Starting phenix.real_space_refine on Tue Jun 10 01:16:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x22_32955/06_2025/7x22_32955_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x22_32955/06_2025/7x22_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_32955/06_2025/7x22_32955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x22_32955/06_2025/7x22_32955.map" model { file = "/net/cci-nas-00/data/ceres_data/7x22_32955/06_2025/7x22_32955_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x22_32955/06_2025/7x22_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-5710/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: 6.40, per 1000 atoms: 0.62 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: 2.55 Conformation dependent library (CDL) restraints added in 1.4 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: 1.16 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: 3.47 Time building geometry restraints manager: 3.00 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: 1.060 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 26.310 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:12.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.800 ------------------------------------------------------------------------------- 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 : 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 1) link_NAG-ASN : angle 1.74343 ( 3) hydrogen bonds : bond 0.15194 ( 486) hydrogen bonds : angle 6.15754 ( 1407) SS BOND : bond 0.00074 ( 3) SS BOND : angle 0.60114 ( 6) covalent geometry : bond 0.00541 (10451) covalent geometry : angle 1.15286 (14121) *********************** 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 : 1.068 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: 1.2983 time to fit residues: 270.1070 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 : 1.088 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.177375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.137672 restraints weight = 11083.096| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.75 r_work: 0.3190 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 10455 Z= 0.118 Angle : 0.792 30.110 14130 Z= 0.346 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 5.00551 ( 3) hydrogen bonds : bond 0.04377 ( 486) hydrogen bonds : angle 4.71739 ( 1407) SS BOND : bond 0.00081 ( 3) SS BOND : angle 0.68571 ( 6) covalent geometry : bond 0.00248 (10451) covalent geometry : angle 0.78873 (14121) *********************** 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 : 1.093 Fit side-chains REVERT: A 66 GLN cc_start: 0.6153 (mm-40) cc_final: 0.5671 (pt0) REVERT: A 180 GLN cc_start: 0.6803 (pt0) cc_final: 0.6461 (mt0) REVERT: A 195 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7106 (mt-10) REVERT: A 219 PHE cc_start: 0.7158 (m-80) cc_final: 0.6824 (m-10) REVERT: A 246 GLU cc_start: 0.6360 (tp30) cc_final: 0.5906 (tp30) REVERT: A 293 LYS cc_start: 0.7512 (mttt) cc_final: 0.7152 (mtmt) REVERT: A 398 MET cc_start: 0.7621 (tpt) cc_final: 0.7384 (tpp) REVERT: A 420 LYS cc_start: 0.6167 (pptt) cc_final: 0.5716 (mtpt) REVERT: A 473 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 519 MET cc_start: 0.6599 (tpp) cc_final: 0.6216 (tpp) REVERT: A 653 VAL cc_start: 0.7267 (p) cc_final: 0.7009 (t) REVERT: A 691 ASP cc_start: 0.7609 (m-30) cc_final: 0.7346 (m-30) REVERT: A 746 MET cc_start: 0.8780 (mmm) cc_final: 0.8513 (mmp) REVERT: A 763 LEU cc_start: 0.7962 (mm) cc_final: 0.7542 (mp) REVERT: A 799 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7516 (tp) REVERT: A 846 ARG cc_start: 0.7705 (mtm-85) cc_final: 0.7009 (mtt180) REVERT: A 847 LYS cc_start: 0.7513 (mtmt) cc_final: 0.7129 (mmpt) REVERT: A 860 GLN cc_start: 0.7686 (mp10) cc_final: 0.7251 (mp10) REVERT: A 872 MET cc_start: 0.8231 (mtt) cc_final: 0.7939 (mtm) REVERT: A 968 TRP cc_start: 0.7774 (m100) cc_final: 0.7434 (m100) REVERT: B 121 MET cc_start: 0.6252 (tpt) cc_final: 0.6006 (mpp) REVERT: B 224 LYS cc_start: 0.7100 (mttm) cc_final: 0.6699 (mtpp) REVERT: B 229 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 233 MET cc_start: 0.7914 (ttp) cc_final: 0.7507 (ttp) REVERT: B 299 LYS cc_start: 