Starting phenix.real_space_refine on Wed Mar 4 05:26:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x22_32955/03_2026/7x22_32955_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x22_32955/03_2026/7x22_32955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x22_32955/03_2026/7x22_32955_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x22_32955/03_2026/7x22_32955_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x22_32955/03_2026/7x22_32955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x22_32955/03_2026/7x22_32955.map" } resolution = 3.0 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= 0.004 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 3 8.98 5 Al 1 5.89 5 P 4 5.49 5 Mg 1 5.21 5 S 49 5.16 5 C 6650 2.51 5 N 1652 2.21 5 O 1893 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 33 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: 10257 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7663 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: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 250 Unusual residues: {' K': 3, ' MG': 1, 'ALF': 1, 'CLR': 1, 'PCW': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 2, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 88 Unusual residues: {'CLR': 1, 'NAG': 1, 'PCW': 1} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.49, per 1000 atoms: 0.24 Number of scatterers: 10257 At special positions: 0 Unit cell: (122.84, 100.43, 170.98, 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 3 19.00 S 49 16.00 P 4 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1893 8.00 N 1652 7.00 C 6650 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: 0.67 Conformation dependent library (CDL) restraints added in 474.0 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: 49 helices and 10 sheets defined 48.9% alpha, 14.7% 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 88 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 113 through 134 Processing helix chain 'A' and resid 141 through 163 Processing helix chain 'A' and resid 169 through 175 removed outlier: 4.201A pdb=" N LYS A 175 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 289 removed outlier: 3.578A pdb=" N VAL A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 324 Processing helix chain 'A' and resid 328 through 344 Processing helix chain 'A' and resid 347 through 366 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 429 through 440 removed outlier: 3.592A pdb=" N LEU A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 476 Processing helix chain 'A' and resid 478 through 486 removed outlier: 3.870A pdb=" N ILE A 482 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 543 through 560 Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 706 through 719 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 757 Processing helix chain 'A' and resid 767 through 809 removed outlier: 4.191A pdb=" N VAL A 771 " --> pdb=" O PHE A 767 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER 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 Processing helix chain 'A' and resid 827 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 867 Processing helix chain 'A' and resid 867 through 888 removed outlier: 3.501A pdb=" N LEU A 871 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET A 872 " --> pdb=" O HIS A 868 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN A 888 " --> pdb=" O VAL A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 896 removed outlier: 3.662A pdb=" N ILE A 896 " --> pdb=" O THR A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 904 Processing helix chain 'A' and resid 919 through 950 removed outlier: 3.642A pdb=" N ALA A 944 " --> pdb=" O ILE A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 964 through 988 removed outlier: 4.143A pdb=" N TRP A 968 " --> pdb=" O ASN A 964 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL A 988 " --> pdb=" O GLY A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 removed outlier: 4.085A pdb=" N PHE A1002 " --> pdb=" O VAL A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1025 Processing helix chain 'A' and resid 1029 through 1035 removed outlier: 3.745A pdb=" N ASN A1033 " --> pdb=" O TRP A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 61 removed outlier: 3.816A pdb=" N THR B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 61 " --> pdb=" O MET B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 4.170A pdb=" N TYR B 98 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 6.264A pdb=" N ASP B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 156 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 225 removed outlier: 4.048A pdb=" N ASP B 223 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) 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 188 through 193 removed outlier: 4.594A pdb=" N LEU A 182 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL A 202 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N CYS A 261 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 224 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU A 263 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 222 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR A 265 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER A 220 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A 267 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP A 214 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 209 through 210 removed outlier: 3.839A pdb=" N ASP A 209 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N CYS A 261 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 224 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU A 263 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 222 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N