Starting phenix.real_space_refine on Sun Dec 29 18:52:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x22_32955/12_2024/7x22_32955_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x22_32955/12_2024/7x22_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x22_32955/12_2024/7x22_32955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x22_32955/12_2024/7x22_32955.map" model { file = "/net/cci-nas-00/data/ceres_data/7x22_32955/12_2024/7x22_32955_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x22_32955/12_2024/7x22_32955_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.45, per 1000 atoms: 0.63 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: 3.25 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.33 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: 4.82 Time building geometry restraints manager: 3.28 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: 0.850 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.450 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.290 ------------------------------------------------------------------------------- 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 10451 Z= 0.357 Angle : 1.153 70.539 14121 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 : 25.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (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 TRP 0.010 0.001 TRP A 968 HIS 0.003 0.001 HIS A 868 PHE 0.014 0.001 PHE A 500 TYR 0.016 0.001 TYR B 167 ARG 0.002 0.000 ARG B 71 *********************** 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 : 1.108 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: 0.6076 (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: 0.7367 (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: 1.2793 time to fit residues: 266.3921 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 : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 113 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 505 HIS A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN B 79 GLN B 104 ASN B 140 ASN B 242 GLN B 283 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10451 Z= 0.163 Angle : 0.789 30.110 14121 Z= 0.345 Chirality : 0.043 0.248 1598 Planarity : 0.004 0.062 1768 Dihedral : 11.334 137.379 1722 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.93 % Allowed : 7.44 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1259 helix: 2.45 (0.22), residues: 547 sheet: 0.72 (0.44), residues: 127 loop : -0.24 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 968 HIS 0.004 0.001 HIS A 245 PHE 0.015 0.002 PHE A 567 TYR 0.019 0.001 TYR A 881 ARG 0.007 0.001 ARG B 143 *********************** 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 174 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.067 Fit side-chains REVERT: A 66 GLN cc_start: 0.5917 (mm-40) cc_final: 0.5358 (pt0) REVERT: A 175 LYS cc_start: 0.6508 (mptt) cc_final: 0.6234 (ttpp) REVERT: A 180 GLN cc_start: 0.6511 (pt0) cc_final: 0.6061 (mt0) REVERT: A 195 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6530 (mt-10) REVERT: A 219 PHE cc_start: 0.6631 (m-80) cc_final: 0.6219 (m-10) REVERT: A 246 GLU cc_start: 0.6098 (tp30) cc_final: 0.5613 (tp30) REVERT: A 293 LYS cc_start: 0.6958 (mttt) cc_final: 0.6488 (mtmt) REVERT: A 398 MET cc_start: 0.7136 (tpt) cc_final: 0.6542 (tpp) REVERT: A 420 LYS cc_start: 0.5812 (pptt) cc_final: 0.5318 (mtpt) REVERT: A 519 MET cc_start: 0.5764 (tpp) cc_final: 0.5272 (tpp) REVERT: A 653 VAL cc_start: 0.6687 (p) cc_final: 0.6476 (t) REVERT: A 683 LYS cc_start: 0.7307 (ttmm) cc_final: 0.7096 (tttp) REVERT: A 691 ASP cc_start: 0.6838 (m-30) cc_final: 0.6541 (m-30) REVERT: A 746 MET cc_start: 0.8370 (mmm) cc_final: 0.7921 (mmp) REVERT: A 763 LEU cc_start: 0.7502 (mm) cc_final: 0.7238 (mp) REVERT: A 799 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6357 (tp) REVERT: A 846 ARG cc_start: 0.6988 (mtm-85) cc_final: 0.6023 (mtt180) REVERT: A 847 LYS cc_start: 0.6827 (mtmt) cc_final: 0.6138 (mmpt) REVERT: A 860 GLN