0.8000 (mtmm) cc_final: 0.7523 (mttp) outliers start: 21 outliers final: 6 residues processed: 162 average time/residue: 1.2049 time to fit residues: 210.2493 Evaluate side-chains 136 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 122 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 51 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 0.0470 chunk 98 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.5256 ------------------------------------------------------------------------------- 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 ** 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 140 ASN B 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.173607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.131370 restraints weight = 11227.850| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.89 r_work: 0.3140 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10455 Z= 0.111 Angle : 0.762 29.980 14130 Z= 0.327 Chirality : 0.041 0.182 1598 Planarity : 0.004 0.060 1768 Dihedral : 10.703 128.147 1722 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.11 % Allowed : 9.65 % Favored : 88.24 % 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: 1.40 (0.24), residues: 1259 helix: 2.32 (0.22), residues: 548 sheet: 0.51 (0.43), residues: 130 loop : -0.31 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1029 HIS 0.004 0.001 HIS A 868 PHE 0.015 0.001 PHE A 335 TYR 0.017 0.001 TYR A 881 ARG 0.003 0.000 ARG A 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00815 ( 1) link_NAG-ASN : angle 5.47898 ( 3) hydrogen bonds : bond 0.04058 ( 486) hydrogen bonds : angle 4.47956 ( 1407) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.68716 ( 6) covalent geometry : bond 0.00242 (10451) covalent geometry : angle 0.75777 (14121) *********************** 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 163 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 1.119 Fit side-chains REVERT: A 66 GLN cc_start: 0.6162 (mm-40) cc_final: 0.5647 (pt0) REVERT: A 176 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6468 (mtp) REVERT: A 180 GLN cc_start: 0.6744 (pt0) cc_final: 0.6356 (mt0) REVERT: A 189 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6738 (mtpt) REVERT: A 216 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.5884 (ttp80) REVERT: A 219 PHE cc_start: 0.7108 (m-80) cc_final: 0.6738 (m-10) REVERT: A 221 GLN cc_start: 0.6901 (mm-40) cc_final: 0.6465 (tp40) REVERT: A 246 GLU cc_start: 0.6341 (tp30) cc_final: 0.5861 (tp30) REVERT: A 254 ILE cc_start: 0.8128 (mt) cc_final: 0.7649 (mm) REVERT: A 293 LYS cc_start: 0.7531 (mttt) cc_final: 0.7204 (mtmt) REVERT: A 420 LYS cc_start: 0.6201 (pptt) cc_final: 0.5694 (mtpt) REVERT: A 442 ARG cc_start: 0.6386 (ttp-170) cc_final: 0.5160 (mtp-110) REVERT: A 653 VAL cc_start: 0.7234 (p) cc_final: 0.6983 (t) REVERT: A 691 ASP cc_start: 0.7689 (m-30) cc_final: 0.7416 (m-30) REVERT: A 763 LEU cc_start: 0.7915 (mm) cc_final: 0.7528 (mp) REVERT: A 846 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7103 (mtt180) REVERT: A 847 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7170 (mmpt) REVERT: A 860 GLN cc_start: 0.7811 (mp10) cc_final: 0.7320 (mp10) REVERT: A 872 MET cc_start: 0.8222 (mtt) cc_final: 0.7970 (mtm) REVERT: A 968 TRP cc_start: 0.7773 (m100) cc_final: 0.7464 (m100) REVERT: B 121 MET cc_start: 0.6333 (tpt) cc_final: 0.5966 (mpp) REVERT: B 131 SER cc_start: 0.7740 (t) cc_final: 0.7512 (p) REVERT: B 224 LYS cc_start: 0.7086 (mttm) cc_final: 0.6650 (mtpp) REVERT: B 229 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7440 (mm-30) REVERT: B 233 MET cc_start: 0.8015 (ttp) cc_final: 0.7604 (ttp) REVERT: B 299 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7415 (mttp) outliers start: 23 outliers final: 13 residues processed: 151 average time/residue: 1.1542 time to fit residues: 188.8375 Evaluate side-chains 149 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 460 VAL Chi-restraints excluded: chain A residue 616 SER 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 184 LEU 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 21 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 449 GLN A 498 