THR A 265 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N SER A 220 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A 267 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP A 214 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 369 through 370 removed outlier: 6.779A pdb=" N VAL A 724 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE A 744 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL A 726 " --> pdb=" O ILE A 744 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N MET A 746 " --> pdb=" O VAL A 726 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY A 728 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE A 384 " --> pdb=" O ALA A 725 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR A 727 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N CYS A 386 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE A 385 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 628 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER A 387 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 625 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N PHE A 702 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N MET A 627 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.582A pdb=" N LEU A 403 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 9.227A pdb=" N PHE A 595 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N TYR A 571 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N PHE A 597 " --> pdb=" O HIS A 569 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N HIS A 569 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 599 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE A 515 " --> pdb=" O LEU A 572 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.582A pdb=" N LEU A 403 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS A 402 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 597 " --> pdb=" O SER A 531 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE A 533 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N GLY A 599 " --> pdb=" O ILE A 533 " (cutoff:3.500A) removed outlier: 11.063A pdb=" N ILE A 535 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 16.892A pdb=" N LEU A 601 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.845A pdb=" N GLU A 444 " --> pdb=" O VAL A 460 " (cutoff:3.500A) 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 Processing sheet with id=AB1, first strand: chain 'B' and resid 123 through 124 494 hydrogen bonds defined for protein. 1407 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: 1.88 Time building geometry restraints manager: 0.92 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: 3220 1.34 - 1.46: 1418 1.46 - 1.57: 5723 1.57 - 1.69: 8 1.69 - 1.81: 82 Bond restraints: 10451 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 4.09e+01 bond pdb=" C11 PCW A1109 " pdb=" O3 PCW A1109 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C11 PCW A1110 " pdb=" O3 PCW A1110 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C11 PCW A1107 " pdb=" O3 PCW A1107 " ideal model delta sigma weight residual 1.326 1.453 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C11 PCW A1111 " pdb=" O3 PCW A1111 " ideal model delta sigma weight residual 1.326 1.452 -0.126 2.00e-02 2.50e+03 3.96e+01 ... (remaining 10446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.11: 14114 14.11 - 28.22: 5 28.22 - 42.32: 0 42.32 - 56.43: 0 56.43 - 70.54: 2 Bond angle restraints: 14121 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.22 -70.54 3.00e+00 1.11e-01 5.53e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.61 -69.98 3.00e+00 1.11e-01 5.44e+02 angle pdb=" C34 PCW A1108 " pdb=" C35 PCW A1108 " pdb=" C36 PCW A1108 " ideal model delta sigma weight residual 113.47 91.23 22.24 3.00e+00 1.11e-01 5.50e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 89.63 19.96 3.00e+00 1.11e-01 4.43e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 90.46 19.75 3.00e+00 1.11e-01 4.33e+01 ... (remaining 14116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.11: 6205 27.11 - 54.21: 223 54.21 - 81.32: 27 81.32 - 108.42: 4 108.42 - 135.53: 5 Dihedral angle restraints: 6464 sinusoidal: 2806 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 93.00 146.44 -53.44 1 1.00e+01 1.00e-02 3.88e+01 dihedral pdb=" C33 PCW A1110 " pdb=" C31 PCW A1110 " pdb=" C32 PCW A1110 " pdb=" O2 PCW A1110 " ideal model delta sinusoidal sigma weight residual 191.83 56.30 135.53 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" N PCW A1110 " pdb=" C4 PCW A1110 " pdb=" C5 PCW A1110 " pdb=" O4P PCW A1110 " ideal model delta sinusoidal sigma weight residual 293.34 160.76 132.58 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 6461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1371 0.054 - 0.109: 197 0.109 - 0.163: 25 0.163 - 0.217: 3 0.217 - 0.271: 2 Chirality restraints: 1598 Sorted by residual: chirality pdb=" C2 PCW B 403 " pdb=" C1 PCW B 403 " pdb=" C3 PCW B 403 " pdb=" O2 PCW B 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.59 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C2 PCW A1110 " pdb=" C1 PCW A1110 " pdb=" C3 PCW A1110 " pdb=" O2 PCW A1110 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C2 PCW A1107 " pdb=" C1 PCW A1107 " pdb=" C3 PCW A1107 " pdb=" O2 PCW A1107 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.20 2.00e-01 2.50e+01 9.62e-01 ... (remaining 1595 not shown) Planarity restraints: 1769 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 177 " -0.043 5.00e-02 4.00e+02 6.60e-02 6.98e+00 pdb=" N PRO A 178 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 206 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 207 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 207 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 