cc_start: 0.6436 (mp10) cc_final: 0.5775 (mp10) REVERT: A 872 MET cc_start: 0.7657 (mtt) cc_final: 0.7355 (mtm) REVERT: A 968 TRP cc_start: 0.6854 (m100) cc_final: 0.6526 (m100) REVERT: B 65 LYS cc_start: 0.7253 (pttm) cc_final: 0.6996 (pttm) REVERT: B 224 LYS cc_start: 0.6630 (mttm) cc_final: 0.6159 (mtpp) REVERT: B 229 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6578 (mm-30) REVERT: B 233 MET cc_start: 0.7372 (ttp) cc_final: 0.6867 (ttp) REVERT: B 293 GLN cc_start: 0.8088 (tt0) cc_final: 0.7823 (tt0) REVERT: B 299 LYS cc_start: 0.7115 (mtmm) cc_final: 0.6545 (mttp) outliers start: 21 outliers final: 6 residues processed: 162 average time/residue: 1.3312 time to fit residues: 232.2173 Evaluate side-chains 138 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain B residue 122 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 112 optimal weight: 0.7980 chunk 38 optimal weight: 0.0770 chunk 91 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 GLN B 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10451 Z= 0.153 Angle : 0.757 30.047 14121 Z= 0.326 Chirality : 0.041 0.188 1598 Planarity : 0.004 0.060 1768 Dihedral : 10.580 125.454 1722 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.48 % Allowed : 9.19 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1259 helix: 2.26 (0.22), residues: 553 sheet: 0.51 (0.42), residues: 130 loop : -0.35 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1029 HIS 0.005 0.001 HIS A 868 PHE 0.016 0.001 PHE A 335 TYR 0.017 0.001 TYR A 881 ARG 0.003 0.000 ARG B 143 *********************** 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 171 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.017 Fit side-chains REVERT: A 66 GLN cc_start: 0.5891 (mm-40) cc_final: 0.5344 (pt0) REVERT: A 175 LYS cc_start: 0.6578 (mptt) cc_final: 0.6247 (ttpp) REVERT: A 180 GLN cc_start: 0.6488 (pt0) cc_final: 0.6010 (mt0) REVERT: A 214 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: A 216 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.4892 (ttp80) REVERT: A 219 PHE cc_start: 0.6541 (m-80) cc_final: 0.6116 (m-10) REVERT: A 221 GLN cc_start: 0.6655 (mm-40) cc_final: 0.6139 (tp40) REVERT: A 246 GLU cc_start: 0.6091 (tp30) cc_final: 0.5552 (tp30) REVERT: A 254 ILE cc_start: 0.7133 (mt) cc_final: 0.6499 (mm) REVERT: A 293 LYS cc_start: 0.6994 (mttt) cc_final: 0.6550 (mtmt) REVERT: A 420 LYS cc_start: 0.5897 (pptt) cc_final: 0.5474 (mtpt) REVERT: A 442 ARG cc_start: 0.6108 (ttp-170) cc_final: 0.4783 (mtp-110) REVERT: A 534 MET cc_start: 0.6490 (tmt) cc_final: 0.6245 (tmt) REVERT: A 653 VAL cc_start: 0.6692 (p) cc_final: 0.6483 (t) REVERT: A 691 ASP cc_start: 0.6871 (m-30) cc_final: 0.6570 (m-30) REVERT: A 799 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6452 (tp) REVERT: A 844 MET cc_start: 0.7075 (mmt) cc_final: 0.6841 (mmp) REVERT: A 846 ARG cc_start: 0.7001 (mtm-85) cc_final: 0.6104 (mtt180) REVERT: A 847 LYS cc_start: 0.6920 (mtmt) cc_final: 0.6209 (mmpt) REVERT: A 860 GLN cc_start: 0.6497 (mp10) cc_final: 0.5752 (mp10) REVERT: A 872 MET cc_start: 0.7585 (mtt) cc_final: 0.7332 (mtm) REVERT: A 968 TRP cc_start: 0.6850 (m100) cc_final: 0.6550 (m100) REVERT: B 65 LYS cc_start: 0.7071 (pttm) cc_final: 0.6780 (pttm) REVERT: B 131 SER cc_start: 0.7060 (t) cc_final: 0.6814 (p) REVERT: B 229 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6712 (mm-30) REVERT: B 293 GLN cc_start: 0.8071 (tt0) cc_final: 0.7810 (tt0) REVERT: B 299 LYS cc_start: 0.7003 (mtmm) cc_final: 0.6353 (mttp) outliers start: 27 outliers final: 12 residues processed: 158 average time/residue: 1.1666 time to fit residues: 199.9795 Evaluate side-chains 147 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 214 ASP 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 460 VAL Chi-restraints excluded: chain A residue 616 SER 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 961 LEU Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 250 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 114 optimal