Starting phenix.real_space_refine on Thu Mar 5 02:43:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7et1_31294/03_2026/7et1_31294.cif Found real_map, /net/cci-nas-00/data/ceres_data/7et1_31294/03_2026/7et1_31294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7et1_31294/03_2026/7et1_31294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7et1_31294/03_2026/7et1_31294.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7et1_31294/03_2026/7et1_31294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7et1_31294/03_2026/7et1_31294.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9994 atoms to isotropic. 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 3 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 6440 2.51 5 N 1649 2.21 5 O 1848 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 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10015 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7652 Classifications: {'peptide': 987} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 47, 'TRANS': 939} Chain: "B" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2100 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 17, 'TRANS': 240} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 138 Unusual residues: {' K': 3, ' MG': 1, 'ALF': 1, 'CLR': 1, 'PCW': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Unusual residues: {'NAG': 5, 'PCW': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.19, per 1000 atoms: 0.22 Number of scatterers: 10015 At special positions: 0 Unit cell: (118.69, 92.96, 174.3, 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 66 16.00 P 3 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1848 8.00 N 1649 7.00 C 6440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 262 " 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=1, symmetry=0 Links applied NAG-ASN " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 161 " " NAG B 304 " - " ASN B 221 " " NAG B 305 " - " ASN B 193 " " NAG B 306 " - " ASN B 146 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 483.3 milliseconds 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2338 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 50.5% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 107 through 130 Processing helix chain 'A' and resid 135 through 161 removed outlier: 3.833A pdb=" N LEU A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 291 through 322 Processing helix chain 'A' and resid 325 through 341 Processing helix chain 'A' and resid 344 through 362 Processing helix chain 'A' and resid 371 through 379 removed outlier: 4.014A pdb=" N THR A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLY A 377 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 459 through 473 Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.573A pdb=" N GLU A 525 " --> pdb=" O GLU A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 607 through 618 Processing helix chain 'A' and resid 629 through 641 Processing helix chain 'A' and resid 649 through 658 Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 676 through 682 Processing helix chain 'A' and resid 683 through 694 Processing helix chain 'A' and resid 703 through 717 Processing helix chain 'A' and resid 730 through 737 Processing helix chain 'A' and resid 748 through 755 Processing helix chain 'A' and resid 765 through 791 removed outlier: 4.074A pdb=" N SER A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 806 removed outlier: 3.526A pdb=" N GLU A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Proline residue: A 798 - end of helix Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 824 through 831 removed outlier: 3.579A pdb=" N SER A 828 " --> pdb=" O ASP A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 865 through 885 Processing helix chain 'A' and resid 888 through 893 removed outlier: 3.594A pdb=" N VAL A 893 " --> pdb=" O PRO A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 900 Processing helix chain 'A' and resid 916 through 946 Processing helix chain 'A' and resid 952 through 957 Processing helix chain 'A' and resid 961 through 981 removed outlier: 3.521A pdb=" N VAL A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 988 Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1001 through 1022 Processing helix chain 'A' and resid 1025 through 1032 Processing helix chain 'B' and resid 33 through 66 Processing helix chain 'B' and resid 102 through 118 removed outlier: 4.247A pdb=" N TRP B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 123 through 128 removed outlier: 4.278A pdb=" N GLY B 127 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 removed outlier: 6.313A pdb=" N ASN B 161 " --> pdb=" O MET B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.816A pdb=" N THR B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 