207 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 980 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C ILE A 980 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE A 980 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU A 981 " 0.006 2.00e-02 2.50e+03 ... (remaining 1766 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.57: 96 2.57 - 3.21: 10289 3.21 - 3.85: 19550 3.85 - 4.50: 27647 4.50 - 5.14: 44081 Nonbonded interactions: 101663 Sorted by model distance: nonbonded pdb=" OD2 ASP A 388 " pdb="MG MG A1102 " model vdw 1.926 2.170 nonbonded pdb=" F1 ALF A1101 " pdb="MG MG A1102 " model vdw 1.980 2.120 nonbonded pdb=" OE1 GLU A 562 " pdb=" OG SER A 602 " model vdw 2.032 3.040 nonbonded pdb=" OG SER A 240 " pdb=" OE1 GLU A 242 " model vdw 2.067 3.040 nonbonded pdb=" O GLY A 380 " pdb=" OG SER A 381 " model vdw 2.070 3.040 ... (remaining 101658 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: 1.120 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.920 Find NCS groups from input model: 0.040 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:8.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 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 10455 Z= 0.271 Angle : 1.153 70.539 14130 Z= 0.449 Chirality : 0.040 0.271 1598 Planarity : 0.003 0.066 1768 Dihedral : 14.019 135.529 4105 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 26.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.84 (0.25), residues: 1259 helix: 2.70 (0.23), residues: 552 sheet: 0.73 (0.46), residues: 126 loop : -0.12 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 71 TYR 0.016 0.001 TYR B 167 PHE 0.014 0.001 PHE A 500 TRP 0.010 0.001 TRP A 968 HIS 0.003 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00541 (10451) covalent geometry : angle 1.15286 (14121) SS BOND : bond 0.00074 ( 3) SS BOND : angle 0.60114 ( 6) hydrogen bonds : bond 0.15194 ( 486) hydrogen bonds : angle 6.15754 ( 1407) link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 1.74343 ( 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 193 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.397 Fit side-chains REVERT: A 66 GLN cc_start: 0.5964 (mm-40) cc_final: 0.5397 (pt0) REVERT: A 175 LYS cc_start: 0.6536 (mptt) cc_final: 0.6296 (ttpp) REVERT: A 180 GLN cc_start: 0.6454 (pt0) cc_final: 0.5984 (mt0) REVERT: A 219 PHE cc_start: 0.6501 (m-80) cc_final: 0.6075 (m-10) REVERT: A 221 GLN cc_start: 0.6553 (mt0) cc_final: 0.6331 (mm-40) REVERT: A 246 GLU cc_start: 0.6277 (tp30) cc_final: 0.5839 (tp30) REVERT: A 293 LYS cc_start: 0.7055 (mttt) cc_final: 0.6598 (mtmt) REVERT: A 387 SER cc_start: 0.8260 (p) cc_final: 0.7726 (t) REVERT: A 398 MET cc_start: 0.7189 (tpt) cc_final: 0.6596 (tpp) REVERT: A 420 LYS cc_start: 0.5617 (pptt) cc_final: 0.5197 (mtpt) REVERT: A 442 ARG cc_start: 0.5983 (ttp-110) cc_final: 0.5340 (ttt-90) REVERT: A 683 LYS cc_start: 0.7366 (ttmm) cc_final: 0.7060 (tttt) REVERT: A 691 ASP cc_start: 0.6728 (m-30) cc_final: 0.6453 (m-30) REVERT: A 746 MET cc_start: 0.8206 (mmm) cc_final: 0.7832 (mmp) REVERT: A 763 LEU cc_start: 0.7726 (mm) cc_final: 0.7458 (mp) REVERT: A 846 ARG cc_start: 0.6911 (mtm-85) cc_final: 0.6358 (mtm-85) REVERT: A 847 LYS cc_start: 0.6897 (mtmt) cc_final: 0.6186 (mmpt) REVERT: A 860 GLN cc_start: 0.6078 (mp10) cc_final: 0.5460 (mp10) REVERT: A 872 MET cc_start: 0.7718 (mtt) cc_final: 0.7463 (mtm) REVERT: A 968 TRP cc_start: 0.6836 (m100) cc_final: 0.6533 (m100) REVERT: A 1017 MET cc_start: 0.7073 (mmm) cc_final: 0.6752 (mpp) REVERT: A 1034 MET cc_start: 0.7309 (mmp) cc_final: 0.6744 (mmp) REVERT: B 65 LYS cc_start: 0.7271 (pttm) cc_final: 0.7035 (pttm) REVERT: B 121 MET cc_start: 0.5917 (tpt) cc_final: 0.5581 (mpp) REVERT: B 132 GLU cc_start: 0.7042 (mp0) cc_final: 0.6836 (mp0) REVERT: B 135 GLU cc_start: 0.6827 (mm-30) cc_final: 0.6355 (tt0) REVERT: B 211 PRO cc_start: 0.8352 (Cg_exo) cc_final: 0.8006 (Cg_endo) REVERT: B 221 ASP cc_start: 0.6393 (m-30) cc_final: 0.6077 (m-30) REVERT: B 224 LYS cc_start: 0.6707 (mttm) cc_final: 0.6319 (mtpp) REVERT: B 229 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6475 (mm-30) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.6098 time to fit residues: 126.2473 Evaluate side-chains 136 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 245 HIS A 402 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 GLN A 501 GLN A 505 HIS A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 HIS A 873 GLN A 964 ASN B 55 GLN B 79 GLN B 104 ASN B 140 ASN B 242 GLN B 283 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.167721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.125232 restraints weight = 11117.097| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.00 r_work: 0.3063 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10455 Z= 0.215 Angle : 0.905 29.936 14130 Z= 0.409 Chirality : 0.048 0.362 1598 Planarity : 0.005 0.066 1768 Dihedral : 11.958 132.418 1722 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.57 % Allowed : 8.00 % Favored : 89.43 % 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: 0.87 (0.23), residues: 1259 helix: 1.63 (0.22), residues: 555 sheet: 0.59 (0.43), residues: 128 loop : -0.44 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 143 TYR 0.029 0.002 TYR B 167 PHE 0.020 0.003 PHE B 264 TRP 0.021 0.002 TRP A 968 HIS 0.014 0.002 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00519 (10451) covalent geometry : angle 0.90033 (14121) SS BOND : bond 0.00236 ( 3) SS BOND : angle 1.23268 ( 6) hydrogen bonds : bond 0.05805 ( 486) hydrogen bonds : angle 4.93546 ( 1407) link_NAG-ASN : bond 0.01978 ( 1) link_NAG-ASN : angle 5.90581 ( 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 186 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.388 Fit side-chains