weight: 0.0000 chunk 120 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.4982 ------------------------------------------------------------------------------- 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 396 ASN A 425 GLN A 449 GLN A 498 ASN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10451 Z= 0.150 Angle : 0.748 30.205 14121 Z= 0.319 Chirality : 0.041 0.204 1598 Planarity : 0.004 0.058 1768 Dihedral : 10.161 120.879 1722 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.03 % Allowed : 9.83 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1259 helix: 2.20 (0.22), residues: 554 sheet: 0.55 (0.42), residues: 130 loop : -0.33 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 968 HIS 0.004 0.001 HIS A 868 PHE 0.018 0.001 PHE A 471 TYR 0.017 0.001 TYR A 881 ARG 0.003 0.000 ARG A 216 *********************** 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 175 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 1.359 Fit side-chains REVERT: A 66 GLN cc_start: 0.5909 (mm-40) cc_final: 0.5349 (pt0) REVERT: A 175 LYS cc_start: 0.6611 (mptt) cc_final: 0.6258 (ttpp) REVERT: A 180 GLN cc_start: 0.6487 (pt0) cc_final: 0.5997 (mt0) REVERT: A 216 ARG cc_start: 0.7255 (OUTLIER) cc_final: 0.4923 (ttp80) REVERT: A 221 GLN cc_start: 0.6658 (mm-40) cc_final: 0.6209 (tp40) REVERT: A 246 GLU cc_start: 0.6068 (tp30) cc_final: 0.5500 (tp30) REVERT: A 254 ILE cc_start: 0.7203 (mt) cc_final: 0.6556 (mm) REVERT: A 293 LYS cc_start: 0.7041 (mttt) cc_final: 0.6586 (mtmt) REVERT: A 420 LYS cc_start: 0.6155 (pptt) cc_final: 0.5508 (mtpt) REVERT: A 442 ARG cc_start: 0.6337 (ttp-170) cc_final: 0.5005 (mtp180) REVERT: A 473 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6442 (mm-30) REVERT: A 653 VAL cc_start: 0.6697 (p) cc_final: 0.6487 (t) REVERT: A 681 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6372 (mt-10) REVERT: A 691 ASP cc_start: 0.6862 (m-30) cc_final: 0.6523 (m-30) REVERT: A 799 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6445 (tp) REVERT: A 846 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6107 (mtt180) REVERT: A 847 LYS cc_start: 0.6889 (mtmt) cc_final: 0.6191 (mmpt) REVERT: A 860 GLN cc_start: 0.6501 (mp10) cc_final: 0.5727 (mp10) REVERT: A 968 TRP cc_start: 0.6864 (m100) cc_final: 0.6563 (m100) REVERT: B 63 GLU cc_start: 0.6902 (pm20) cc_final: 0.6701 (pt0) REVERT: B 65 LYS cc_start: 0.6966 (pttm) cc_final: 0.6718 (pttm) REVERT: B 131 SER cc_start: 0.7018 (t) cc_final: 0.6794 (p) REVERT: B 229 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6770 (mm-30) REVERT: B 293 GLN cc_start: 0.8074 (tt0) cc_final: 0.7811 (tt0) REVERT: B 299 LYS cc_start: 0.6934 (mtmm) cc_final: 0.6172 (mttm) REVERT: B 302 VAL cc_start: 0.6849 (m) cc_final: 0.6409 (p) outliers start: 33 outliers final: 19 residues processed: 158 average time/residue: 1.2734 time to fit residues: 217.1876 Evaluate side-chains 152 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 260 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 394 THR 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 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 68 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 425 GLN A 501 GLN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 HIS B 55 GLN B 79 GLN B 140 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10451 Z= 0.372 Angle : 0.885 30.649 14121 Z= 0.399 Chirality : 0.047 0.236 1598 Planarity : 0.005 0.062 1768 Dihedral : 11.644 121.359 1722 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.58 % Allowed : 11.21 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1259 helix: 1.53 (0.22), residues: 542 sheet: 0.46 (0.41), residues: 129 loop : -0.48 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 968 HIS 0.008 0.002 HIS A 868 PHE 0.020 0.003 PHE A 471 TYR 0.026 0.002 TYR B 167 ARG 0.009 0.001 ARG A 849 *********************** 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 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6157 (mm-40) cc_final: 0.5760 (mp10) REVERT: A 175 LYS cc_start: 0.6778 (mptt) cc_final: 0.6299 (ttpp) REVERT: A 180 GLN cc_start: 0.6344 (pt0) cc_final: 0.5822 (mt0) REVERT: A 219 PHE cc_start: 0.6623 (m-80) cc_final: 0.6322 (m-10) REVERT: A 221 GLN cc_start: 0.6632 (mm-40) cc_final: 0.6195 (tp40) REVERT: A 293 LYS cc_start: 0.7047 (mttt) cc_final: 0.6405 (mtmt) REVERT: A 365 LYS cc_start: 0.5486 (ttmm) cc_final: 0.4863 (mptt) REVERT: A 420 LYS cc_start: 0.6096 (pptt) cc_final: 0.5372 (mtpt) REVERT: A 666 GLN cc_start: 0.5749 (mt0) cc_final: 0.4706 (tp40) REVERT: A 691 ASP cc_start: 0.6798 (m-30) cc_final: 0.6459 (m-30) REVERT: A 846 ARG cc_start: 0.7159 (mtm-85) cc_final: 0.6226 (mtt180) REVERT: A 847 LYS cc_start: 0.7207 (mtmt) cc_final: 0.6402 (mmpt) REVERT: A 860 GLN cc_start: 0.6536 (mp10) cc_final: 0.5807 (mp10) REVERT: B 65 LYS cc_start: 0.7049 (pttm) cc_final: 0.6797 (pttm) REVERT: B 93 ASN cc_start: 0.6412 (m110) cc_final: 0.5510 (m-40) REVERT: B 131 SER cc_start: 0.7023 (OUTLIER) cc_final: 0.6798 (p) REVERT: B 135 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6013 (tt0) REVERT: B 229 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6821 (mm-30) outliers start: 39 outliers final: 20 residues processed: 162 average time/residue: 1.2340 time to fit residues: 215.9764 Evaluate side-chains 146 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU 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 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 817 ILE Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 823 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN A 425 GLN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10451 Z= 0.180 Angle : 0.774 30.514 14121 Z= 0.336 Chirality : 0.042 0.249 1598 Planarity : 0.004 0.061 1768 Dihedral : 11.185 127.772 1722 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.12 % Allowed : 13.14 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1259 helix: 1.71 (0.22), residues: 551 sheet: 0.43 (0.42), residues: 128 loop : -0.51 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 968 HIS 0.003 0.001 HIS A 569 PHE 0.023 0.002 PHE A 335 TYR 0.018 0.001 TYR A 881 ARG 0.003 0.000 ARG A1018 *********************** 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 170 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6069 (mm-40) cc_final: 0.5380 (pt0) REVERT: A 175 LYS cc_start: 0.6729 (mptt) cc_final: 0.6284 (ttpp) REVERT: A 176 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5724 (mtp) REVERT: A 180 GLN cc_start: 0.6349 (pt0) cc_final: 0.5876 (mt0) REVERT: A 219 PHE cc_start: 0.6726 (m-80) cc_final: 0.6414 (m-10) REVERT: A 221 GLN cc_start: 0.6561 (mm-40) cc_final: 0.6212 (tp40) REVERT: A 223 CYS cc_start: 0.7311 (t) cc_final: 0.6893 (t) REVERT: A 293 LYS cc_start: 0.7093 (mttt) cc_final: 0.6601 (mtmt) REVERT: A 365 LYS cc_start: 0.5323 (ttmm) cc_final: 0.4719 (mptt) REVERT: A 411 VAL cc_start: 0.7499 (t) cc_final: 0.7194 (p) REVERT: A 420 LYS cc_start: 0.5987 (pptt) cc_final: 0.5271 (mtpt) REVERT: A 666 GLN cc_start: 0.5787 (mt0) cc_final: 0.4805 (tp40) REVERT: A 691 ASP cc_start: 0.6744 (m-30) cc_final: 0.6433 (m-30) REVERT: A 846 ARG cc_start: 0.6967 (mtm-85) cc_final: 0.6055 (mtt180) REVERT: A 847 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6439 (mmpt) REVERT: A 860 GLN cc_start: 0.6607 (mp10) cc_final: 0.5852 (mp10) REVERT: B 65 LYS cc_start: 0.7001 (pttm) cc_final: 0.6675 (pttm) REVERT: B 93 ASN cc_start: 0.6366 (m110) cc_final: 0.5469 (m-40) REVERT: B 131 SER cc_start: 0.7028 (OUTLIER) cc_final: 0.6808 (p) REVERT: B 229 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6809 (mm-30) outliers start: 34 outliers final: 21 residues processed: 157 average time/residue: 1.1801 time to fit residues: 200.6722 Evaluate side-chains 149 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 176 MET 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 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 680 MET Chi-restraints excluded: chain A residue 796 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10451 Z= 0.195 Angle : 0.776 30.361 14121 Z= 0.337 Chirality : 0.042 0.233 1598 Planarity : 0.004 0.060 1768 Dihedral : 10.829 127.867 1722 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.58 % Allowed : 13.