Starting phenix.real_space_refine on Wed Aug 5 21:15:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qgr_53147/08_2026/9qgr_53147_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qgr_53147/08_2026/9qgr_53147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qgr_53147/08_2026/9qgr_53147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qgr_53147/08_2026/9qgr_53147.map" model { file = "/net/cci-nas-00/data/ceres_data/9qgr_53147/08_2026/9qgr_53147_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qgr_53147/08_2026/9qgr_53147_neut.cif" } resolution = 3.1 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= 0.020 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 51 5.16 5 C 7185 2.51 5 N 1934 2.21 5 O 2140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11311 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2423 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 275} Chain: "B" Number of atoms: 7661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 976, 7661 Classifications: {'peptide': 976} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 48, 'TRANS': 925} Chain breaks: 1 Chain: "C" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.57, per 1000 atoms: 0.23 Number of scatterers: 11311 At special positions: 0 Unit cell: (91.3, 98.77, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 P 1 15.00 O 2140 8.00 N 1934 7.00 C 7185 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 509.3 milliseconds 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2682 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 11 sheets defined 47.0% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 4582 through 4593 removed outlier: 4.523A pdb=" N LYS A4593 " --> pdb=" O GLU A4589 " (cutoff:3.500A) Processing helix chain 'A' and resid 4618 through 4626 Processing helix chain 'A' and resid 4630 through 4648 removed outlier: 4.159A pdb=" N VAL A4634 " --> pdb=" O HIS A4630 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS A4635 " --> pdb=" O PRO A4631 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A4646 " --> pdb=" O VAL A4642 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU A4648 " --> pdb=" O LEU A4644 " (cutoff:3.500A) Processing helix chain 'A' and resid 4746 through 4758 Processing helix chain 'A' and resid 4762 through 4767 removed outlier: 3.510A pdb=" N PHE A4765 " --> pdb=" O GLU A4762 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A4767 " --> pdb=" O TYR A4764 " (cutoff:3.500A) Processing helix chain 'A' and resid 4769 through 4774 removed outlier: 3.759A pdb=" N ARG A4772 " --> pdb=" O GLY A4769 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A4774 " --> pdb=" O GLU A4771 " (cutoff:3.500A) Processing helix chain 'A' and resid 4776 through 4798 removed outlier: 3.558A pdb=" N GLN A4792 " --> pdb=" O SER A4788 " (cutoff:3.500A) Processing helix chain 'A' and resid 4799 through 4805 Processing helix chain 'A' and resid 4810 through 4821 Processing helix chain 'A' and resid 4821 through 4837 Processing helix chain 'A' and resid 4842 through 4869 removed outlier: 3.748A pdb=" N THR A4848 " --> pdb=" O ARG A4844 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS A4862 " --> pdb=" O ARG A4858 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A4869 " --> pdb=" O GLU A4865 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 208 removed outlier: 7.028A pdb=" N ARG B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 216 Processing helix chain 'B' and resid 226 through 240 Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.615A pdb=" N SER B 258 " --> pdb=" O HIS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 271 through 282 removed outlier: 4.275A pdb=" N ALA B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 469 through 488 removed outlier: 3.680A pdb=" N THR B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS B 483 " --> pdb=" O ASN B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 512 Processing helix chain 'B' and resid 517 through 528 Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.580A pdb=" N ASP B 536 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 570 Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.630A pdb=" N GLN B 581 " --> pdb=" O ALA B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 595 removed outlier: 3.879A pdb=" N ILE B 593 " --> pdb=" O SER B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 604 Processing helix chain 'B' and resid 613 through 627 Processing helix chain 'B' and resid 644 through 650 removed outlier: 3.653A pdb=" N ASN B 649 