REVERT: A 66 GLN cc_start: 0.6259 (mm-40) cc_final: 0.5678 (pt0) REVERT: A 175 LYS cc_start: 0.6740 (mptt) cc_final: 0.6463 (ttpp) REVERT: A 180 GLN cc_start: 0.6755 (pt0) cc_final: 0.6375 (mt0) REVERT: A 219 PHE cc_start: 0.7025 (m-80) cc_final: 0.6785 (m-10) REVERT: A 221 GLN cc_start: 0.6990 (mt0) cc_final: 0.6689 (tp40) REVERT: A 293 LYS cc_start: 0.7647 (mttt) cc_final: 0.7188 (mtmt) REVERT: A 365 LYS cc_start: 0.6274 (ttmm) cc_final: 0.5676 (mptt) REVERT: A 398 MET cc_start: 0.7776 (tpt) cc_final: 0.7472 (tpp) REVERT: A 411 VAL cc_start: 0.7851 (t) cc_final: 0.7546 (p) REVERT: A 420 LYS cc_start: 0.6307 (pptt) cc_final: 0.5706 (mtpt) REVERT: A 653 VAL cc_start: 0.7251 (p) cc_final: 0.6988 (t) REVERT: A 691 ASP cc_start: 0.7722 (m-30) cc_final: 0.7374 (m-30) REVERT: A 746 MET cc_start: 0.8787 (mmm) cc_final: 0.8528 (mmp) REVERT: A 760 MET cc_start: 0.8725 (ttm) cc_final: 0.8516 (ttm) REVERT: A 799 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7852 (tp) REVERT: A 844 MET cc_start: 0.7663 (mmt) cc_final: 0.7412 (mmp) REVERT: A 846 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7235 (mtt180) REVERT: A 847 LYS cc_start: 0.7616 (mtmt) cc_final: 0.7172 (mmpt) REVERT: A 853 LYS cc_start: 0.7437 (mtpp) cc_final: 0.6630 (tttm) REVERT: A 860 GLN cc_start: 0.7890 (mp10) cc_final: 0.7411 (mp10) REVERT: A 968 TRP cc_start: 0.8066 (m100) cc_final: 0.7841 (m100) REVERT: B 34 LYS cc_start: 0.7936 (mppt) cc_final: 0.7586 (mtmm) REVERT: B 93 ASN cc_start: 0.6336 (m110) cc_final: 0.5604 (m-40) REVERT: B 121 MET cc_start: 0.6324 (tpt) cc_final: 0.5916 (mpp) REVERT: B 135 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6578 (tt0) REVERT: B 229 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7635 (mm-30) outliers start: 28 outliers final: 13 residues processed: 172 average time/residue: 0.5445 time to fit residues: 101.4497 Evaluate side-chains 148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 203 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 17 optimal weight: 0.0570 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 402 HIS ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.179099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.137829 restraints weight = 10965.616| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.63 r_work: 0.3107 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10455 Z= 0.143 Angle : 0.796 30.791 14130 Z= 0.349 Chirality : 0.043 0.236 1598 Planarity : 0.004 0.066 1768 Dihedral : 11.529 124.515 1722 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.12 % Allowed : 10.66 % Favored : 86.21 % 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: 0.98 (0.23), residues: 1259 helix: 1.88 (0.22), residues: 539 sheet: 0.39 (0.42), residues: 128 loop : -0.42 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 216 TYR 0.020 0.001 TYR B 167 PHE 0.013 0.002 PHE A 471 TRP 0.017 0.002 TRP A 968 HIS 0.005 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00328 (10451) covalent geometry : angle 0.79209 (14121) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.96636 ( 6) hydrogen bonds : bond 0.04838 ( 486) hydrogen bonds : angle 4.64987 ( 1407) link_NAG-ASN : bond 0.01203 ( 1) link_NAG-ASN : angle 5.44463 ( 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 172 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.395 Fit side-chains REVERT: A 66 GLN cc_start: 0.6186 (mm-40) cc_final: 0.5673 (pt0) REVERT: A 80 ARG cc_start: 0.6540 (tpt170) cc_final: 0.6201 (tpp-160) REVERT: A 175 LYS cc_start: 0.6805 (mptt) cc_final: 0.6528 (ttpp) REVERT: A 180 GLN cc_start: 0.6731 (pt0) cc_final: 0.6356 (mt0) REVERT: A 189 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6618 (mtpt) REVERT: A 221 GLN cc_start: 0.7005 (mt0) cc_final: 0.6703 (tp40) REVERT: A 243 PHE cc_start: 0.7445 (t80) cc_final: 0.7231 (t80) REVERT: A 293 LYS cc_start: 0.7594 (mttt) cc_final: 0.7126 (mtmt) REVERT: A 365 LYS cc_start: 0.6250 (ttmm) cc_final: 0.5604 (mptt) REVERT: A 411 VAL cc_start: 0.7732 (t) cc_final: 0.7463 (p) REVERT: A 420 LYS cc_start: 0.6262 (pptt) cc_final: 0.5669 (mtpt) REVERT: A 442 ARG cc_start: 0.6451 (ttp-170) cc_final: 0.5168 (mtp-110) REVERT: A 653 VAL cc_start: 0.7242 (p) cc_final: 0.6954 (t) REVERT: A 691 ASP cc_start: 0.7608 (m-30) cc_final: 0.7283 (m-30) REVERT: A 746 MET cc_start: 0.8824 (mmm) cc_final: 0.8537 (mmp) REVERT: A 799 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7793 (tp) REVERT: A 838 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7447 (mttm) REVERT: A 846 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7178 (mtt180) REVERT: A 847 LYS cc_start: 0.7696 (mtmt) cc_final: 0.7246 (mmpt) REVERT: A 860 GLN cc_start: 0.7839 (mp10) cc_final: 0.7356 (mp10) REVERT: A 872 MET cc_start: 0.8251 (mtt) cc_final: 0.7984 (mtm) REVERT: A 968 TRP cc_start: 0.7845 (m100) cc_final: 0.7605 (m100) REVERT: B 34 LYS cc_start: 0.7918 (mppt) cc_final: 0.7711 (mtmm) REVERT: B 93 ASN cc_start: 0.6233 (m110) cc_final: 0.5514 (m-40) REVERT: B 121 MET cc_start: 0.6340 (tpt) cc_final: 0.5926 (mpp) REVERT: B 131 SER cc_start: 0.7749 (t) cc_final: 0.7512 (p) REVERT: B 135 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6407 (tt0) REVERT: B 229 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7602 (mm-30) outliers start: 34 outliers final: 17 residues processed: 151 average time/residue: 0.5563 time to fit residues: 91.0330 Evaluate side-chains 147 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 288 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 25 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.0010 chunk 63 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 498 ASN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.175639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.134615 restraints weight = 