ASN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.172467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.130339 restraints weight = 11052.449| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.89 r_work: 0.3134 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10455 Z= 0.115 Angle : 0.765 30.244 14130 Z= 0.329 Chirality : 0.042 0.193 1598 Planarity : 0.004 0.059 1768 Dihedral : 10.279 119.277 1722 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.85 % Allowed : 10.57 % Favored : 86.58 % 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: 1.27 (0.24), residues: 1259 helix: 2.19 (0.22), residues: 547 sheet: 0.50 (0.42), residues: 130 loop : -0.37 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1029 HIS 0.006 0.001 HIS A 868 PHE 0.017 0.002 PHE A 595 TYR 0.018 0.001 TYR A 881 ARG 0.004 0.000 ARG A 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 1) link_NAG-ASN : angle 3.72428 ( 3) hydrogen bonds : bond 0.04106 ( 486) hydrogen bonds : angle 4.33473 ( 1407) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.83850 ( 6) covalent geometry : bond 0.00254 (10451) covalent geometry : angle 0.76270 (14121) *********************** 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 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6161 (mm-40) cc_final: 0.5658 (pt0) REVERT: A 180 GLN cc_start: 0.6780 (pt0) cc_final: 0.6381 (mt0) REVERT: A 189 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6709 (mtpt) REVERT: A 221 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6529 (tp40) REVERT: A 293 LYS cc_start: 0.7588 (mttt) cc_final: 0.7238 (mtmt) REVERT: A 420 LYS cc_start: 0.6348 (pptt) cc_final: 0.5798 (mtpt) REVERT: A 442 ARG cc_start: 0.6616 (ttp-170) cc_final: 0.5391 (mtp180) REVERT: A 563 ARG cc_start: 0.5659 (ttm-80) cc_final: 0.5292 (tpp80) REVERT: A 653 VAL cc_start: 0.7279 (p) cc_final: 0.7036 (t) REVERT: A 691 ASP cc_start: 0.7696 (m-30) cc_final: 0.7381 (m-30) REVERT: A 763 LEU cc_start: 0.7903 (mm) cc_final: 0.7573 (mp) REVERT: A 844 MET cc_start: 0.7709 (mmt) cc_final: 0.7492 (mmp) REVERT: A 846 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7183 (mtt180) REVERT: A 847 LYS cc_start: 0.7623 (mtmt) cc_final: 0.7187 (mmpt) REVERT: A 860 GLN cc_start: 0.7809 (mp10) cc_final: 0.7310 (mp10) REVERT: A 872 MET cc_start: 0.8251 (mtt) cc_final: 0.8014 (mtm) REVERT: A 911 GLU cc_start: 0.8387 (tt0) cc_final: 0.7973 (tt0) REVERT: A 968 TRP cc_start: 0.7742 (m100) cc_final: 0.7467 (m100) REVERT: B 34 LYS cc_start: 0.7920 (mppt) cc_final: 0.7711 (mtmm) REVERT: B 121 MET cc_start: 0.6390 (tpt) cc_final: 0.5989 (mpp) REVERT: B 131 SER cc_start: 0.7706 (t) cc_final: 0.7465 (p) REVERT: B 229 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7577 (mm-30) REVERT: B 299 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7289 (mttm) outliers start: 31 outliers final: 19 residues processed: 162 average time/residue: 1.1375 time to fit residues: 199.6850 Evaluate side-chains 152 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 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 616 SER 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 250 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 35 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.0000 chunk 80 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 0.0010 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 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 = 0.3939 r_free = 0.3939 target = 0.181237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.141063 restraints weight = 11022.211| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.57 r_work: 0.3195 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10455 Z= 0.098 Angle : 0.744 30.190 14130 Z= 0.316 Chirality : 0.041 0.216 1598 Planarity : 0.004 0.056 1768 Dihedral : 9.922 124.513 1722 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.67 % Allowed : 12.41 % Favored : 84.93 % 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: 1.32 (0.24), residues: 1259 helix: 2.19 (0.22), residues: 554 sheet: 0.56 (0.42), residues: 131 loop : -0.34 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1029 HIS 0.003 0.001 HIS A 868 PHE 0.021 0.001 PHE A 500 TYR 0.015 0.001 TYR A 