Starting phenix.real_space_refine on Tue Jul 29 06:05:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c2k_30275/07_2025/7c2k_30275.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c2k_30275/07_2025/7c2k_30275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c2k_30275/07_2025/7c2k_30275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c2k_30275/07_2025/7c2k_30275.map" model { file = "/net/cci-nas-00/data/ceres_data/7c2k_30275/07_2025/7c2k_30275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c2k_30275/07_2025/7c2k_30275.cif" } resolution = 2.93 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= 0.002 sd= 0.092 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 32 5.49 5 S 77 5.16 5 C 6667 2.51 5 N 1806 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10692 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7464 Classifications: {'peptide': 927} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 905 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 111} Chain: "C" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 554 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 12} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "G" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {'F86': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p_pur': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2538 SG CYS A 310 75.724 40.795 50.289 1.00 27.08 S ATOM 3946 SG CYS A 487 88.847 46.521 69.558 1.00 31.06 S ATOM 5199 SG CYS A 645 90.765 48.370 66.495 1.00 36.06 S ATOM 5205 SG CYS A 646 88.957 44.100 65.770 1.00 34.53 S Time building chain proxies: 6.78, per 1000 atoms: 0.63 Number of scatterers: 10692 At special positions: 0 Unit cell: (104.14, 100.86, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 77 16.00 P 32 15.00 O 2108 8.00 N 1806 7.00 C 6667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 3 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 51.2% alpha, 15.1% beta 14 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.719A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.650A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.065A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.460A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.234A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.570A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.503A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.049A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.701A pdb=" N GLN A 492 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 493' Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.741A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.566A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.512A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.598A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.618A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.628A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.885A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A 901 " --> pdb=" O GLY A 897 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 918 through 924 Processing helix chain 'B' and resid 77 through 97 removed outlier: 3.981A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.566A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.537A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.553A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'D' and resid 54 through 83 removed outlier: 3.658A pdb=" N GLN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.771A pdb=" N ASN D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.039A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.650A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.251A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.650A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.650A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.605A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 143 " --> pdb=" O THR D 146 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1689 1.27 - 1.40: 2878 1.40 - 1.54: 6175 1.54 - 1.67: 125 1.67 - 1.81: 118 Bond restraints: 10985 Sorted by residual: bond pdb=" C1 F86 G 4 " pdb=" C5 F86 G 4 " ideal model delta sigma weight residual 1.507 1.381 0.126 1.00e-02 1.00e+04 1.59e+02 bond pdb=" C4 F86 G 4 " pdb=" O1 F86 G 4 " ideal model delta sigma weight residual 1.435 1.284 0.151 1.20e-02 6.94e+03 1.57e+02 bond pdb=" C11 F86 G 4 " pdb=" N5 F86 G 4 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.00e-02 1.00e+04 1.30e+02 bond pdb=" C3 F86 G 4 " pdb=" C4 F86 G 4 " ideal model delta sigma weight residual 1.526 1.670 -0.144 1.40e-02 5.10e+03 1.05e+02 bond pdb=" O7 F86 G 4 " pdb=" P1 F86 G 4 " ideal model delta sigma weight residual 1.491 1.649 -0.158 1.70e-02 3.46e+03 8.66e+01 ... (remaining 10980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.26: 15030 5.26 - 10.53: 18 10.53 - 15.79: 0 15.79 - 21.06: 0 21.06 - 26.32: 1 Bond angle restraints: 15049 Sorted by residual: angle pdb=" O2' C F -2 " pdb=" C2' C F -2 " pdb=" C1' C F -2 " ideal model delta sigma weight residual 108.40 82.08 26.32 1.50e+00 4.44e-01 3.08e+02 angle pdb=" C12 F86 G 4 " pdb=" N2 F86 G 4 " pdb=" N1 F86 G 4 " ideal model delta sigma weight residual 111.53 121.71 -10.18 1.00e+00 1.00e+00 1.04e+02 angle pdb=" N2 F86 G 4 " pdb=" C12 F86 G 4 " pdb=" N4 F86 G 4 " ideal model delta sigma weight residual 128.74 120.63 8.11 1.17e+00 7.33e-01 4.82e+01 angle pdb=" C3' C F -2 " pdb=" C2' C F -2 " pdb=" O2' C F -2 " ideal model delta sigma weight residual 110.70 119.92 -9.22 1.50e+00 4.44e-01 3.78e+01 angle pdb=" C9 F86 G 4 " pdb=" N1 F86 G 4 " pdb=" N2 F86 G 4 " ideal model delta sigma weight residual 124.86 119.91 4.95 1.00e+00 1.00e+00 2.45e+01 ... (remaining 15044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5876 17.75 - 35.50: 558 35.50 - 53.26: 102 53.26 - 71.01: 51 71.01 - 88.76: 16 Dihedral angle restraints: 6603 sinusoidal: 2875 harmonic: 3728 Sorted by residual: dihedral pdb=" CA TRP D 182 " pdb=" C TRP D 182 " pdb=" N PRO D 183 " pdb=" CA PRO D 183 " ideal model delta harmonic sigma weight residual 180.00 143.54 36.46 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASP A 109 " pdb=" C ASP A 109 " pdb=" N MET A 110 " pdb=" CA MET A 110 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 6600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1468 0.060 - 0.120: 229 0.120 - 0.180: 18 0.180 - 0.239: 3 0.239 - 0.299: 2 Chirality restraints: 1720 Sorted by residual: chirality pdb=" P C F -3 " pdb=" OP1 C F -3 " pdb=" OP2 C F -3 " pdb=" O5' C F -3 " both_signs ideal model delta sigma weight residual True 2.41 -2.11 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB THR A 120 " pdb=" CA THR A 120 " pdb=" OG1 THR A 120 " pdb=" CG2 THR A 120 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3 F86 G 4 " pdb=" C2 F86 G 4 " pdb=" C4 F86 G 4 " pdb=" O3 F86 G 4 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1717 not shown) Planarity restraints: 1807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " 0.055 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO D 183 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C F -2 " 0.040 2.00e-02 2.50e+03 2.09e-02 9.78e+00 pdb=" N1 C F -2 " -0.042 2.00e-02 2.50e+03 pdb=" C2 C F -2 " -0.014 2.00e-02 2.50e+03 pdb=" O2 C F -2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C F -2 " 0.011 2.00e-02 2.50e+03 pdb=" C4 C F -2 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C F -2 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C F -2 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C F -2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C F -3 " 0.015 2.00e-02 2.50e+03 1.69e-02 6.39e+00 pdb=" N1 C F -3 " -0.022 2.00e-02 2.50e+03 pdb=" C2 C F -3 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C F -3 " -0.009 2.00e-02 2.50e+03 pdb=" N3 C F -3 " 0.022 2.00e-02 2.50e+03 pdb=" C4 C F -3 " -0.033 2.00e-02 2.50e+03 pdb=" N4 C F -3 " 0.013 2.00e-02 2.50e+03 pdb=" C5 C F -3 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C F -3 " 0.006 2.00e-02 2.50e+03 ... (remaining 1804 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2573 2.78 - 3.31: 9523 3.31 - 3.84: 17807 3.84 - 4.37: 22073 4.37 - 4.90: 36991 Nonbonded interactions: 88967 Sorted by model distance: nonbonded pdb=" OD2 ASP A 170 " pdb=" NH2 ARG A 173 " model vdw 2.256 3.120 nonbonded pdb=" O SER C 54 " pdb=" OG SER C 57 " model vdw 2.291 3.040 nonbonded pdb=" NH2 ARG A 279 " pdb=" OG SER A 318 " model vdw 2.302 3.120 nonbonded pdb=" O SER D 151 " pdb=" OG SER D 151 " model vdw 2.305 3.040 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.312 3.040 ... (remaining 88962 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: 1.320 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.700 Find NCS groups from input model: 0.100 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:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 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 : 0.013 0.550 10993 Z= 0.552 Angle : 0.698 26.321 15052 Z= 0.411 Chirality : 0.044 0.299 1720 Planarity : 0.004 0.083 1807 Dihedral : 15.538 88.760 4191 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.91 (0.20), residues: 1246 helix: -1.20 (0.19), residues: 588 sheet: -2.00 (0.39), residues: 129 loop : -2.70 (0.22), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.017 0.001 PHE A 741 TYR 0.013 0.001 TYR A 788 ARG 0.002 0.000 ARG A 640 Details of bonding type rmsd hydrogen bonds : bond 0.17915 ( 526) hydrogen bonds : angle 6.54575 ( 1496) metal coordination : bond 0.49129 ( 6) metal coordination : angle 12.71581 ( 3) covalent geometry : bond 0.00674 (10985) covalent geometry : angle 0.67492 (15049) Misc. bond : bond 0.06369 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.185 