11.121A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N CYS A 258 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS A 221 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU A 260 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY A 219 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA A 217 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN A 264 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP A 211 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS A 220 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 11.121A pdb=" N GLN A 177 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N LYS A 203 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 179 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU A 199 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N CYS A 258 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS A 221 " --> pdb=" O CYS A 258 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU A 260 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLY A 219 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N THR A 262 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA A 217 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN A 264 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP A 211 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.229A pdb=" N GLY A 740 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU A 759 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A 742 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 721 " --> pdb=" O ILE A 739 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 741 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 723 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N MET A 743 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLY A 725 " --> pdb=" O MET A 743 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL A 381 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR A 724 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N CYS A 383 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A 382 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 625 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER A 384 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 622 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N PHE A 699 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N MET A 624 " --> pdb=" O PHE A 699 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.449A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS A 487 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 503 " --> pdb=" O LYS A 485 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS A 485 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408 removed outlier: 5.449A pdb=" N VAL A 397 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE A 601 " --> pdb=" O VAL A 397 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU A 592 " --> pdb=" O CYS A 527 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 441 through 442 removed outlier: 3.810A pdb=" N ALA A 441 " --> pdb=" O ILE A 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 907 through 908 Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 85 Processing sheet with id=AA9, first strand: chain 'B' and resid 94 through 99 removed outlier: 6.529A pdb=" N LEU B 94 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LYS B 287 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 96 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLN B 289 " --> pdb=" O ILE B 96 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR B 98 " --> pdb=" O GLN B 289 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.18 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: 3160 1.34 - 1.46: 1933 1.46 - 1.58: 5036 1.58 - 1.70: 6 1.70 - 1.82: 99 Bond restraints: 10234 Sorted by residual: bond pdb=" C11 PCW A1102 " pdb=" O3 PCW A1102 " ideal model delta sigma weight residual 1.326 1.458 -0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" C11 PCW A1103 " pdb=" O3 PCW A1103 " ideal model delta sigma weight residual 1.326 1.455 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" C31 PCW A1103 " pdb=" O2 PCW A1103 " ideal model delta sigma weight residual 1.333 1.458 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C31 PCW A1102 " pdb=" O2 PCW A1102 " ideal model delta sigma weight residual 1.333 1.455 -0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" C31 PCW B 301 " pdb=" O2 PCW B 301 " ideal model delta sigma weight residual 1.333 1.454 -0.121 2.00e-02 2.50e+03 3.67e+01 ... (remaining 10229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.97: 13882 13.97 - 27.93: 4 27.93 - 41.90: 0 41.90 - 55.86: 0 55.86 - 69.83: 2 Bond angle restraints: 13888 Sorted by residual: angle pdb=" F3 ALF A1105 " pdb="AL ALF A1105 " pdb=" F4 ALF A1105 " ideal model delta sigma weight residual 109.63 179.46 -69.83 3.00e+00 1.11e-01 5.42e+02 angle pdb=" F1 ALF A1105 " pdb="AL ALF A1105 " pdb=" F2 ALF A1105 " ideal model delta sigma weight residual 108.68 177.50 -68.82 3.00e+00 1.11e-01 5.26e+02 angle pdb=" F2 ALF A1105 " pdb="AL ALF A1105 " pdb=" F4 ALF A1105 " ideal model delta sigma weight residual 110.21 89.85 20.36 3.00e+00 1.11e-01 4.60e+01 angle pdb=" F1 ALF A1105 " pdb="AL ALF A1105 " pdb=" F4 ALF A1105 " ideal model delta sigma weight residual 109.02 89.33 19.69 3.00e+00 1.11e-01 4.31e+01 angle pdb=" F2 ALF A1105 " pdb="AL ALF A1105 " pdb=" F3 ALF A1105 " ideal model delta sigma weight residual 109.59 90.33 19.26 3.00e+00 1.11e-01 4.12e+01 ... (remaining 13883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 6011 34.08 - 68.17: 256 68.17 - 102.25: 15 102.25 - 136.33: 4 136.33 - 170.42: 1 Dihedral angle restraints: 6287 sinusoidal: 2660 harmonic: 3627 Sorted by residual: dihedral pdb=" N PCW B 301 " pdb=" C4 PCW B 301 " pdb=" C5 PCW B 301 " pdb=" O4P PCW B 301 " ideal model delta sinusoidal sigma weight residual -66.66 103.76 -170.42 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C33 PCW A1102 " pdb=" C31 PCW A1102 " pdb=" C32 PCW A1102 " pdb=" O2 PCW A1102 " ideal model delta sinusoidal sigma weight residual 191.83 57.87 133.96 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" N PCW A1103 " pdb=" C4 PCW A1103 " pdb=" C5 PCW A1103 " pdb=" O4P PCW A1103 " ideal model delta sinusoidal sigma weight residual 293.34 164.18 129.16 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 6284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1501 0.112 - 0.223: 67 0.223 - 0.335: 3 0.335 - 0.446: 2 0.446 - 0.558: 1 Chirality restraints: 1574 Sorted by residual: chirality pdb=" C1 NAG B 303 " pdb=" ND2 ASN B 161 " pdb=" C2 NAG B 303 " pdb=" O5 NAG B 303 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG B 304 " pdb=" ND2 ASN B 221 " pdb=" C2 NAG B 304 " pdb=" O5 NAG B 304 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C20 CLR A1106 " pdb=" C17 CLR A1106 " pdb=" C21 CLR A1106 " pdb=" C22 CLR A1106 " both_signs ideal model delta sigma weight residual False 2.59 2.25 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1571 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 161 " -0.033 2.00e-02 2.50e+03 3.11e-02 1.21e+01 pdb=" CG ASN B 161 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 161 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 161 " 0.028 2.00e-02 2.50e+03 pdb=" C1 NAG B 303 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 121 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 122 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 449 " -0.052 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 450 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " -0.043 5.00e-02 4.00e+02 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 57 2.58 - 3.22: 9381 3.22 - 3.86: 19960 3.86 - 4.50: 27552 4.50 - 5.14: 43645 Nonbonded interactions: 100595 Sorted by model distance: nonbonded pdb="MG MG A1101 " pdb=" F3 ALF A1105 " model vdw 1.936 2.120 nonbonded pdb=" OE2 GLU A 230 " pdb=" O HOH A1201 " model vdw 2.052 3.040 nonbonded pdb=" OD1 ASP A 726 " pdb="MG MG A1101 " model vdw 2.072 2.170 nonbonded pdb=" OD2 ASP A 385 " pdb=" F3 ALF A1105 " model vdw 2.078 2.990 nonbonded pdb=" OG1 THR A 235 " pdb=" NE ARG A 249 " model vdw 2.079 3.120 ... (remaining 100590 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.040 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.009 0.606 10243 Z= 0.680 Angle : 1.256 69.831 13909 Z= 0.539 Chirality : 0.055 0.558 1574 Planarity : 0.007 0.083 1768 Dihedral : 17.047 170.419 3940 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.19 % Allowed : 20.70 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1245 helix: 1.14 (0.21), residues: 573 sheet: -0.09 (0.39), residues: 145 loop : -0.22 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 850 TYR 0.020 0.002 TYR A 802 PHE 0.025 0.002 PHE A 300 TRP 0.018 0.002 TRP A 401 HIS 0.008 0.002 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00686 (10234) covalent geometry : angle 1.25029 (13888) SS BOND : bond 0.00291 ( 3) SS BOND : angle 2.28148 ( 6) hydrogen bonds : bond 0.15594 ( 509) hydrogen bonds : angle 6.14085 ( 1524) Misc. bond : bond 0.60625 ( 1) link_NAG-ASN : bond 0.00558 ( 5) link_NAG-ASN : angle 3.65612 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.7949 (m-30) cc_final: 0.7686 (m-30) REVERT: A 401 TRP cc_start: 0.8503 (t60) cc_final: 0.8270 (t60) REVERT: A 505 GLU cc_start: 0.7691 (tt0) cc_final: 0.6833 (tm-30) REVERT: A 532 ILE cc_start: 0.8744 (mt) cc_final: 0.7817 (mm) outliers start: 2 outliers final: 1 residues processed: 134 average time/residue: 0.8397 time to fit residues: 118.3584 Evaluate