881 ARG 0.003 0.000 ARG A 563 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 1) link_NAG-ASN : angle 2.95190 ( 3) hydrogen bonds : bond 0.03627 ( 486) hydrogen bonds : angle 4.18385 ( 1407) SS BOND : bond 0.00062 ( 3) SS BOND : angle 0.59909 ( 6) covalent geometry : bond 0.00206 (10451) covalent geometry : angle 0.74296 (14121) *********************** 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 167 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.075 Fit side-chains REVERT: A 66 GLN cc_start: 0.6145 (mm-40) cc_final: 0.5658 (pt0) REVERT: A 180 GLN cc_start: 0.6734 (pt0) cc_final: 0.6348 (mt0) REVERT: A 189 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6764 (mtpt) REVERT: A 221 GLN cc_start: 0.6828 (mm-40) cc_final: 0.6553 (tp40) REVERT: A 293 LYS cc_start: 0.7494 (mttt) cc_final: 0.7202 (mtmt) REVERT: A 420 LYS cc_start: 0.6316 (pptt) cc_final: 0.5760 (mtpt) REVERT: A 442 ARG cc_start: 0.6687 (ttp-170) cc_final: 0.5332 (mtp180) REVERT: A 473 GLU cc_start: 0.7146 (mm-30) cc_final: 0.5890 (tp30) REVERT: A 563 ARG cc_start: 0.5630 (ttm-80) cc_final: 0.5319 (tpp80) REVERT: A 653 VAL cc_start: 0.7231 (p) cc_final: 0.7024 (t) REVERT: A 691 ASP cc_start: 0.7543 (m-30) cc_final: 0.7256 (m-30) REVERT: A 763 LEU cc_start: 0.7766 (mm) cc_final: 0.7506 (mp) REVERT: A 799 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7436 (tp) REVERT: A 846 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7114 (mtt180) REVERT: A 847 LYS cc_start: 0.7554 (mtmt) cc_final: 0.7088 (mmpt) REVERT: A 860 GLN cc_start: 0.7759 (mp10) cc_final: 0.7251 (mp10) REVERT: A 968 TRP cc_start: 0.7653 (m100) cc_final: 0.7393 (m100) REVERT: B 117 GLN cc_start: 0.7928 (mt0) cc_final: 0.7654 (mt0) REVERT: B 121 MET cc_start: 0.6359 (tpt) cc_final: 0.5962 (mpp) REVERT: B 131 SER cc_start: 0.7716 (OUTLIER) cc_final: 0.7449 (p) REVERT: B 229 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7505 (mm-30) REVERT: B 299 LYS cc_start: 0.7895 (mtmm) cc_final: 0.7272 (mttm) outliers start: 29 outliers final: 14 residues processed: 156 average time/residue: 1.1857 time to fit residues: 199.4102 Evaluate side-chains 145 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LYS 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 454 ILE Chi-restraints excluded: chain A residue 460 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 129 MET Chi-restraints excluded: chain B residue 131 SER 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 105 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 85 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN ** A 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN A 501 GLN A 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.178507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.139566 restraints weight = 11041.290| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.63 r_work: 0.3254 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10455 Z= 0.108 Angle : 0.754 30.314 14130 Z= 0.322 Chirality : 0.041 0.206 1598 Planarity : 0.004 0.056 1768 Dihedral : 9.860 123.087 1722 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.94 % Allowed : 13.14 % Favored : 83.92 % 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: 1.24 (0.24), residues: 1259 helix: 2.04 (0.22), residues: 559 sheet: 0.66 (0.43), residues: 130 loop : -0.34 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1029 HIS 0.004 0.001 HIS A 868 PHE 0.022 0.002 PHE A 500 TYR 0.018 0.001 TYR A 881 ARG 0.003 0.000 ARG A 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00589 ( 1) link_NAG-ASN : angle 2.32115 ( 3) hydrogen bonds : bond 0.03834 ( 486) hydrogen bonds : angle 4.15535 ( 1407) SS BOND : bond 0.00092 ( 3) SS BOND : angle 0.71634 ( 6) covalent geometry : bond 0.00237 (10451) covalent geometry : angle 0.75295 (14121) *********************** 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 163 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 1.114 Fit side-chains REVERT: A 66 GLN cc_start: 0.6174 (mm-40) cc_final: 0.5729 (pt0) REVERT: A 180 GLN cc_start: 0.6799 (pt0) cc_final: 0.6485 (mt0) REVERT: A 216 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.6137 (ttp80) REVERT: A 221 GLN cc_start: 