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 650 " --> pdb=" O ASN B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.743A pdb=" N VAL B 659 " --> pdb=" O PRO B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 675 Processing helix chain 'B' and resid 688 through 692 removed outlier: 3.832A pdb=" N GLU B 692 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 removed outlier: 3.687A pdb=" N LYS B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 727 removed outlier: 3.661A pdb=" N ARG B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 756 removed outlier: 3.798A pdb=" N SER B 756 " --> pdb=" O TYR B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 771 Processing helix chain 'B' and resid 775 through 792 Processing helix chain 'B' and resid 792 through 804 removed outlier: 4.789A pdb=" N ASN B 797 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA B 798 " --> pdb=" O SER B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 812 Processing helix chain 'B' and resid 817 through 831 removed outlier: 3.853A pdb=" N SER B 825 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 854 Processing helix chain 'B' and resid 854 through 864 Processing helix chain 'B' and resid 893 through 912 Processing helix chain 'B' and resid 918 through 927 removed outlier: 3.548A pdb=" N GLN B 927 " --> pdb=" O ALA B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 976 Processing helix chain 'B' and resid 996 through 1012 Processing helix chain 'B' and resid 1018 through 1027 Processing helix chain 'B' and resid 1033 through 1054 removed outlier: 3.533A pdb=" N GLY B1054 " --> pdb=" O LYS B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1116 Processing helix chain 'B' and resid 1136 through 1144 Processing helix chain 'B' and resid 1147 through 1157 Processing helix chain 'C' and resid 22 through 32 Processing helix chain 'E' and resid 22 through 34 Processing helix chain 'E' and resid 37 through 41 Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.901A pdb=" N TYR E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4596 through 4599 removed outlier: 6.693A pdb=" N ILE A4667 " --> pdb=" O ASP A4661 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4602 through 4604 Processing sheet with id=AA3, first strand: chain 'B' and resid 288 through 292 removed outlier: 6.733A pdb=" N ILE B 220 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N HIS B 247 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU B 222 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP B 219 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N VAL B 308 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 221 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR B 563 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 353 Processing sheet with id=AA5, first strand: chain 'B' and resid 410 through 411 removed outlier: 4.631A pdb=" N TYR B 392 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL B 398 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY B 434 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLY B 435 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B 378 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE B 369 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL B 376 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 680 through 683 removed outlier: 6.238A pdb=" N ILE B 635 " --> pdb=" O THR B 681 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N TYR B 683 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 637 " --> pdb=" O TYR B 683 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LYS B 606 " --> pdb=" O GLY B 705 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ALA B 707 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 608 " --> pdb=" O ALA B 707 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 733 " --> pdb=" O ASN B 708 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1084 through 1086 Processing sheet with id=AA8, first strand: chain 'B' and resid 1097 through 1099 removed outlier: 6.292A pdb=" N PHE B1097 " --> pdb=" O ARG B1187 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR B1189 " --> pdb=" O PHE B1097 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B1099 " --> pdb=" O THR B1189 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLU B1170 " --> pdb=" O LEU B1123 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B1123 " --> pdb=" O GLU B1170 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS B1172 " --> pdb=" O THR B1121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1097 through 