side-chains 81 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 GLN B 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.105926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.070343 restraints weight = 18087.348| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.48 r_work: 0.2862 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10243 Z= 0.139 Angle : 0.791 31.120 13909 Z= 0.341 Chirality : 0.045 0.279 1574 Planarity : 0.005 0.044 1768 Dihedral : 11.027 160.325 1653 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.73 % Allowed : 19.76 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.24), residues: 1245 helix: 1.78 (0.21), residues: 577 sheet: 0.06 (0.40), residues: 147 loop : 0.10 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 439 TYR 0.014 0.001 TYR A 802 PHE 0.016 0.001 PHE A 300 TRP 0.010 0.001 TRP A 915 HIS 0.004 0.001 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00324 (10234) covalent geometry : angle 0.78584 (13888) SS BOND : bond 0.00410 ( 3) SS BOND : angle 1.80248 ( 6) hydrogen bonds : bond 0.04281 ( 509) hydrogen bonds : angle 4.67266 ( 1524) Misc. bond : bond 0.00070 ( 1) link_NAG-ASN : bond 0.00448 ( 5) link_NAG-ASN : angle 2.76051 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 126 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7838 (mt) REVERT: A 505 GLU cc_start: 0.7863 (tt0) cc_final: 0.6975 (tm-30) REVERT: A 512 HIS cc_start: 0.6232 (m90) cc_final: 0.5513 (m-70) REVERT: B 29 MET cc_start: 0.7742 (tpp) cc_final: 0.7371 (tpt) REVERT: B 216 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: B 267 GLU cc_start: 0.8791 (tt0) cc_final: 0.8568 (tt0) outliers start: 29 outliers final: 7 residues processed: 102 average time/residue: 0.7649 time to fit residues: 82.7944 Evaluate side-chains 75 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 437 CYS Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 60 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 120 optimal weight: 0.0770 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.102936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.067723 restraints weight = 18293.434| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.44 r_work: 0.2817 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10243 Z= 0.171 Angle : 0.789 32.306 13909 Z= 0.338 Chirality : 0.045 0.226 1574 Planarity : 0.004 0.038 1768 Dihedral : 10.764 160.855 1653 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.54 % Allowed : 19.57 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1245 helix: 1.90 (0.22), residues: 577 sheet: 0.05 (0.39), residues: 152 loop : 0.16 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 439 TYR 0.016 0.001 TYR A 802 PHE 0.018 0.001 PHE A 300 TRP 0.010 0.001 TRP A 915 HIS 0.005 0.001 HIS A 903 Details of bonding type rmsd covalent geometry : bond 0.00413 (10234) covalent geometry : angle 0.78461 (13888) SS BOND : bond 0.00545 ( 3) SS BOND : angle 2.01098 ( 6) hydrogen bonds : bond 0.04541 ( 509) hydrogen bonds : angle 4.49649 ( 1524) Misc. bond : bond 0.00027 ( 1) link_NAG-ASN : bond 0.00303 ( 5) link_NAG-ASN : angle 2.28846 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.6918 (mp0) cc_final: 0.6345 (pp20) REVERT: A 232 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8420 (tp30) REVERT: A 371 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8406 (mm-30) REVERT: A 415 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: A 505 GLU cc_start: 0.7852 (tt0) cc_final: 0.7028 (tm-30) REVERT: B 267 GLU cc_start: 0.8844 (tt0) cc_final: 0.8585 (tt0) REVERT: B 285 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8617 (mtmm) outliers start: 27 outliers final: 9 residues processed: 93 average time/residue: 0.7806 time to fit residues: 76.7175 Evaluate side-chains 73 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 285 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN A 923 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.100920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.066047 restraints weight = 18492.752| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.42 r_work: 0.2776 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10243 Z= 0.231 Angle : 0.813 32.888 13909 Z= 0.353 Chirality : 0.047 0.232 1574 Planarity : 0.005 0.038 1768 Dihedral : 10.750 157.157 1653 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.73 % Allowed : 18.63 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.24), residues: 1245 helix: 1.82 (0.22), residues: 577 sheet: 0.09 (0.40), residues: 150 loop : 0.09 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 439 TYR 0.019 0.002 TYR A 802 PHE 0.022 0.001 PHE A 300 TRP 0.011 0.002 TRP A 799 HIS 0.006 0.001 HIS A 903 Details of bonding type rmsd covalent geometry : bond 0.00563 (10234) covalent geometry : angle 0.80863 (13888) SS