0.6768 (mm-40) cc_final: 0.6508 (tp40) REVERT: A 293 LYS cc_start: 0.7622 (mttt) cc_final: 0.7317 (mtmt) REVERT: A 420 LYS cc_start: 0.6351 (pptt) cc_final: 0.5802 (mtpt) REVERT: A 563 ARG cc_start: 0.5802 (ttm-80) cc_final: 0.5511 (ttm-80) REVERT: A 691 ASP cc_start: 0.7606 (m-30) cc_final: 0.7356 (m-30) REVERT: A 748 ILE cc_start: 0.7948 (mt) cc_final: 0.7700 (mm) REVERT: A 763 LEU cc_start: 0.7871 (mm) cc_final: 0.7545 (mp) REVERT: A 799 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7532 (tp) REVERT: A 846 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7225 (mtt180) REVERT: A 847 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7202 (mmpt) REVERT: A 860 GLN cc_start: 0.7808 (mp10) cc_final: 0.7277 (mp10) REVERT: A 968 TRP cc_start: 0.7758 (m100) cc_final: 0.7506 (m100) REVERT: B 34 LYS cc_start: 0.7920 (mppt) cc_final: 0.7688 (mtmm) REVERT: B 121 MET cc_start: 0.6477 (tpt) cc_final: 0.6153 (mpp) REVERT: B 131 SER cc_start: 0.7806 (OUTLIER) cc_final: 0.7567 (p) REVERT: B 229 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7580 (mm-30) REVERT: B 299 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7425 (mttm) outliers start: 32 outliers final: 19 residues processed: 150 average time/residue: 1.2001 time to fit residues: 194.1871 Evaluate side-chains 146 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 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 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 131 SER 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 12 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 114 optimal weight: 0.2980 chunk 98 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 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 = 0.3909 r_free = 0.3909 target = 0.178215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.139659 restraints weight = 11103.480| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.82 r_work: 0.3173 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10455 Z= 0.116 Angle : 0.763 30.273 14130 Z= 0.328 Chirality : 0.042 0.215 1598 Planarity : 0.004 0.056 1768 Dihedral : 9.945 123.549 1722 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.76 % Allowed : 13.88 % Favored : 83.36 % 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: 1.21 (0.24), residues: 1259 helix: 2.00 (0.22), residues: 557 sheet: 0.77 (0.42), residues: 128 loop : -0.37 (0.26), residues: 574 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 0.020 0.002 PHE A 500 TYR 0.018 0.001 TYR A 881 ARG 0.003 0.000 ARG A 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 1) link_NAG-ASN : angle 2.27001 ( 3) hydrogen bonds : bond 0.04045 ( 486) hydrogen bonds : angle 4.20627 ( 1407) SS BOND : bond 0.00125 ( 3) SS BOND : angle 0.85463 ( 6) covalent geometry : bond 0.00263 (10451) covalent geometry : angle 0.76258 (14121) *********************** 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 163 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 1.759 Fit side-chains revert: symmetry clash REVERT: A 66 GLN cc_start: 0.6131 (mm-40) cc_final: 0.5761 (pt0) REVERT: A 180 GLN cc_start: 0.6671 (pt0) cc_final: 0.6347 (mt0) REVERT: A 216 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.5998 (ttp80) REVERT: A 221 GLN cc_start: 0.6723 (mm-40) cc_final: 0.6379 (tp40) REVERT: A 223 CYS cc_start: 0.7524 (t) cc_final: 0.7123 (t) REVERT: A 293 LYS cc_start: 0.7557 (mttt) cc_final: 0.7241 (mtmt) REVERT: A 365 LYS cc_start: 0.6433 (ptmm) cc_final: 0.5773 (mptt) REVERT: A 411 VAL cc_start: 0.7684 (t) cc_final: 0.7362 (p) REVERT: A 420 LYS cc_start: 0.6255 (pptt) cc_final: 0.5680 (mtpt) REVERT: A 563 ARG cc_start: 0.5642 (ttm-80) cc_final: 0.5327 (ttm-80) REVERT: A 666 GLN cc_start: 0.6027 (mt0) cc_final: 0.4891 (tp40) REVERT: A 691 ASP cc_start: 0.7465 (m-30) cc_final: 0.7194 (m-30) REVERT: A 763 LEU cc_start: 0.7836 (mm) cc_final: 0.7631 (mp) REVERT: A 799 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7544 (tp) REVERT: A 846 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7151 (mtt180) REVERT: A 847 LYS cc_start: 0.7680 (mtmt) cc_final: 0.7178 (mmpt) REVERT: A 860 GLN cc_start: 0.7766 (mp10) cc_final: 0.7227 (mp10) REVERT: A 911 GLU cc_start: 0.8298 (tt0) cc_final: 0.7821 (tt0) REVERT: A 968 TRP cc_start: 0.7741 (m100) cc_final: 0.7492 (m100) REVERT: B 34 LYS cc_start: 0.7816 (mppt) cc_final: 0.7574 (mtmm) REVERT: B 121 MET cc_start: 0.6365 (tpt) cc_final: 0.5657 (mpp) REVERT: B 129 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6856 (mmm) REVERT: B 131 SER cc_start: 0.7655 (t) cc_final: 0.7433 (p) REVERT: B 229 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7522 (mm-30) REVERT: B 299 LYS cc_start: 0.7867 (mtmm) cc_final: 0.7256 (mttm) outliers start: 30 outliers final: 20 residues processed: 153 average time/residue: 1.6231 time to fit residues: 270.8546 Evaluate side-chains 148 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 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 400 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 669 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 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 203 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 89 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 540 GLN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.179689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.140568 restraints weight = 11007.083| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.59 r_work: 0.3280 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10455 Z= 0.116 Angle : 0.767 30.199 14130 Z= 0.329 Chirality : 0.042 0.216 1598 Planarity : 0.004 0.057 1768 Dihedral : 9.893 122.937 1722 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.48 % Allowed : 14.89 % Favored : 82.63 % 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: 1.21 (0.24), residues: 1259 helix: 2.02 (0.22), residues: 550 sheet: 0.66 (0.42), residues: 128 loop : -0.33 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1029 HIS 0.003 0.001 HIS A 868 PHE 0.019 0.002 PHE A 500 TYR 0.018 0.001 TYR A 881 ARG 0.003 0.000 ARG A 849 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 1) link_NAG-ASN : angle 2.28881 ( 3) hydrogen bonds : bond 0.04022 ( 486) hydrogen bonds : angle 4.20986 ( 1407) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.87915 ( 6) covalent geometry : bond 0.00262 (10451) covalent geometry : angle 0.76598 (14121) *********************** 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 152 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.949 Fit side-chains REVERT: A 66 GLN cc_start: 0.6310 (mm-40) cc_final: 0.5967 (pt0) REVERT: A 180 GLN cc_start: 0.6709 (pt0) cc_final: 0.6435 (mt0) REVERT: A 216 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.6055 (ttp80) REVERT: A 221 GLN cc_start: 0.6743 (mm-40) cc_final: 0.6454 (tp40) REVERT: A 223 CYS cc_start: 0.7515 (t) cc_final: 0.7153 (t) REVERT: A 293 LYS cc_start: 0.7639 (mttt) cc_final: 0.7351 (mtmt) REVERT: A 411 VAL cc_start: 0.7693 (t) cc_final: 0.7375 (p) REVERT: A 420 LYS cc_start: 0.6314 (pptt) cc_final: 0.5679 (mtpt) REVERT: A 563 ARG cc_start: 0.5744 (ttm-80) cc_final: 0.5513 (ttm-80) REVERT: A 666 GLN cc_start: 0.5957 (mt0) cc_final: 0.4918 (tp40) REVERT: A 691 ASP cc_start: 0.7561 (m-30) cc_final: 0.7315 (m-30) REVERT: A 799 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7632 (tp) REVERT: A 846 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7227 (mtt180) REVERT: A 847 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7315 (mmpt) REVERT: A 860 GLN cc_start: 0.7818 (mp10) cc_final: 0.7365 (mp10) REVERT: A 911 GLU cc_start: 0.8321 (tt0) cc_final: 0.7842 (tt0) REVERT: A 968 TRP cc_start: 0.7813 (m100) cc_final: 0.7563 (m100) REVERT: B 34 LYS cc_start: 0.7918 (mppt) cc_final: 0.7683 (mtmm) REVERT: B 121 MET cc_start: 0.6422 (tpt) cc_final: 0.5740 (mpp) REVERT: B 129 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6938 (mmm) REVERT: B 131 SER cc_start: 0.7791 (t) cc_final: 0.7591 (p) REVERT: B 229 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 299 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7403 (mttm) outliers start: 27 outliers final: 19 residues processed: 142 average time/residue: 1.2907 time to fit residues: 197.6718 Evaluate side-chains 141 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 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 400 