11065.911| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.68 r_work: 0.3096 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10455 Z= 0.166 Angle : 0.820 30.110 14130 Z= 0.362 Chirality : 0.044 0.285 1598 Planarity : 0.005 0.065 1768 Dihedral : 11.605 124.696 1722 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.22 % Allowed : 11.76 % Favored : 85.02 % 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: 0.74 (0.23), residues: 1259 helix: 1.63 (0.22), residues: 544 sheet: 0.20 (0.39), residues: 138 loop : -0.50 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 216 TYR 0.021 0.002 TYR B 167 PHE 0.015 0.002 PHE B 264 TRP 0.019 0.002 TRP A 968 HIS 0.005 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00400 (10451) covalent geometry : angle 0.81658 (14121) SS BOND : bond 0.00174 ( 3) SS BOND : angle 1.09288 ( 6) hydrogen bonds : bond 0.05048 ( 486) hydrogen bonds : angle 4.61511 ( 1407) link_NAG-ASN : bond 0.00873 ( 1) link_NAG-ASN : angle 5.30764 ( 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 172 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.458 Fit side-chains REVERT: A 58 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6807 (ptt-90) REVERT: A 66 GLN cc_start: 0.6370 (mm-40) cc_final: 0.5761 (pt0) REVERT: A 175 LYS cc_start: 0.6828 (mptt) cc_final: 0.6519 (ttpp) REVERT: A 180 GLN cc_start: 0.6680 (pt0) cc_final: 0.6290 (mt0) REVERT: A 219 PHE cc_start: 0.7239 (m-80) cc_final: 0.6897 (m-10) REVERT: A 221 GLN cc_start: 0.7068 (mt0) cc_final: 0.6732 (tp40) REVERT: A 293 LYS cc_start: 0.7571 (mttt) cc_final: 0.7119 (mtmt) REVERT: A 365 LYS cc_start: 0.6245 (ttmm) cc_final: 0.5878 (ptmm) REVERT: A 411 VAL cc_start: 0.7852 (t) cc_final: 0.7522 (p) REVERT: A 420 LYS cc_start: 0.6268 (pptt) cc_final: 0.5585 (mtpt) REVERT: A 442 ARG cc_start: 0.6687 (ttp-170) cc_final: 0.5332 (mtp180) REVERT: A 666 GLN cc_start: 0.5969 (mt0) cc_final: 0.4856 (tp40) REVERT: A 691 ASP cc_start: 0.7593 (m-30) cc_final: 0.7284 (m-30) REVERT: A 799 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7802 (tp) REVERT: A 838 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7451 (mttm) REVERT: A 846 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7231 (mtt180) REVERT: A 847 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7372 (mmpt) REVERT: A 853 LYS cc_start: 0.7272 (mtpp) cc_final: 0.7035 (mtpt) REVERT: A 860 GLN cc_start: 0.7824 (mp10) cc_final: 0.7361 (mp10) REVERT: A 872 MET cc_start: 0.8349 (mtt) cc_final: 0.8092 (mtm) REVERT: B 63 GLU cc_start: 0.7688 (pm20) cc_final: 0.7437 (pt0) REVERT: B 93 ASN cc_start: 0.6489 (m110) cc_final: 0.5681 (m-40) REVERT: B 121 MET cc_start: 0.6484 (tpt) cc_final: 0.5731 (mpp) REVERT: B 129 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7044 (mmm) REVERT: B 135 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6279 (tt0) REVERT: B 221 ASP cc_start: 0.6514 (m-30) cc_final: 0.6234 (m-30) REVERT: B 229 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7657 (mm-30) outliers start: 35 outliers final: 23 residues processed: 159 average time/residue: 0.5622 time to fit residues: 96.5813 Evaluate side-chains 154 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 35 optimal weight: 5.9990 chunk 77 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 0.0000 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 418 GLN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.179345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.137831 restraints weight = 10954.643| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.68 r_work: 0.3102 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10455 Z= 0.133 Angle : 0.786 30.546 14130 Z= 0.342 Chirality : 0.042 0.198 1598 Planarity : 0.004 0.063 1768 Dihedral : 11.283 125.913 1722 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.77 % Allowed : 11.58 % Favored : 84.65 % 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: 0.81 (0.23), residues: 1259 helix: 1.69 (0.22), residues: 551 sheet: 0.27 (0.39), residues: 137 loop : -0.52 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.018 0.001 TYR A 881 PHE 0.019 0.002 PHE A 500 TRP 0.015 0.001 TRP A 968 HIS 0.003 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00308 (10451) covalent geometry : angle 0.78205 (14121) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.96182 ( 6) hydrogen bonds : bond 0.04596 ( 486) hydrogen bonds : angle 4.47965 ( 1407) link_NAG-ASN : bond 0.00485 ( 1) link_NAG-ASN : angle 5.55653 ( 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 175 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.313 Fit side-chains REVERT: A 58 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6809 (ptt-90) REVERT: A 66 GLN cc_start: 0.6342 (mm-40) cc_final: 0.5712 (pt0) REVERT: A 175 LYS cc_start: 0.6843 (mptt) cc_final: 0.6523 (ttpp) REVERT: A 180 GLN cc_start: 0.6636 (pt0) cc_final: 0.6290 (mt0) REVERT: A 221 GLN cc_start: 0.7080 (mt0) cc_final: 0.6734 (tp40) REVERT: A 223 CYS cc_start: 0.7476 (t) cc_final: 0.7165 (t) REVERT: A 293 LYS cc_start: 0.7541 (mttt) cc_final: 0.7070 (mtmt) REVERT: A 365 LYS cc_start: 0.6209 (ttmm) cc_final: 0.5862 (ptmm) REVERT: A 411 VAL cc_start: 0.7806 (t) cc_final: 0.7482 (p) REVERT: A 420 LYS cc_start: 0.6245 (pptt) cc_final: 0.5681 (mtpt) REVERT: A 442 ARG cc_start: 0.6712 (ttp-170) cc_final: 0.5330 (mtp180) REVERT: A 666 GLN cc_start: 0.6020 (mt0) cc_final: 0.4921 (tp40) REVERT: A 691 ASP cc_start: 0.7567 (m-30) cc_final: 0.7268 (m-30) REVERT: A 799 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7780 (tp) REVERT: A 838 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7428 (mttm) REVERT: A 846 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7169 (mtt180) REVERT: A 847 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7377 (mmpt) REVERT: A 853 LYS cc_start: 0.7321 (mtpp) cc_final: 0.7049 (mtpt) REVERT: A 860 GLN cc_start: 0.7810 (mp10) cc_final: 0.7339 (mp10) REVERT: A 872 MET cc_start: 0.8243 (mtt) cc_final: 0.8026 (mtm) REVERT: B 63 GLU cc_start: 0.7687 (pm20) cc_final: 0.7466 (pt0) REVERT: B 93 ASN cc_start: 0.6495 (m110) cc_final: 0.5687 (m-40) REVERT: B 121 MET cc_start: 0.6361 (tpt) cc_final: 0.5621 (mpp) REVERT: B 129 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7122 (mmm) REVERT: B 131 SER cc_start: 0.7744 (OUTLIER) cc_final: 0.7514 (p) REVERT: B 221 ASP cc_start: 0.6430 (m-30) cc_final: 0.6106 (m-30) REVERT: B 229 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7667 (mm-30) outliers start: 41 outliers final: 23 residues processed: 160 average time/residue: 0.5785 time to fit residues: 99.9045 Evaluate side-chains 155 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 288 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 GLN B 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.176548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135724 restraints weight = 11128.069| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.61 r_work: 0.3078 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10455 Z= 0.210 Angle : 0.859 30.947 14130 Z= 0.385 Chirality : 0.046 0.206 1598 Planarity : 0.005 0.064 1768 Dihedral : 11.772 128.783 1722 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.92 % Favored : 95.00 % Rotamer: Outliers : 4.41 % Allowed : 12.41 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.23), residues: 1259 helix: 1.30 (0.22), residues: 557 sheet: 0.14 (0.41), residues: 129 loop : -0.73 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 849 TYR 0.022 0.002 TYR B 167 PHE 0.018 0.003 PHE B 264 TRP 0.021 0.002 TRP A 968 HIS 0.004 0.002 HIS A 850 Details of bonding type rmsd covalent geometry : bond 0.00510 (10451) covalent geometry : angle 0.85410 (14121) SS BOND : bond 0.00246 ( 3) SS BOND : angle 1.33353 ( 6) hydrogen bonds : bond 0.05604 ( 486) hydrogen bonds : angle 4.71227 ( 1407) link_NAG-ASN : bond 0.00532 ( 1) link_NAG-ASN : angle 6.28833 ( 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 181 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.374 Fit side-chains REVERT: A 58 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6847 (ptt-90) REVERT: A 66 GLN cc_start: 0.6537 (mm-40) cc_final: 0.6290 (mp10) REVERT: A 175 LYS cc_start: 0.6832 (mptt) cc_final: 0.6522 (ttpp) REVERT: A 180 GLN cc_start: 0.6693 (pt0) cc_final: 0.6295 (mt0) REVERT: A 221 GLN cc_start: 0.7143 (mt0) cc_final: 0.6775 (tp40) REVERT: A 293 LYS cc_start: 0.7590 (mttt) cc_final: 0.7123 (mtmt) REVERT: A 365 LYS cc_start: 0.6420 (ttmm) cc_final: 0.5706 (mptt) REVERT: A 420 LYS cc_start: 0.6358 (pptt) cc_final: 0.5716 (mtpt) REVERT: A 666 GLN cc_start: 0.5923 (mt0) cc_final: 0.4943 (tp40) REVERT: A 673 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7734 (mttm) REVERT: A 691 ASP cc_start: 0.7570 (m-30) cc_final: 0.7278 (m-30) REVERT: A 838 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7482 (mttm) REVERT: A 846 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.7335 (mtt180) REVERT: A 847 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7450 (mmpt) REVERT: A 853 LYS cc_start: 0.7364 (mtpp) cc_final: 0.7062 (mtpp) REVERT: A 860 GLN cc_start: 0.7874 (mp10) cc_final: 0.7409 (mp10) REVERT: B 93 ASN cc_start: 0.6609 (m110) cc_final: 0.5832 (m-40) REVERT: B 121 MET cc_start: 0.6448 (tpt) cc_final: 0.5668 (mpp) REVERT: B 129 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7184 (mmm) REVERT: B 221 ASP cc_start: 0.6589 (m-30) cc_final: 0.6192 (m-30) outliers start: 48 outliers final: 30 residues processed: 166 average time/residue: 0.6176 time to fit residues: 110.3070 Evaluate side-chains 157 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 95 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 501 GLN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.168728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.126090 restraints weight = 11089.679| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.84 r_work: 0.3088 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10455 Z= 0.142 Angle : 0.803 30.669 14130 Z= 0.352 Chirality : 0.043 0.200 1598 Planarity : 0.004 0.063 1768 Dihedral : 11.391 127.305 1722 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.77 % Allowed : 13.88 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1259 helix: 1.51 (0.22), residues: 550 sheet: 0.22 (0.42), residues: 123 loop : -0.66 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.018 0.001 TYR A 881 PHE 0.023 0.002 PHE A 335 TRP 0.018 0.002 TRP A 968 HIS 0.003 0.001 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00332 (10451) covalent geometry : angle 0.79717 (14121) SS BOND : bond 0.00122 ( 3) SS BOND : angle 1.01438 ( 6) hydrogen bonds : bond 0.04775 ( 486) hydrogen bonds : angle 4.54132 ( 1407) link_NAG-ASN : bond 0.00242 ( 1) link_NAG-ASN : angle 6.77877 ( 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 176 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 135 time to evaluate : 0.403 Fit side-chains REVERT: A 58 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6851 (ptt-90) REVERT: A 66 GLN cc_start: 0.6530 (mm-40) cc_final: 0.6282 (mp10) REVERT: A 175 LYS cc_start: 0.6875 (mptt) cc_final: 0.6524 (ttpp) REVERT: A 180 GLN cc_start: 0.6644 (pt0) cc_final: 0.6253 (mt0) REVERT: A 221 GLN cc_start: 0.7154 (mt0) cc_final: 0.6769 (tp40) REVERT: A 293 LYS cc_start: 0.7578 (mttt) cc_final: 0.7089 (mtmt) REVERT: A 365 LYS cc_start: 0.6335 (ttmm) cc_final: 0.5926 (ptmm) REVERT: A 420 LYS cc_start: 0.6319 (pptt) cc_final: 0.5639 (mtpt) REVERT: A 666 GLN cc_start: 0.5874 (mt0) cc_final: 0.4898 (tp40) REVERT: A 673 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7747 (mttm) REVERT: A 688 GLU