1099 removed outlier: 6.292A pdb=" N PHE B1097 " --> pdb=" O ARG B1187 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR B1189 " --> pdb=" O PHE B1097 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL B1099 " --> pdb=" O THR B1189 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS B1173 " --> pdb=" O VAL B1181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 12 through 16 Processing sheet with id=AB2, first strand: chain 'E' and resid 12 through 16 removed outlier: 4.036A pdb=" N ARG E 42 " --> pdb=" O VAL E 70 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1506 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: 2.38 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2907 1.33 - 1.45: 2119 1.45 - 1.58: 6450 1.58 - 1.70: 1 1.70 - 1.82: 76 Bond restraints: 11553 Sorted by residual: bond pdb=" CB CYS B 767 " pdb=" SG CYS B 767 " ideal model delta sigma weight residual 1.808 1.419 0.389 3.30e-02 9.18e+02 1.39e+02 bond pdb=" CA SER E 20 " pdb=" CB SER E 20 " ideal model delta sigma weight residual 1.533 1.484 0.049 1.63e-02 3.76e+03 8.99e+00 bond pdb=" CZ ARG E 72 " pdb=" NH2 ARG E 72 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 8.91e+00 bond pdb=" CZ ARG E 42 " pdb=" NH2 ARG E 42 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.12e+00 bond pdb=" CA THR E 22 " pdb=" C THR E 22 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.21e-02 6.83e+03 5.89e+00 ... (remaining 11548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 15387 2.55 - 5.11: 229 5.11 - 7.66: 19 7.66 - 10.21: 2 10.21 - 12.77: 2 Bond angle restraints: 15639 Sorted by residual: angle pdb=" OE1 GLN B 545 " pdb=" CD GLN B 545 " pdb=" NE2 GLN B 545 " ideal model delta sigma weight residual 122.60 118.44 4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" CA PHE B 555 " pdb=" CB PHE B 555 " pdb=" CG PHE B 555 " ideal model delta sigma weight residual 113.80 117.96 -4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" OE1 GLN E 49 " pdb=" CD GLN E 49 " pdb=" NE2 GLN E 49 " ideal model delta sigma weight residual 122.60 118.56 4.04 1.00e+00 1.00e+00 1.63e+01 angle pdb=" CA LYS A4871 " pdb=" CB LYS A4871 " pdb=" CG LYS A4871 " ideal model delta sigma weight residual 114.10 121.96 -7.86 2.00e+00 2.50e-01 1.54e+01 angle pdb=" CA THR E 22 " pdb=" CB THR E 22 " pdb=" OG1 THR E 22 " ideal model delta sigma weight residual 109.60 103.86 5.74 1.50e+00 4.44e-01 1.46e+01 ... (remaining 15634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 6276 17.24 - 34.47: 559 34.47 - 51.71: 122 51.71 - 68.95: 39 68.95 - 86.19: 21 Dihedral angle restraints: 7017 sinusoidal: 2879 harmonic: 4138 Sorted by residual: dihedral pdb=" CD ARG C 74 " pdb=" NE ARG C 74 " pdb=" CZ ARG C 74 " pdb=" NH1 ARG C 74 " ideal model delta sinusoidal sigma weight residual 0.00 51.67 -51.67 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CA GLU C 34 " pdb=" C GLU C 34 " pdb=" N GLY C 35 " pdb=" CA GLY C 35 " ideal model delta harmonic sigma weight residual 180.00 151.60 28.40 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA LEU B1070 " pdb=" C LEU B1070 " pdb=" N PRO B1071 " pdb=" CA PRO B1071 " ideal model delta harmonic sigma weight residual 0.00 -25.78 25.78 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 7014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1494 0.063 - 0.126: 225 0.126 - 0.189: 13 0.189 - 0.253: 3 0.253 - 0.316: 1 Chirality restraints: 1736 Sorted by residual: chirality pdb=" CA VAL E 17 " pdb=" N VAL E 17 " pdb=" C VAL E 17 " pdb=" CB VAL E 17 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA LEU B1070 " pdb=" N LEU B1070 " pdb=" C LEU B1070 " pdb=" CB LEU B1070 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ILE C 36 " pdb=" N ILE C 36 " pdb=" C ILE C 36 " pdb=" CB ILE C 36 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1733 not shown) Planarity restraints: 2037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 74 " -0.873 9.50e-02 1.11e+02 3.91e-01 9.29e+01 pdb=" NE ARG C 74 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG C 74 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 74 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 74 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A4719 " 0.070 2.00e-02 2.50e+03 3.77e-02 2.85e+01 pdb=" CG TYR A4719 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A4719 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A4719 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A4719 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR A4719 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A4719 