VAL Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 460 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 203 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.0970 overall best weight: 1.1180 ------------------------------------------------------------------------------- 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 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 = 0.3816 r_free = 0.3816 target = 0.170242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.128143 restraints weight = 11179.666| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.90 r_work: 0.3102 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10455 Z= 0.138 Angle : 0.793 30.324 14130 Z= 0.345 Chirality : 0.043 0.222 1598 Planarity : 0.004 0.058 1768 Dihedral : 10.361 123.904 1722 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.85 % Allowed : 14.89 % 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: 1.03 (0.23), residues: 1259 helix: 1.85 (0.22), residues: 550 sheet: 0.53 (0.41), residues: 128 loop : -0.39 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1029 HIS 0.007 0.001 HIS A 868 PHE 0.019 0.002 PHE A 335 TYR 0.020 0.001 TYR A 881 ARG 0.003 0.000 ARG A1018 Details of bonding type rmsd link_NAG-ASN : bond 0.00545 ( 1) link_NAG-ASN : angle 2.45243 ( 3) hydrogen bonds : bond 0.04500 ( 486) hydrogen bonds : angle 4.35126 ( 1407) SS BOND : bond 0.00171 ( 3) SS BOND : angle 1.11354 ( 6) covalent geometry : bond 0.00322 (10451) covalent geometry : angle 0.79176 (14121) *********************** 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 161 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6855 (ptt-90) REVERT: A 66 GLN cc_start: 0.6348 (mm-40) cc_final: 0.5682 (pt0) REVERT: A 180 GLN cc_start: 0.6693 (pt0) cc_final: 0.6324 (mt0) REVERT: A 216 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.5794 (ttp80) REVERT: A 221 GLN cc_start: 0.6704 (mm-40) cc_final: 0.6355 (tp40) REVERT: A 223 CYS cc_start: 0.7574 (t) cc_final: 0.7228 (t) REVERT: A 293 LYS cc_start: 0.7583 (mttt) cc_final: 0.7248 (mtmt) REVERT: A 420 LYS cc_start: 0.6170 (pptt) cc_final: 0.5516 (mtpt) REVERT: A 425 GLN cc_start: 0.5163 (mt0) cc_final: 0.4943 (mt0) REVERT: A 534 MET cc_start: 0.6496 (tmt) cc_final: 0.6019 (ppp) REVERT: A 563 ARG cc_start: 0.5671 (ttm-80) cc_final: 0.5386 (tpp80) REVERT: A 666 GLN cc_start: 0.5853 (mt0) cc_final: 0.4863 (tp40) REVERT: A 691 ASP cc_start: 0.7536 (m-30) cc_final: 0.7259 (m-30) REVERT: A 799 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7710 (tp) REVERT: A 846 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7135 (mtt180) REVERT: A 847 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7323 (mmpt) REVERT: A 860 GLN cc_start: 0.7881 (mp10) cc_final: 0.7368 (mp10) REVERT: A 968 TRP cc_start: 0.7882 (m100) cc_final: 0.7654 (m100) REVERT: B 34 LYS cc_start: 0.7839 (mppt) cc_final: 0.7627 (mtmm) REVERT: B 121 MET cc_start: 0.6537 (tpt) cc_final: 0.5660 (mpp) REVERT: B 129 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6986 (mmm) REVERT: B 229 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 299 LYS cc_start: 0.7881 (mtmm) cc_final: 0.7492 (mtmm) outliers start: 31 outliers final: 21 residues processed: 149 average time/residue: 1.2163 time to fit residues: 195.4215 Evaluate side-chains 151 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 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 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 203 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 7 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 61 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 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 = 0.3896 r_free = 0.3896 target = 0.177027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.137224 restraints weight = 11121.049| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.81 r_work: 0.3170 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 10455 Z= 0.111 Angle : 0.767 30.415 14130 Z= 0.329 Chirality : 0.041 0.220 1598 Planarity : 0.004 0.057 1768 Dihedral : 10.124 122.853 1722 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.11 % Allowed : 15.62 % 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: 