cc_start: 0.6993 (mp0) cc_final: 0.5851 (mm-30) REVERT: A 691 ASP cc_start: 0.7535 (m-30) cc_final: 0.7244 (m-30) REVERT: A 799 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7766 (tp) REVERT: A 838 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7464 (mttm) REVERT: A 846 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7308 (mtt180) REVERT: A 847 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7429 (mmpt) REVERT: A 853 LYS cc_start: 0.7428 (mtpp) cc_final: 0.7116 (mtpp) REVERT: A 860 GLN cc_start: 0.7834 (mp10) cc_final: 0.7371 (mp10) REVERT: A 872 MET cc_start: 0.8260 (mtt) cc_final: 0.8047 (mtm) REVERT: B 93 ASN cc_start: 0.6605 (m110) cc_final: 0.5818 (m-40) REVERT: B 121 MET cc_start: 0.6341 (tpt) cc_final: 0.5526 (mpp) REVERT: B 129 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7097 (mmm) REVERT: B 221 ASP cc_start: 0.6509 (m-30) cc_final: 0.6088 (m-30) outliers start: 41 outliers final: 26 residues processed: 161 average time/residue: 0.5965 time to fit residues: 103.6161 Evaluate side-chains 161 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.177669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.136457 restraints weight = 10914.060| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.60 r_work: 0.3133 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10455 Z= 0.121 Angle : 0.781 30.502 14130 Z= 0.339 Chirality : 0.042 0.197 1598 Planarity : 0.004 0.061 1768 Dihedral : 10.794 125.188 1722 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.77 % Allowed : 14.43 % Favored : 81.80 % 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: 0.74 (0.23), residues: 1259 helix: 1.70 (0.22), residues: 550 sheet: 0.17 (0.39), residues: 144 loop : -0.61 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.017 0.001 TYR A 881 PHE 0.023 0.002 PHE A 335 TRP 0.026 0.002 TRP A1029 HIS 0.003 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00277 (10451) covalent geometry : angle 0.77625 (14121) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.99448 ( 6) hydrogen bonds : bond 0.04296 ( 486) hydrogen bonds : angle 4.39586 ( 1407) link_NAG-ASN : bond 0.00811 ( 1) link_NAG-ASN : angle 6.17422 ( 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 175 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.328 Fit side-chains REVERT: A 58 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6854 (ptt-90) REVERT: A 66 GLN cc_start: 0.6485 (mm-40) cc_final: 0.5861 (pt0) REVERT: A 175 LYS cc_start: 0.6829 (mptt) cc_final: 0.6496 (ttpp) REVERT: A 180 GLN cc_start: 0.6653 (pt0) cc_final: 0.6276 (mt0) REVERT: A 221 GLN cc_start: 0.7229 (mt0) cc_final: 0.6821 (tp40) REVERT: A 293 LYS cc_start: 0.7572 (mttt) cc_final: 0.7121 (mtmt) REVERT: A 420 LYS cc_start: 0.6307 (pptt) cc_final: 0.5653 (mtpt) REVERT: A 666 GLN cc_start: 0.5847 (mt0) cc_final: 0.4894 (tp40) REVERT: A 673 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7761 (mttm) REVERT: A 688 GLU cc_start: 0.6942 (mp0) cc_final: 0.5806 (mm-30) REVERT: A 691 ASP cc_start: 0.7459 (m-30) cc_final: 0.7195 (m-30) REVERT: A 799 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7686 (tp) REVERT: A 838 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7423 (mttm) REVERT: A 846 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7195 (mtt180) REVERT: A 847 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7414 (mmpt) REVERT: A 853 LYS cc_start: 0.7456 (mtpp) cc_final: 0.7241 (mtpp) REVERT: A 860 GLN cc_start: 0.7817 (mp10) cc_final: 0.7339 (mp10) REVERT: B 120 ASP cc_start: 0.5318 (OUTLIER) cc_final: 0.5113 (m-30) REVERT: B 121 MET cc_start: 0.6314 (tpt) cc_final: 0.5534 (mpp) REVERT: B 129 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7079 (mmm) REVERT: B 221 ASP cc_start: 0.6507 (m-30) cc_final: 0.6082 (m-30) outliers start: 41 outliers final: 24 residues processed: 159 average time/residue: 0.5865 time to fit residues: 100.8952 Evaluate side-chains 155 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 288 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 33 optimal weight: 0.0770 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 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 196 GLN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.182255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142275 restraints weight = 10894.659| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.60 r_work: 0.3153 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 10455 Z= 0.109 Angle : 0.772 30.489 14130 Z= 0.332 Chirality : 0.041 0.192 1598 Planarity : 0.004 0.059 1768 Dihedral : 10.335 121.400 1722 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.03 % Allowed : 15.62 % Favored : 81.34 % 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: 0.91 (0.24), residues: 1259 helix: 1.83 (0.22), residues: 551 sheet: 0.31 (0.40), residues: 143 loop : -0.52 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.016 0.001 TYR A 881 PHE 0.024 0.001 PHE A 500 TRP 0.035 0.002 TRP A1029 HIS 0.002 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00244 (10451) covalent geometry : angle 0.76722 (14121) SS BOND : bond 0.00088 ( 3) SS BOND : angle 0.84703 ( 6) hydrogen bonds : bond 0.03999 ( 486) hydrogen bonds : angle 4.28521 ( 1407) link_NAG-ASN : bond 0.00603 ( 1) link_NAG-ASN : angle 5.79130 ( 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 163 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.403 Fit side-chains REVERT: A 66 GLN cc_start: 0.6386 (mm-40) cc_final: 0.5888 (pt0) REVERT: A 80 ARG cc_start: 0.6471 (tpt170) cc_final: 0.6255 (tpp-160) REVERT: A 175 LYS cc_start: 0.6842 (mptt) cc_final: 0.6500 (ttpp) REVERT: A 180 GLN cc_start: 0.6684 (pt0) cc_final: 0.6351 (mt0) REVERT: A 221 GLN cc_start: 0.7210 (mt0) cc_final: 0.6818 (tp40) REVERT: A 223 CYS cc_start: 0.7490 (t) cc_final: 