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1259 helix: 1.74 (0.22), residues: 551 sheet: 0.39 (0.41), residues: 128 loop : -0.47 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1029 HIS 0.003 0.001 HIS A 868 PHE 0.023 0.002 PHE A 500 TYR 0.018 0.001 TYR A 881 ARG 0.003 0.000 ARG B 218 *********************** 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 169 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6065 (mm-40) cc_final: 0.5384 (pt0) REVERT: A 175 LYS cc_start: 0.6756 (mptt) cc_final: 0.6307 (ttpp) REVERT: A 180 GLN cc_start: 0.6359 (pt0) cc_final: 0.5884 (mt0) REVERT: A 221 GLN cc_start: 0.6541 (mm-40) cc_final: 0.6083 (tp40) REVERT: A 223 CYS cc_start: 0.7311 (t) cc_final: 0.6914 (t) REVERT: A 293 LYS cc_start: 0.7085 (mttt) cc_final: 0.6556 (mtmt) REVERT: A 365 LYS cc_start: 0.5239 (ttmm) cc_final: 0.4973 (ptmm) REVERT: A 411 VAL cc_start: 0.7494 (t) cc_final: 0.7173 (p) REVERT: A 420 LYS cc_start: 0.5999 (pptt) cc_final: 0.5264 (mtpt) REVERT: A 563 ARG cc_start: 0.4656 (ttm-80) cc_final: 0.4397 (tpp80) REVERT: A 666 GLN cc_start: 0.5762 (mt0) cc_final: 0.4825 (tp40) REVERT: A 691 ASP cc_start: 0.6732 (m-30) cc_final: 0.6426 (m-30) REVERT: A 748 ILE cc_start: 0.7146 (mt) cc_final: 0.6910 (mm) REVERT: A 838 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7075 (mttm) REVERT: A 846 ARG cc_start: 0.7034 (mtm-85) cc_final: 0.6128 (mtt180) REVERT: A 847 LYS cc_start: 0.7263 (mtmt) cc_final: 0.6429 (mmpt) REVERT: A 860 GLN cc_start: 0.6625 (mp10) cc_final: 0.5877 (mp10) REVERT: B 65 LYS cc_start: 0.6950 (pttm) cc_final: 0.6639 (pttm) REVERT: B 93 ASN cc_start: 0.6486 (m110) cc_final: 0.5600 (m-40) REVERT: B 129 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6655 (mmm) REVERT: B 131 SER cc_start: 0.6966 (OUTLIER) cc_final: 0.6753 (p) REVERT: B 229 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6822 (mm-30) outliers start: 39 outliers final: 25 residues processed: 150 average time/residue: 1.2073 time to fit residues: 195.6642 Evaluate side-chains 154 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU 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 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 680 MET Chi-restraints excluded: chain A residue 796 ILE 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 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 131 SER Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 224 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 11 optimal weight: 0.0060 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.8198 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10451 Z= 0.179 Angle : 0.766 30.454 14121 Z= 0.330 Chirality : 0.042 0.229 1598 Planarity : 0.004 0.058 1768 Dihedral : 10.460 126.818 1722 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.12 % Allowed : 13.88 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1259 helix: 1.81 (0.22), residues: 551 sheet: 0.44 (0.41), residues: 128 loop : -0.45 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1029 HIS 0.003 0.001 HIS A 569 PHE 0.024 0.002 PHE A 500 TYR 0.017 0.001 TYR A 881 ARG 0.003 0.000 ARG A 849 *********************** 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 156 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6070 (mm-40) cc_final: 0.5386 (pt0) REVERT: A 175 LYS cc_start: 0.6719 (mptt) cc_final: 0.6288 (ttpp) REVERT: A 180 GLN cc_start: 0.6306 (pt0) cc_final: 0.5851 (mt0) REVERT: A 221 GLN cc_start: 0.6487 (mm-40) cc_final: 0.6037 (tp40) REVERT: A 223 CYS cc_start: 0.7289 (t) cc_final: 0.6902 (t) REVERT: A 293 LYS cc_start: 0.7100 (mttt) cc_final: 0.6597 (mtmt) REVERT: A 411 VAL cc_start: 0.7468 (t) cc_final: 0.7161 (p) REVERT: A 420 LYS cc_start: 0.5985 (pptt) cc_final: 0.5259 (mtpt) REVERT: A 563 ARG cc_start: 0.4492 (ttm-80) cc_final: 0.4277 (tpp80) REVERT: A 666 GLN cc_start: 0.5762 (mt0) cc_final: 0.4853 (tp40) REVERT: A 691 ASP cc_start: 0.6681 (m-30) cc_final: 0.6389 (m-30) REVERT: A 748 ILE cc_start: 0.7144 (mt) cc_final: 0.6866 (mm) REVERT: A 838 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7070 (mttm) REVERT: A 846 ARG cc_start: 0.6940 (mtm-85) cc_final: 0.6100 (mtt180) REVERT: A 847 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6493 (mmpt) REVERT: A 860 GLN cc_start: 0.6602 (mp10) cc_final: 0.5863 (mp10) REVERT: B 65 LYS cc_start: 0.6873 (pttm) cc_final: 0.6583 (pttm) REVERT: B 129 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6637 (mmm) REVERT: B 131 SER cc_start: 0.6948 (OUTLIER) cc_final: 0.6743 (p) REVERT: B 229 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6889 (mm-30) outliers start: 34 outliers final: 24 residues processed: 142 average time/residue: 1.2187 time to fit residues: 187.3928 Evaluate side-chains 148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU 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 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 669 LYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 796 ILE 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 823 ASP 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.1980 chunk 115 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 118 optimal weight: 0.1980 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10451 Z= 0.183 Angle : 0.768 30.342 14121 Z= 0.332 Chirality : 0.042 0.218 1598 Planarity : 0.004 0.058 1768 Dihedral : 10.317 125.030 1722 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.31 % Allowed : 13.88 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1259 helix: 1.81 (0.22), residues: 551 sheet: 0.45 (0.41), residues: 128 loop : -0.43 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1029 HIS 0.003 0.001 HIS A 569 PHE 0.022 0.002 PHE A 335 TYR 0.017 0.001 TYR A 881 ARG 0.003 0.000 ARG A 216 *********************** 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 156 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6066 (mm-40) cc_final: 0.5384 (pt0) REVERT: A 175 LYS cc_start: 0.6766 (mptt) cc_final: 0.6271 (ttpp) REVERT: A 180 GLN cc_start: 0.6292 (pt0) cc_final: 0.5845 (mt0) REVERT: A 219 PHE cc_start: 0.6715 (m-80) cc_final: 0.6361 (m-10) REVERT: A 221 GLN cc_start: 0.6477 (mm-40) cc_final: 0.6009 (tp40) REVERT: A 223 CYS cc_start: 0.7288 (t) cc_final: 0.6906 (t) REVERT: A 293 LYS cc_start: 0.7058 (mttt) cc_final: 0.6550 (mtmt) REVERT: A 411 VAL cc_start: 0.7484 (t) cc_final: 0.7177 (p) REVERT: A 420 LYS cc_start: 0.6035 (pptt) cc_final: 0.5277 (mtpt) REVERT: A 563 ARG cc_start: 0.4544 (ttm-80) cc_final: 0.4344 (tpp80) REVERT: A 666 GLN cc_start: 0.5770 (mt0) cc_final: 0.4866 (tp40) REVERT: A 691 ASP cc_start: 0.6686 (m-30) cc_final: 0.6405 (m-30) REVERT: A 748 ILE cc_start: 0.7149 (mt) cc_final: 0.6914 (mm) REVERT: A 763 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7387 (mp) REVERT: A 838 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.7077 (mttm) REVERT: A 846 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6164 (mtt180) REVERT: A 847 LYS cc_start: 0.7302 (mtmt) cc_final: 0.6470 (mmpt) REVERT: A 860 GLN cc_start: 0.6554 (mp10) cc_final: 0.5816 (mp10) REVERT: B 65 LYS cc_start: 0.6939 (pttm) cc_final: 0.6655 (pttm) REVERT: B 129 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6637 (mmm) REVERT: B 131 SER cc_start: 0.6940 (OUTLIER) cc_final: 0.6734 (p) REVERT: B 229 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6911 (mm-30) outliers start: 36 outliers final: 27 residues processed: 142 average time/residue: 1.3118 time to fit residues: 201.2376 Evaluate side-chains 149 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU 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 669 LYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 796 ILE 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 823 ASP 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 