BOND : bond 0.00586 ( 3) SS BOND : angle 1.91630 ( 6) hydrogen bonds : bond 0.04877 ( 509) hydrogen bonds : angle 4.54743 ( 1524) Misc. bond : bond 0.00008 ( 1) link_NAG-ASN : bond 0.00341 ( 5) link_NAG-ASN : angle 2.30369 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 371 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8453 (mm-30) REVERT: A 415 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: A 505 GLU cc_start: 0.7833 (tt0) cc_final: 0.7029 (tm-30) REVERT: B 267 GLU cc_start: 0.8905 (tt0) cc_final: 0.8654 (tt0) REVERT: B 285 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8699 (mtmm) outliers start: 29 outliers final: 8 residues processed: 90 average time/residue: 0.7256 time to fit residues: 68.9541 Evaluate side-chains 73 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 285 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.101908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.067248 restraints weight = 18179.045| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.40 r_work: 0.2807 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10243 Z= 0.152 Angle : 0.773 31.782 13909 Z= 0.328 Chirality : 0.044 0.228 1574 Planarity : 0.004 0.041 1768 Dihedral : 10.426 158.233 1653 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.54 % Allowed : 19.47 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.24), residues: 1245 helix: 1.97 (0.22), residues: 579 sheet: 0.15 (0.39), residues: 150 loop : 0.18 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 560 TYR 0.014 0.001 TYR A 802 PHE 0.018 0.001 PHE A 300 TRP 0.010 0.001 TRP A 899 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00368 (10234) covalent geometry : angle 0.76937 (13888) SS BOND : bond 0.00415 ( 3) SS BOND : angle 1.40287 ( 6) hydrogen bonds : bond 0.04175 ( 509) hydrogen bonds : angle 4.35013 ( 1524) Misc. bond : bond 0.00009 ( 1) link_NAG-ASN : bond 0.00223 ( 5) link_NAG-ASN : angle 2.15093 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 242 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.8079 (t-90) REVERT: A 371 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8429 (mm-30) REVERT: A 415 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7281 (mp-120) REVERT: A 504 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8024 (tt) REVERT: A 505 GLU cc_start: 0.7866 (tt0) cc_final: 0.7124 (tm-30) REVERT: A 531 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8106 (tp) REVERT: B 267 GLU cc_start: 0.8892 (tt0) cc_final: 0.8641 (tt0) REVERT: B 285 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8691 (mtmm) outliers start: 27 outliers final: 8 residues processed: 89 average time/residue: 0.7547 time to fit residues: 71.0469 Evaluate side-chains 75 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 415 GLN Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 285 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 0.0980 chunk 96 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 0.0670 chunk 23 optimal weight: 5.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 GLN ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.103049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.068376 restraints weight = 18261.359| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.44 r_work: 0.2834 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10243 Z= 0.108 Angle : 0.757 31.368 13909 Z= 0.317 Chirality : 0.043 0.234 1574 Planarity : 0.004 0.045 1768 Dihedral : 10.109 158.107 1653 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.45 % Allowed : 20.04 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.24), residues: 1245 helix: 2.11 (0.22), residues: 578 sheet: 0.27 (0.42), residues: 135 loop : 0.16 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 560 TYR 0.012 0.001 TYR A 878 PHE 0.016 0.001 PHE A 300 TRP 0.009 0.001 TRP A 899 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00252 (10234) covalent geometry : angle 0.75424 (13888) SS BOND : bond 0.00284 ( 3) SS BOND : angle 0.97614 ( 6) hydrogen bonds : bond 0.03719 ( 509) hydrogen bonds : angle 4.21458 ( 1524) Misc. bond : bond 0.00032 ( 1) link_NAG-ASN : bond 0.00223 ( 5) link_NAG-ASN : angle 2.12569 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 242 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.8050 (t-90) REVERT: A 257 MET cc_start: 0.8529 (mmm) cc_final: 0.8256 (tpp) REVERT: A 371 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8491 (mm-30) REVERT: A 504 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8065 (tt) REVERT: A 505 GLU cc_start: 0.7873 (tt0) cc_final: 0.7143 (tm-30) REVERT: A 531 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8116 (tp) REVERT: B 29 MET cc_start: 0.7777 (tpp) cc_final: 0.7390 (tpt) REVERT: B 285 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8691 (mtmm) outliers