1.11 (0.23), residues: 1259 helix: 2.02 (0.22), residues: 543 sheet: 0.47 (0.41), residues: 128 loop : -0.40 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A1029 HIS 0.003 0.001 HIS A 868 PHE 0.023 0.001 PHE A 335 TYR 0.016 0.001 TYR A 881 ARG 0.003 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 1) link_NAG-ASN : angle 2.21862 ( 3) hydrogen bonds : bond 0.03954 ( 486) hydrogen bonds : angle 4.22457 ( 1407) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.80377 ( 6) covalent geometry : bond 0.00246 (10451) covalent geometry : angle 0.76598 (14121) ********************** 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: 23 poor density : 126 time to evaluate : 1.101 Fit side-chains REVERT: A 66 GLN cc_start: 0.6208 (mm-40) cc_final: 0.5846 (pt0) REVERT: A 180 GLN cc_start: 0.6613 (pt0) cc_final: 0.6272 (mt0) REVERT: A 216 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.5741 (ttp80) REVERT: A 221 GLN cc_start: 0.6658 (mm-40) cc_final: 0.6336 (tp40) REVERT: A 223 CYS cc_start: 0.7541 (t) cc_final: 0.7178 (t) REVERT: A 293 LYS cc_start: 0.7536 (mttt) cc_final: 0.7222 (mtmt) REVERT: A 411 VAL cc_start: 0.7697 (t) cc_final: 0.7368 (p) REVERT: A 420 LYS cc_start: 0.6175 (pptt) cc_final: 0.5566 (mtpt) REVERT: A 534 MET cc_start: 0.6448 (tmt) cc_final: 0.6026 (ppp) REVERT: A 563 ARG cc_start: 0.5597 (ttm-80) cc_final: 0.5312 (tpp80) REVERT: A 653 VAL cc_start: 0.7192 (p) cc_final: 0.6987 (t) REVERT: A 666 GLN cc_start: 0.5862 (mt0) cc_final: 0.4882 (tp40) REVERT: A 691 ASP cc_start: 0.7422 (m-30) cc_final: 0.7156 (m-30) REVERT: A 748 ILE cc_start: 0.7935 (mt) cc_final: 0.7716 (mm) REVERT: A 799 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7577 (tp) REVERT: A 846 ARG cc_start: 0.7720 (mtm-85) cc_final: 0.7071 (mtt180) REVERT: A 847 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7236 (mmpt) REVERT: A 860 GLN cc_start: 0.7764 (mp10) cc_final: 0.7244 (mp10) REVERT: A 968 TRP cc_start: 0.7722 (m100) cc_final: 0.7412 (m100) REVERT: B 34 LYS cc_start: 0.7772 (mppt) cc_final: 0.7546 (mtmm) REVERT: B 64 LEU cc_start: 0.8099 (mt) cc_final: 0.7838 (mt) REVERT: B 121 MET cc_start: 0.6503 (tpt) cc_final: 0.5609 (mpp) REVERT: B 129 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6938 (mmm) REVERT: B 229 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7562 (mm-30) REVERT: B 299 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7209 (mttm) outliers start: 23 outliers final: 18 residues processed: 140 average time/residue: 1.2362 time to fit residues: 187.0240 Evaluate side-chains 142 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 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 122 ILE Chi-restraints excluded: chain B residue 129 MET 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 94 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 84 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 = 0.3877 r_free = 0.3877 target = 0.175398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.136093 restraints weight = 11018.656| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.82 r_work: 0.3152 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10455 Z= 0.112 Angle : 0.769 30.256 14130 Z= 0.330 Chirality : 0.041 0.209 1598 Planarity : 0.004 0.056 1768 Dihedral : 10.035 121.552 1722 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.21 % Allowed : 15.99 % 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 (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 (0.23), residues: 1259 helix: 1.97 (0.22), residues: 545 sheet: 0.34 (0.42), residues: 122 loop : -0.36 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A1029 HIS 0.003 0.001 HIS A 868 PHE 0.021 0.002 PHE A 335 TYR 0.017 0.001 TYR A 881 ARG 0.003 0.000 ARG A 704 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 1) link_NAG-ASN : angle 2.06895 ( 3) hydrogen bonds : bond 0.03942 ( 486) hydrogen bonds : angle 4.20160 ( 1407) SS BOND : bond 0.00116 ( 3) SS BOND : angle 0.85015 ( 6) covalent geometry : bond 0.00252 (10451) covalent geometry : angle 0.76865 (14121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9275.79 seconds wall clock time: 161 minutes 48.47 seconds (9708.47 seconds total)