1024 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 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 99 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10451 Z= 0.158 Angle : 0.760 30.348 14121 Z= 0.326 Chirality : 0.041 0.211 1598 Planarity : 0.004 0.057 1768 Dihedral : 9.886 121.828 1722 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.94 % Allowed : 14.52 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1259 helix: 1.89 (0.22), residues: 556 sheet: 0.53 (0.42), residues: 128 loop : -0.46 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A1029 HIS 0.003 0.001 HIS A 505 PHE 0.023 0.001 PHE A 335 TYR 0.015 0.001 TYR A 881 ARG 0.002 0.000 ARG A 216 ********************** 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 149 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.184 Fit side-chains REVERT: A 66 GLN cc_start: 0.6011 (mm-40) cc_final: 0.5627 (pt0) REVERT: A 175 LYS cc_start: 0.6776 (mptt) cc_final: 0.6284 (ttpp) REVERT: A 180 GLN cc_start: 0.6380 (pt0) cc_final: 0.5882 (mt0) REVERT: A 216 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.5169 (ttp80) REVERT: A 219 PHE cc_start: 0.6852 (m-80) cc_final: 0.6511 (m-10) REVERT: A 221 GLN cc_start: 0.6454 (mm-40) cc_final: 0.6114 (tp40) REVERT: A 223 CYS cc_start: 0.7281 (t) cc_final: 0.6899 (t) REVERT: A 293 LYS cc_start: 0.7018 (mttt) cc_final: 0.6547 (mtmt) REVERT: A 411 VAL cc_start: 0.7454 (t) cc_final: 0.7148 (p) REVERT: A 420 LYS cc_start: 0.6003 (pptt) cc_final: 0.5265 (mtpt) REVERT: A 455 MET cc_start: 0.7673 (mmp) cc_final: 0.7472 (mmp) REVERT: A 563 ARG cc_start: 0.4584 (ttm-80) cc_final: 0.4373 (tpp80) REVERT: A 666 GLN cc_start: 0.5753 (mt0) cc_final: 0.4841 (tp40) REVERT: A 691 ASP cc_start: 0.6701 (m-30) cc_final: 0.6425 (m-30) REVERT: A 748 ILE cc_start: 0.7162 (mt) cc_final: 0.6877 (mm) REVERT: A 763 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7304 (mp) REVERT: A 838 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6989 (mttm) REVERT: A 846 ARG cc_start: 0.6937 (mtm-85) cc_final: 0.6109 (mtt180) REVERT: A 847 LYS cc_start: 0.7220 (mtmt) cc_final: 0.6438 (mmtm) REVERT: A 860 GLN cc_start: 0.6537 (mp10) cc_final: 0.5795 (mp10) REVERT: A 968 TRP cc_start: 0.6986 (m100) cc_final: 0.6701 (m100) REVERT: B 65 LYS cc_start: 0.6907 (pttm) cc_final: 0.6623 (pttm) REVERT: B 129 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6592 (mmm) REVERT: B 131 SER cc_start: 0.7004 (OUTLIER) cc_final: 0.6776 (p) REVERT: B 229 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6844 (mm-30) outliers start: 32 outliers final: 23 residues processed: 138 average time/residue: 1.3063 time to fit residues: 194.1722 Evaluate side-chains 142 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU 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 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 669 LYS Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 796 ILE 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 893 THR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1024 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 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.173957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.134231 restraints weight = 10958.813| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.78 r_work: 0.3149 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 10451 Z= 0.157 Angle : 0.757 30.237 14121 Z= 0.324 Chirality : 0.041 0.204 1598 Planarity : 0.004 0.057 1768 Dihedral : 9.547 120.113 1722 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.94 % Allowed : 14.80 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1259 helix: 1.93 (0.22), residues: 557 sheet: 0.61 (0.42), residues: 128 loop : -0.44 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A1029 HIS 0.003 0.001 HIS A 569 PHE 0.022 0.001 PHE A 335 TYR 0.016 0.001 TYR A 881 ARG 0.002 0.000 ARG A 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3915.94 seconds wall clock time: 71 minutes 48.60 seconds (4308.60 seconds total)