start: 26 outliers final: 8 residues processed: 90 average time/residue: 0.7995 time to fit residues: 75.8657 Evaluate side-chains 74 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 285 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.066093 restraints weight = 18314.411| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.45 r_work: 0.2794 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10243 Z= 0.178 Angle : 0.792 32.294 13909 Z= 0.338 Chirality : 0.045 0.216 1574 Planarity : 0.004 0.052 1768 Dihedral : 10.157 156.531 1653 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.45 % Allowed : 20.23 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1245 helix: 2.04 (0.22), residues: 580 sheet: 0.21 (0.40), residues: 149 loop : 0.23 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 560 TYR 0.016 0.001 TYR A 802 PHE 0.019 0.001 PHE A 300 TRP 0.009 0.001 TRP A 799 HIS 0.004 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00434 (10234) covalent geometry : angle 0.78848 (13888) SS BOND : bond 0.00446 ( 3) SS BOND : angle 1.39603 ( 6) hydrogen bonds : bond 0.04337 ( 509) hydrogen bonds : angle 4.28535 ( 1524) Misc. bond : bond 0.00011 ( 1) link_NAG-ASN : bond 0.00227 ( 5) link_NAG-ASN : angle 2.12700 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 242 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7862 (t-90) REVERT: A 457 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8523 (pp) REVERT: A 504 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8063 (tt) REVERT: A 505 GLU cc_start: 0.7942 (tt0) cc_final: 0.7206 (tm-30) REVERT: A 531 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8071 (tp) REVERT: A 1013 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: B 285 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8625 (mtmm) outliers start: 26 outliers final: 10 residues processed: 88 average time/residue: 0.7560 time to fit residues: 70.2759 Evaluate side-chains 76 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 285 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 80 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 218 GLN A 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.067319 restraints weight = 18173.140| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.45 r_work: 0.2817 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10243 Z= 0.131 Angle : 0.774 31.668 13909 Z= 0.327 Chirality : 0.043 0.225 1574 Planarity : 0.004 0.051 1768 Dihedral : 9.858 157.204 1653 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.16 % Allowed : 20.23 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.24), residues: 1245 helix: 2.16 (0.22), residues: 578 sheet: 0.27 (0.40), residues: 159 loop : 0.24 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 560 TYR 0.013 0.001 TYR A 802 PHE 0.015 0.001 PHE A 300 TRP 0.010 0.001 TRP A 899 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00318 (10234) covalent geometry : angle 0.77108 (13888) SS BOND : bond 0.00315 ( 3) SS BOND : angle 1.03811 ( 6) hydrogen bonds : bond 0.03859 ( 509) hydrogen bonds : angle 4.18991 ( 1524) Misc. bond : bond 0.00014 ( 1) link_NAG-ASN : bond 0.00218 ( 5) link_NAG-ASN : angle 2.08750 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7343 (pmm150) cc_final: 0.7005 (mpp-170) REVERT: A 242 HIS cc_start: 0.8295 (OUTLIER) cc_final: 0.7820 (t-90) REVERT: A 457 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8523 (pp) REVERT: A 504 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8070 (tt) REVERT: A 505 GLU cc_start: 0.7913 (tt0) cc_final: 0.7192 (tm-30) REVERT: A 531 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8067 (tp) REVERT: A 1013 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8293 (tm-30) REVERT: B 29 MET cc_start: 0.7732 (tpp) cc_final: 0.7326 (tpt) REVERT: B 285 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8642 (mtmm) outliers start: 23 outliers final: 10 residues processed: 82 average time/residue: 0.8216 time to fit residues: 71.2015 Evaluate side-chains 75 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 285 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.102466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.067851 restraints weight = 18216.027| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.43 r_work: 0.2825 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10243 Z= 0.129 Angle : 0.774 31.716 13909 Z= 0.327 Chirality : 0.043 0.219 1574 Planarity : 0.004 0.054 1768 Dihedral : 9.645 156.995 1653 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.79 % Allowed : 20.60 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.24), residues: 1245 helix: 2.21 (0.22), residues: 578 sheet: 0.33 (0.40), residues: 159 loop : 0.29 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 560 TYR 0.013 0.001 TYR A 802 PHE 0.015 0.001 