0.7150 (t) REVERT: A 293 LYS cc_start: 0.7547 (mttt) cc_final: 0.7033 (mtmt) REVERT: A 420 LYS cc_start: 0.6288 (pptt) cc_final: 0.5689 (mtpt) REVERT: A 666 GLN cc_start: 0.5926 (mt0) cc_final: 0.4926 (tp40) REVERT: A 673 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7697 (mttm) REVERT: A 688 GLU cc_start: 0.6933 (mp0) cc_final: 0.5792 (mm-30) REVERT: A 691 ASP cc_start: 0.7482 (m-30) cc_final: 0.7224 (m-30) REVERT: A 799 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7631 (tp) REVERT: A 838 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7366 (mttm) REVERT: A 846 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7242 (mtt180) REVERT: A 847 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7462 (mmpt) REVERT: A 853 LYS cc_start: 0.7568 (mtpp) cc_final: 0.7339 (mtpp) REVERT: A 860 GLN cc_start: 0.7791 (mp10) cc_final: 0.7315 (mp10) REVERT: A 968 TRP cc_start: 0.7814 (m100) cc_final: 0.7575 (m100) REVERT: B 121 MET cc_start: 0.6256 (tpt) cc_final: 0.5469 (mpp) REVERT: B 129 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7021 (mmm) REVERT: B 221 ASP cc_start: 0.6384 (m-30) cc_final: 0.5978 (m-30) outliers start: 33 outliers final: 21 residues processed: 154 average time/residue: 0.6297 time to fit residues: 104.3939 Evaluate side-chains 152 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 33 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 106 optimal weight: 0.0020 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 210 GLN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 GLN B 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.180482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141471 restraints weight = 10857.956| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.74 r_work: 0.3128 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10455 Z= 0.133 Angle : 0.798 30.369 14130 Z= 0.347 Chirality : 0.042 0.186 1598 Planarity : 0.004 0.060 1768 Dihedral : 10.512 121.620 1722 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.94 % Allowed : 16.27 % Favored : 80.79 % 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: 0.86 (0.23), residues: 1259 helix: 1.72 (0.22), residues: 551 sheet: 0.38 (0.42), residues: 128 loop : -0.48 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 216 TYR 0.018 0.001 TYR A 881 PHE 0.023 0.002 PHE A 500 TRP 0.041 0.002 TRP A1029 HIS 0.002 0.001 HIS A 868 Details of bonding type rmsd covalent geometry : bond 0.00310 (10451) covalent geometry : angle 0.79319 (14121) SS BOND : bond 0.00150 ( 3) SS BOND : angle 1.04483 ( 6) hydrogen bonds : bond 0.04426 ( 486) hydrogen bonds : angle 4.35928 ( 1407) link_NAG-ASN : bond 0.00943 ( 1) link_NAG-ASN : angle 5.78667 ( 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 157 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.458 Fit side-chains REVERT: A 66 GLN cc_start: 0.6352 (mm-40) cc_final: 0.5887 (pt0) REVERT: A 175 LYS cc_start: 0.6860 (mptt) cc_final: 0.6496 (ttpp) REVERT: A 180 GLN cc_start: 0.6696 (pt0) cc_final: 0.6349 (mt0) REVERT: A 219 PHE cc_start: 0.7288 (m-80) cc_final: 0.6977 (m-10) REVERT: A 221 GLN cc_start: 0.7231 (mt0) cc_final: 0.6797 (tp40) REVERT: A 293 LYS cc_start: 0.7502 (mttt) cc_final: 0.7043 (mtmt) REVERT: A 420 LYS cc_start: 0.6285 (pptt) cc_final: 0.5604 (mtpt) REVERT: A 666 GLN cc_start: 0.5915 (mt0) cc_final: 0.4907 (tp40) REVERT: A 673 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7708 (mttm) REVERT: A 691 ASP cc_start: 0.7500 (m-30) cc_final: 0.7228 (m-30) REVERT: A 799 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7715 (tp) REVERT: A 838 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7389 (mttm) REVERT: A 846 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7293 (mtt180) REVERT: A 847 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7428 (mmpt) REVERT: A 853 LYS cc_start: 0.7508 (mtpp) cc_final: 0.7182 (mtpp) REVERT: A 860 GLN cc_start: 0.7766 (mp10) cc_final: 0.7284 (mp10) REVERT: B 121 MET cc_start: 0.6243 (tpt) cc_final: 0.5444 (mpp) REVERT: B 129 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7008 (mmm) REVERT: B 221 ASP cc_start: 0.6411 (m-30) cc_final: 0.5970 (m-30) outliers start: 32 outliers final: 23 residues processed: 147 average time/residue: 0.5877 time to fit residues: 93.4190 Evaluate side-chains 150 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 673 LYS Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 823 ASP Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 203 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 ASN 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 = 0.179927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.140052 restraints weight = 10948.126| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.59 r_work: 0.3173 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 10455 Z= 0.107 Angle : 0.771 30.585 14130 Z= 0.330 Chirality : 0.041 0.190 1598 Planarity : 0.004 0.058 1768 Dihedral : 10.158 120.143 1722 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.57 % Allowed : 16.73 % Favored : 80.70 % 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: 1.00 (0.24), residues: 1259 helix: 1.89 (0.22), residues: 551 sheet: 0.41 (0.40), residues: 143 loop : -0.48 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 899 TYR 0.015 0.001 TYR A 881 PHE 0.025 0.001 PHE A 335 TRP 0.045 0.002 TRP A1029 HIS 0.002 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00236 (10451) covalent geometry : angle 0.76752 (14121) SS BOND : bond 0.00093 ( 3) SS BOND : angle 0.84306 ( 6) hydrogen bonds : bond 0.03876 ( 486) hydrogen bonds : angle 4.23026 ( 1407) link_NAG-ASN : bond 0.00677 ( 1) link_NAG-ASN : angle 5.19430 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4358.39 seconds wall clock time: 74 minutes 56.41 seconds (4496.41 seconds total)