Fit side-chains REVERT: A 794 MET cc_start: 0.9111 (ttp) cc_final: 0.8884 (ttp) outliers start: 0 outliers final: 1 residues processed: 146 average time/residue: 1.3843 time to fit residues: 216.5601 Evaluate side-chains 120 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 9 ASN A 75 HIS A 81 GLN A 99 HIS A 138 ASN A 168 ASN A 312 ASN A 356 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 534 ASN A 613 HIS A 725 HIS B 140 ASN B 158 GLN B 192 ASN C 31 GLN C 69 ASN D 105 ASN D 108 ASN D 109 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.089738 restraints weight = 13213.372| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.93 r_work: 0.2909 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10993 Z= 0.138 Angle : 0.545 7.589 15052 Z= 0.285 Chirality : 0.041 0.159 1720 Planarity : 0.004 0.074 1807 Dihedral : 13.004 82.802 1858 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.90 % Allowed : 10.40 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.55 (0.22), residues: 1246 helix: 0.03 (0.21), residues: 593 sheet: -1.21 (0.41), residues: 131 loop : -2.21 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG A 10 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 526) hydrogen bonds : angle 4.50449 ( 1496) metal coordination : bond 0.00666 ( 6) metal coordination : angle 1.15342 ( 3) covalent geometry : bond 0.00315 (10985) covalent geometry : angle 0.54453 (15049) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.149 Fit side-chains REVERT: A 408 GLN cc_start: 0.9005 (tt0) cc_final: 0.8686 (tt0) REVERT: A 794 MET cc_start: 0.9358 (ttp) cc_final: 0.9072 (ttp) REVERT: B 98 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7327 (tp) REVERT: B 155 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8046 (mt-10) REVERT: B 168 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7929 (mm-40) REVERT: C 21 ARG cc_start: 0.7897 (mmp80) cc_final: 0.7683 (mmp-170) outliers start: 21 outliers final: 9 residues processed: 147 average time/residue: 1.2218 time to fit residues: 194.4725 Evaluate side-chains 127 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain D residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 9 optimal weight: 0.2980 chunk 48 optimal weight: 0.4980 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 497 ASN A 734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091970 restraints weight = 13365.470| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.95 r_work: 0.2938 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10993 Z= 0.109 Angle : 0.506 8.149 15052 Z= 0.265 Chirality : 0.039 0.152 1720 Planarity : 0.004 0.067 1807 Dihedral : 12.873 76.512 1858 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.17 % Allowed : 12.30 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1246 helix: 0.63 (0.22), residues: 594 sheet: -0.85 (0.44), residues: 131 loop : -1.92 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 182 HIS 0.006 0.001 HIS C 36 PHE 0.013 0.001 PHE A 753 TYR 0.013 0.001 TYR A 788 ARG 0.004 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 526) hydrogen bonds : angle 4.08968 ( 1496) metal coordination : bond 0.00369 ( 6) metal coordination : angle 1.05980 ( 3) covalent geometry : bond 0.00243 (10985) covalent geometry : angle 0.50536 (15049) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.071 Fit side-chains REVERT: A 22 CYS cc_start: 0.8107 (t) cc_final: 0.7880 (t) REVERT: A 138 ASN cc_start: 0.7804 (t0) cc_final: 0.7465 (t0) REVERT: A 408 GLN cc_start: 0.8981 (tt0) cc_final: 0.8638 (tt0) REVERT: A 543 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7514 (m110) REVERT: A 794 MET cc_start: 0.9348 (ttp) cc_final: 0.9078 (ttp) REVERT: B 155 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8064 (mt-10) REVERT: C 21 ARG cc_start: 0.7845 (mmp80) cc_final: 0.7633 (mmp-170) outliers start: 24 outliers final: 10 residues processed: 152 average time/residue: 1.1889 time to fit residues: 195.6005 Evaluate side-chains 137 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 790 ASN ** C 36 HIS ** 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 = 0.3430 r_free = 0.3430 target = 0.118972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089666 restraints weight = 13325.936| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.94 r_work: 0.2911 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10993 Z= 0.139 Angle : 0.521 7.531 15052 Z= 0.274 Chirality : 0.040 0.157 1720 Planarity : 0.004 0.064 1807 Dihedral : 12.845 73.180 1856 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.71 % Allowed : 13.20 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1246 helix: 0.74 (0.22), residues: 598 sheet: -0.67 (0.43), residues: 132 loop : -1.82 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.002 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 526) hydrogen bonds : angle 4.06816 ( 1496) metal coordination : bond 0.00228 ( 6) metal coordination : angle 0.79318 ( 3) covalent geometry : bond 0.00324 (10985) covalent geometry : angle 0.52138 (15049) Misc. bond : bond 0.00008 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.123 Fit side-chains REVERT: A 138 ASN cc_start: 0.7925 (t0) cc_final: 0.7510 (t0) REVERT: A 543 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7587 (m110) REVERT: A 555 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7349 (mtp-110) REVERT: A 794 MET cc_start: 0.9367 (ttp) cc_final: 0.9064 (ttp) REVERT: B 155 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8086 (mt-10) REVERT: B 168 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7938 (mm-40) REVERT: C 21 ARG cc_start: 0.7853 (mmp80) cc_final: 0.7651 (mmp-170) REVERT: D 129 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7933 (mtp) outliers start: 30 outliers final: 14 residues processed: 146 average time/residue: 1.1870 time to fit residues: 187.7404 Evaluate side-chains 145 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 136 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 497 ASN A 790 ASN C 36 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.086449 restraints weight = 13228.042| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.92 r_work: 0.2869 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10993 Z= 0.196 Angle : 0.570 9.056 15052 Z= 0.298 Chirality : 0.042 0.161 1720 Planarity : 0.004 0.065 1807 Dihedral : 12.859 73.262 1856 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.07 % Allowed : 14.38 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1246 helix: 0.69 (0.22), residues: 599 sheet: -0.56 (0.43), residues: 132 loop : -1.77 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 916 HIS 0.008 0.001 HIS A 309 PHE 0.018 0.002 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.002 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 526) hydrogen bonds : angle 4.18946 ( 1496) metal coordination : bond 0.00338 ( 6) metal coordination : angle 0.73924 ( 3) covalent geometry : bond 0.00470 (10985) covalent geometry : angle 0.56972 (15049) Misc. bond : bond 0.00020 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.444 Fit side-chains REVERT: A 138 ASN cc_start: 0.8018 (t0) cc_final: 0.7593 (t0) REVERT: A 360 ASN cc_start: 0.7977 (p0) cc_final: 0.7736 (p0) REVERT: A 542 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7858 (mmm) REVERT: A 543 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7546 (m110) REVERT: A 555 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7401 (mtp-110) REVERT: A 734 ASN cc_start: 0.8206 (t0) cc_final: 0.7979 (t160) REVERT: A 794 MET cc_start: 0.9410 (ttp) cc_final: 0.9105 (ttp) REVERT: B 127 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8843 (ttpt) REVERT: C 18 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8480 (tp40) REVERT: C 21 ARG cc_start: 0.7884 (mmp80) cc_final: 0.7603 (mmm160) REVERT: D 129 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8068 (mtp) outliers start: 34 outliers final: 15 residues processed: 146 average time/residue: 1.1944 time to fit residues: 188.6220 Evaluate side-chains 141 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 129 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 568 ASN A 790 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.088673 restraints weight = 13324.615| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.92 r_work: 0.2890 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10993 Z= 0.164 Angle : 0.543 8.247 15052 Z= 0.284 Chirality : 0.041 0.160 1720 Planarity : 0.004 0.061 1807 Dihedral : 12.811 73.209 1856 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.35 % Allowed : 14.38 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1246 helix: 0.80 (0.22), residues: 593 sheet: -0.41 (0.43), residues: 134 loop : -1.65 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 290 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.001 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.002 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 526) hydrogen bonds : angle 4.09677 ( 1496) metal coordination : bond 0.00223 ( 6) metal coordination : angle 0.53062 ( 3) covalent geometry : bond 0.00389 (10985) covalent geometry : angle 0.54282 (15049) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.090 Fit side-chains REVERT: A 138 ASN cc_start: 0.7977 (t0) cc_final: 0.7557 (t0) REVERT: A 408 GLN cc_start: 0.9015 (tt0) cc_final: 0.8775 (tt0) REVERT: A 543 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7608 (m110) REVERT: A 555 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7400 (mtp-110) REVERT: A 734 ASN cc_start: 0.8154 (t0) cc_final: 0.7927 (t0) REVERT: A 794 MET cc_start: 0.9397 (ttp) cc_final: 0.9092 (ttp) REVERT: B 168 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7958 (mm-40) REVERT: C 18 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8463 (tp40) REVERT: C 21 ARG cc_start: 0.7896 (mmp80) cc_final: 0.7611 (mmm160) REVERT: D 129 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7995 (mtp) outliers start: 37 outliers final: 21 residues processed: 146 average time/residue: 1.1894 time to fit residues: 188.3868 Evaluate side-chains 146 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 129 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 36 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 705 ASN A 790 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090091 restraints weight = 13487.612| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.95 r_work: 0.2915 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10993 Z= 0.126 Angle : 0.517 7.392 15052 Z= 0.270 Chirality : 0.040 0.157 1720 Planarity : 0.003 0.059 1807 Dihedral : 12.736 73.138 1856 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.44 % Allowed : 15.37 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1246 helix: 0.95 (0.22), residues: 598 sheet: -0.38 (0.43), residues: 132 loop : -1.59 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 182 HIS 0.006 0.001 HIS A 309 PHE 0.019 0.001 PHE A 340 TYR 0.014 0.001 TYR A 788 ARG 0.002 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 526) hydrogen bonds : angle 3.97299 ( 1496) metal coordination : bond 0.00152 ( 6) metal coordination : angle 0.58074 ( 3) covalent geometry : bond 0.00294 (10985) covalent geometry : angle 0.51730 (15049) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.158 Fit side-chains REVERT: A 18 ARG cc_start: 0.8240 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: A 138 ASN cc_start: 0.7903 (t0) cc_final: 0.7481 (t0) REVERT: A 543 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7755 (m110) REVERT: A 794 MET cc_start: 0.9377 (ttp) cc_final: 0.9079 (ttp) REVERT: B 127 LYS cc_start: 0.9127 (ttmm) cc_final: 0.8837 (tppt) REVERT: B 168 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7986 (mm-40) REVERT: C 21 ARG cc_start: 0.7833 (mmp80) cc_final: 0.7624 (mmp-170) REVERT: D 67 MET cc_start: 0.7386 (ttp) cc_final: 0.6727 (tpp) REVERT: D 129 MET cc_start: 0.8456 (mtm) cc_final: 0.7820 (mtt) outliers start: 27 outliers final: 20 residues processed: 142 average time/residue: 1.1860 time to fit residues: 182.0998 Evaluate side-chains 144 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 136 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 568 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.119726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090535 restraints weight = 13350.793| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.94 r_work: 0.2924 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10993 Z= 0.123 Angle : 0.518 8.697 15052 Z= 0.269 Chirality : 0.040 0.156 1720 Planarity : 0.003 0.057 1807 Dihedral : 12.685 73.144 1856 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.99 % Allowed : 16.00 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1246 helix: 1.06 (0.22), residues: 595 sheet: -0.27 (0.44), residues: 132 loop : -1.55 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 182 HIS 0.006 0.001 HIS A 309 PHE 0.018 0.001 PHE A 340 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 526) hydrogen bonds : angle 3.93289 ( 1496) metal coordination : bond 0.00148 ( 6) metal coordination : angle 0.53721 ( 3) covalent geometry : bond 0.00284 (10985) covalent geometry : angle 0.51760 (15049) Misc. bond : bond 0.00011 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.095 Fit side-chains REVERT: A 18 ARG cc_start: 0.8214 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: A 138 ASN cc_start: 0.7871 (t0) cc_final: 0.7462 (t0) REVERT: A 543 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7764 (m110) REVERT: A 794 MET cc_start: 0.9375 (ttp) cc_final: 0.9067 (ttp) REVERT: B 127 LYS cc_start: 0.9129 (ttmm) cc_final: 0.8845 (tppt) REVERT: C 21 ARG cc_start: 0.7861 (mmp80) cc_final: 0.7654 (mmp-170) REVERT: D 67 MET cc_start: 0.7301 (ttp) cc_final: 0.6657 (tpp) outliers start: 22 outliers final: 18 residues processed: 136 average time/residue: 1.4133 time to fit residues: 207.8185 Evaluate side-chains 141 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 136 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 86 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 90 optimal weight: 0.3980 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.090415 restraints weight = 13417.346| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.95 r_work: 0.2936 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10993 Z= 0.113 Angle : 0.516 10.347 15052 Z= 0.267 Chirality : 0.039 0.155 1720 Planarity : 0.003 0.056 1807 Dihedral : 12.638 73.127 1856 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.08 % Allowed : 16.00 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1246 helix: 1.19 (0.22), residues: 592 