PHE A 300 TRP 0.009 0.001 TRP A 427 HIS 0.003 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00313 (10234) covalent geometry : angle 0.77145 (13888) SS BOND : bond 0.00315 ( 3) SS BOND : angle 1.02373 ( 6) hydrogen bonds : bond 0.03809 ( 509) hydrogen bonds : angle 4.14202 ( 1524) Misc. bond : bond 0.00017 ( 1) link_NAG-ASN : bond 0.00232 ( 5) link_NAG-ASN : angle 2.02444 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 242 HIS cc_start: 0.8240 (OUTLIER) cc_final: 0.7909 (t-90) REVERT: A 457 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8555 (pp) REVERT: A 505 GLU cc_start: 0.7931 (tt0) cc_final: 0.7230 (tm-30) REVERT: A 531 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8121 (tp) REVERT: B 29 MET cc_start: 0.7708 (tpp) cc_final: 0.7286 (tpt) REVERT: B 285 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8647 (mtmm) outliers start: 19 outliers final: 9 residues processed: 80 average time/residue: 0.7764 time to fit residues: 65.6197 Evaluate side-chains 72 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 285 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 102 optimal weight: 0.0170 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 114 optimal weight: 0.0470 chunk 59 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN A 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.104779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.070488 restraints weight = 18104.532| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.44 r_work: 0.2877 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10243 Z= 0.095 Angle : 0.761 30.678 13909 Z= 0.316 Chirality : 0.042 0.229 1574 Planarity : 0.004 0.060 1768 Dihedral : 9.226 158.100 1653 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.03 % Allowed : 21.64 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.24), residues: 1245 helix: 2.36 (0.22), residues: 578 sheet: 0.40 (0.42), residues: 145 loop : 0.26 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 560 TYR 0.013 0.001 TYR A 878 PHE 0.012 0.001 PHE A 300 TRP 0.011 0.001 TRP A 899 HIS 0.002 0.000 HIS A 502 Details of bonding type rmsd covalent geometry : bond 0.00216 (10234) covalent geometry : angle 0.75885 (13888) SS BOND : bond 0.00175 ( 3) SS BOND : angle 0.61303 ( 6) hydrogen bonds : bond 0.03167 ( 509) hydrogen bonds : angle 3.97726 ( 1524) Misc. bond : bond 0.00023 ( 1) link_NAG-ASN : bond 0.00339 ( 5) link_NAG-ASN : angle 1.92871 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2490 Ramachandran restraints generated. 1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.396 Fit side-chains REVERT: A 242 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7784 (t-90) REVERT: A 457 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8545 (pp) REVERT: A 505 GLU cc_start: 0.7988 (tt0) cc_final: 0.7216 (tm-30) REVERT: A 531 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8120 (tp) REVERT: A 560 ARG cc_start: 0.8058 (mtp-110) cc_final: 0.7631 (mtm180) REVERT: A 1013 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8309 (tm-30) REVERT: B 29 MET cc_start: 0.7677 (tpp) cc_final: 0.7245 (tpt) REVERT: B 251 ASN cc_start: 0.7703 (t0) cc_final: 0.6528 (t0) outliers start: 11 outliers final: 4 residues processed: 78 average time/residue: 0.8573 time to fit residues: 70.3683 Evaluate side-chains 68 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 HIS Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 1013 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 261 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN B 147 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.101392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.066447 restraints weight = 18330.751| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.44 r_work: 0.2798 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10243 Z= 0.181 Angle : 0.795 32.552 13909 Z= 0.340 Chirality : 0.045 0.203 1574 Planarity : 0.005 0.060 1768 Dihedral : 9.558 154.656 1651 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.03 % Allowed : 21.83 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.24), residues: 1245 helix: 2.22 (0.22), residues: 579 sheet: 0.39 (0.40), residues: 154 loop : 0.33 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 560 TYR 0.017 0.001 TYR A 802 PHE 0.018 0.001 PHE A 315 TRP 0.009 0.001 TRP A 799 HIS 0.005 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00442 (10234) covalent geometry : angle 0.79250 (13888) SS BOND : bond 0.00410 ( 3) SS BOND : angle 1.31106 ( 6) hydrogen bonds : bond 0.04299 ( 509) hydrogen bonds : angle 4.19691 ( 1524) Misc. bond : bond 0.00014 ( 1) link_NAG-ASN : bond 0.00222 ( 5) link_NAG-ASN : angle 2.05767 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4573.54 seconds wall clock time: 78 minutes 24.94 seconds (4704.94 seconds total)