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A4719 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B1062 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C LYS B1062 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS B1062 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN B1063 " 0.021 2.00e-02 2.50e+03 ... (remaining 2034 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1353 2.76 - 3.47: 15972 3.47 - 4.19: 26992 4.19 - 4.90: 49367 Nonbonded interactions: 93686 Sorted by model distance: nonbonded pdb=" SG CYS B 767 " pdb=" C ALA C 76 " model vdw 1.326 3.630 nonbonded pdb=" SG CYS A4725 " pdb=" CB ALA C 76 " model vdw 1.816 3.820 nonbonded pdb=" SG CYS B 767 " pdb=" O ALA C 76 " model vdw 2.225 3.400 nonbonded pdb=" CB CYS B 767 " pdb=" C ALA C 76 " model vdw 2.293 3.670 nonbonded pdb=" O LEU B 710 " pdb=" CB ALA E 76 " model vdw 2.399 3.460 ... (remaining 93681 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 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) } 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: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.389 11554 Z= 0.220 Angle : 0.677 12.767 15639 Z= 0.387 Chirality : 0.045 0.316 1736 Planarity : 0.010 0.391 2037 Dihedral : 14.975 86.187 4335 Min Nonbonded Distance : 1.326 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.64 % Allowed : 12.61 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.60 (0.22), residues: 1412 helix: 1.59 (0.22), residues: 576 sheet: 1.44 (0.36), residues: 229 loop : 0.52 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1159 TYR 0.070 0.002 TYR A4719 PHE 0.036 0.002 PHE B 555 TRP 0.015 0.001 TRP A4732 HIS 0.002 0.001 HIS A4817 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (11553) covalent geometry : angle 0.67741 / 0.39 (15639) hydrogen bonds : bond 0.13911 / 9.09 ( 534) hydrogen bonds : angle 5.80100 / 4.18 ( 1506) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9241 (pmm) cc_final: 0.8926 (pmm) REVERT: A 4791 TYR cc_start: 0.7937 (m-10) cc_final: 0.7413 (m-80) REVERT: B 418 TYR cc_start: 0.7494 (m-80) cc_final: 0.7267 (m-80) REVERT: B 428 PHE cc_start: 0.8467 (m-80) cc_final: 0.7982 (m-80) REVERT: B 519 LYS cc_start: 0.9329 (ttmm) cc_final: 0.8947 (tptp) REVERT: B 640 MET cc_start: 0.8902 (pmt) cc_final: 0.8202 (pmt) REVERT: B 796 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 806 GLN cc_start: 0.7889 (pp30) cc_final: 0.7530 (pp30) REVERT: B 810 ARG cc_start: 0.8791 (mtm110) cc_final: 0.8381 (ttp80) REVERT: B 828 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9081 (tttm) REVERT: B 833 ASP cc_start: 0.7982 (m-30) cc_final: 0.7722 (m-30) REVERT: B 989 GLU cc_start: 0.8748 (tp30) cc_final: 0.8237 (tm-30) REVERT: C 3 ILE cc_start: 0.9255 (pt) cc_final: 0.9018 (mm) REVERT: C 6 LYS cc_start: 0.9217 (mttp) cc_final: 0.8949 (mtpp) REVERT: C 72 ARG cc_start: 0.8361 (ttp-110) cc_final: 0.8011 (ttp-110) REVERT: E 2 GLN cc_start: 0.9059 (tt0) cc_final: 0.8822 (tt0) REVERT: E 7 THR cc_start: 0.9549 (m) cc_final: 0.9050 (p) REVERT: E 11 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7842 (ptmm) REVERT: E 21 ASP cc_start: 0.8653 (m-30) cc_final: 0.8396 (m-30) REVERT: E 51 GLU cc_start: 0.9124 (pt0) cc_final: 0.8741 (pm20) REVERT: E 54 ARG cc_start: 0.8462 (mmm-85) cc_final: 0.7998 (mtp85) REVERT: E 55 THR cc_start: 0.8692 (p) cc_final: 0.8356 (t) REVERT: E 62 GLN cc_start: 0.8799 (pt0) cc_final: 0.8558 (pt0) REVERT: E 64 GLU cc_start: 0.9049 (mp0) cc_final: 0.8761 (mp0) REVERT: E 65 SER cc_start: 0.8891 (m) cc_final: 0.8550 (p) outliers start: 8 outliers final: 4 residues processed: 124 average time/residue: 0.1234 time to fit residues: 21.4284 Evaluate side-chains 111 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4663 ASP Chi-restraints excluded: chain B residue 828 LYS Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 22 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 647 ASN B 852 GLN ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.055182 restraints weight = 30450.874| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.55 r_work: 0.2667 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11554 Z= 0.148 Angle : 0.517 8.653 15639 Z= 0.268 Chirality : 0.042 0.161 1736 Planarity : 0.004 0.082 2037 Dihedral : 4.776 45.323 1554 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.20 % Allowed : 11.73 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.68 (0.23), residues: 1412 helix: 1.80 (0.22), residues: 583 sheet: 0.97 (0.34), residues: 249 loop : 0.61 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 