sheet: -0.21 (0.44), residues: 132 loop : -1.43 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 182 HIS 0.006 0.001 HIS A 309 PHE 0.017 0.001 PHE A 340 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 526) hydrogen bonds : angle 3.87485 ( 1496) metal coordination : bond 0.00136 ( 6) metal coordination : angle 0.57668 ( 3) covalent geometry : bond 0.00257 (10985) covalent geometry : angle 0.51632 (15049) Misc. bond : bond 0.00011 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.224 Fit side-chains REVERT: A 18 ARG cc_start: 0.8194 (mtm-85) cc_final: 0.7857 (mtm-85) REVERT: A 138 ASN cc_start: 0.7797 (t0) cc_final: 0.7389 (t0) REVERT: A 543 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7759 (m110) REVERT: A 794 MET cc_start: 0.9365 (ttp) cc_final: 0.9053 (ttp) REVERT: B 88 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6991 (tt0) REVERT: B 127 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8832 (tppt) REVERT: B 168 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7966 (mm-40) REVERT: C 21 ARG cc_start: 0.7828 (mmp80) cc_final: 0.7613 (mmp-170) REVERT: D 55 MET cc_start: 0.6363 (pmt) cc_final: 0.5803 (ppp) REVERT: D 67 MET cc_start: 0.7317 (ttp) cc_final: 0.6723 (tpp) outliers start: 23 outliers final: 18 residues processed: 139 average time/residue: 1.2664 time to fit residues: 190.6139 Evaluate side-chains 140 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 136 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 123 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 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 497 ASN A 568 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091250 restraints weight = 13353.171| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.95 r_work: 0.2955 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10993 Z= 0.105 Angle : 0.507 11.433 15052 Z= 0.261 Chirality : 0.039 0.153 1720 Planarity : 0.003 0.055 1807 Dihedral : 12.573 73.111 1856 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.90 % Allowed : 16.64 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1246 helix: 1.26 (0.23), residues: 592 sheet: -0.16 (0.45), residues: 132 loop : -1.36 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 182 HIS 0.005 0.001 HIS A 309 PHE 0.017 0.001 PHE A 340 TYR 0.013 0.001 TYR A 788 ARG 0.004 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 526) hydrogen bonds : angle 3.80806 ( 1496) metal coordination : bond 0.00124 ( 6) metal coordination : angle 0.58851 ( 3) covalent geometry : bond 0.00236 (10985) covalent geometry : angle 0.50740 (15049) Misc. bond : bond 0.00012 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.241 Fit side-chains REVERT: A 18 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7698 (mtm-85) REVERT: A 138 ASN cc_start: 0.7751 (t0) cc_final: 0.7351 (t0) REVERT: A 543 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7801 (m110) REVERT: A 555 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7453 (mtp-110) REVERT: B 88 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6963 (tt0) REVERT: B 127 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8812 (tppt) REVERT: B 168 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7888 (mm-40) REVERT: C 21 ARG cc_start: 0.7797 (mmp80) cc_final: 0.7571 (mmp-170) REVERT: D 55 MET cc_start: 0.6287 (pmt) cc_final: 0.5694 (ppp) REVERT: D 67 MET cc_start: 0.7263 (ttp) cc_final: 0.6675 (tpp) outliers start: 21 outliers final: 18 residues processed: 136 average time/residue: 1.3197 time to fit residues: 193.3079 Evaluate side-chains 138 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 136 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 39 optimal weight: 0.3980 chunk 46 optimal weight: 0.0670 chunk 23 optimal weight: 0.8980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.093776 restraints weight = 13290.705| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.95 r_work: 0.2990 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10993 Z= 0.093 Angle : 0.496 8.639 15052 Z= 0.255 Chirality : 0.038 0.152 1720 Planarity : 0.003 0.053 1807 Dihedral : 12.509 73.075 1856 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.63 % Allowed : 17.18 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1246 helix: 1.34 (0.23), residues: 592 sheet: -0.17 (0.45), residues: 127 loop : -1.30 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.005 0.001 HIS A 309 PHE 0.014 0.001 PHE A 340 TYR 0.013 0.001 TYR A 788 ARG 0.004 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 526) hydrogen bonds : angle 3.73212 ( 1496) metal coordination : bond 0.00131 ( 6) metal coordination : angle 0.74900 ( 3) covalent geometry : bond 0.00200 (10985) covalent geometry : angle 0.49546 (15049) Misc. bond : bond 0.00019 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7290.41 seconds wall clock time: 125 minutes 20.80 seconds (7520.80 seconds total)