74 TYR 0.014 0.001 TYR B 901 PHE 0.013 0.001 PHE B1108 TRP 0.006 0.001 TRP B 782 HIS 0.002 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (11553) covalent geometry : angle 0.51653 / 0.27 (15639) hydrogen bonds : bond 0.03904 / 2.60 ( 534) hydrogen bonds : angle 4.61922 / 3.32 ( 1506) Misc. bond : bond 0.00082 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9238 (pmm) cc_final: 0.8915 (pmm) REVERT: A 4791 TYR cc_start: 0.8055 (m-10) cc_final: 0.7509 (m-80) REVERT: B 391 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: B 418 TYR cc_start: 0.7636 (m-80) cc_final: 0.7280 (m-80) REVERT: B 519 LYS cc_start: 0.9326 (ttmm) cc_final: 0.8907 (tptp) REVERT: B 640 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8098 (pmt) REVERT: B 761 GLU cc_start: 0.7916 (tp30) cc_final: 0.7713 (tp30) REVERT: B 806 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7206 (pp30) REVERT: B 989 GLU cc_start: 0.8759 (tp30) cc_final: 0.8235 (tm-30) REVERT: B 998 MET cc_start: 0.8604 (mmm) cc_final: 0.8235 (mmm) REVERT: C 3 ILE cc_start: 0.9250 (pt) cc_final: 0.8964 (mm) REVERT: C 21 ASP cc_start: 0.9203 (OUTLIER) cc_final: 0.8793 (t70) REVERT: E 2 GLN cc_start: 0.9137 (tt0) cc_final: 0.8742 (tt0) REVERT: E 16 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8834 (mm-30) REVERT: E 18 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8729 (mm-30) REVERT: E 21 ASP cc_start: 0.8860 (m-30) cc_final: 0.8557 (m-30) REVERT: E 51 GLU cc_start: 0.9126 (pt0) cc_final: 0.8745 (pm20) REVERT: E 54 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8064 (mtp85) REVERT: E 64 GLU cc_start: 0.9104 (mp0) cc_final: 0.8809 (mp0) REVERT: E 65 SER cc_start: 0.8948 (m) cc_final: 0.8652 (p) outliers start: 15 outliers final: 5 residues processed: 117 average time/residue: 0.1208 time to fit residues: 20.1219 Evaluate side-chains 111 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4756 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.055299 restraints weight = 30794.604| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.57 r_work: 0.2683 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11554 Z= 0.109 Angle : 0.484 9.129 15639 Z= 0.249 Chirality : 0.041 0.151 1736 Planarity : 0.003 0.048 2037 Dihedral : 4.429 44.942 1544 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.12 % Allowed : 11.81 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.76 (0.23), residues: 1412 helix: 1.88 (0.22), residues: 585 sheet: 1.08 (0.34), residues: 243 loop : 0.60 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.013 0.001 TYR B 901 PHE 0.012 0.001 PHE B1108 TRP 0.005 0.001 TRP B 607 HIS 0.002 0.000 HIS A4817 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (11553) covalent geometry : angle 0.48443 / 0.25 (15639) hydrogen bonds : bond 0.03468 / 2.30 ( 534) hydrogen bonds : angle 4.37300 / 3.15 ( 1506) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9248 (pmm) cc_final: 0.8903 (pmm) REVERT: A 4791 TYR cc_start: 0.8059 (m-10) cc_final: 0.7511 (m-80) REVERT: B 391 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: B 418 TYR cc_start: 0.7595 (m-80) cc_final: 0.7219 (m-80) REVERT: B 457 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8551 (pm20) REVERT: B 519 LYS cc_start: 0.9302 (ttmm) cc_final: 0.8991 (tmtt) REVERT: B 610 VAL cc_start: 0.9458 (OUTLIER) cc_final: 0.9177 (m) REVERT: B 640 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8038 (pmt) REVERT: B 761 GLU cc_start: 0.7934 (tp30) cc_final: 0.7656 (tp30) REVERT: B 806 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7224 (pp30) REVERT: B 989 GLU cc_start: 0.8753 (tp30) cc_final: 0.8201 (tm-30) REVERT: B 998 MET cc_start: 0.8583 (mmm) cc_final: 0.8069 (mmm) REVERT: C 3 ILE cc_start: 0.9182 (pt) cc_final: 0.8946 (mm) REVERT: C 24 GLU cc_start: 0.8834 (pm20) cc_final: 0.8076 (pm20) REVERT: E 2 GLN cc_start: 0.9104 (tt0) cc_final: 0.8858 (tt0) REVERT: E 16 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8914 (mm-30) REVERT: E 18 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8755 (mm-30) REVERT: E 21 ASP cc_start: 0.8731 (m-30) cc_final: 0.8361 (m-30) REVERT: E 51 GLU cc_start: 0.9106 (pt0) cc_final: 0.8699 (pm20) REVERT: E 64 GLU cc_start: 0.9110 (mp0) cc_final: 0.8805 (mp0) REVERT: E 65 SER cc_start: 0.8988 (m) cc_final: 0.8701 (p) outliers start: 14 outliers final: 5 residues processed: 120 average time/residue: 0.1275 time to fit residues: 21.7618 Evaluate side-chains 114 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4756 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4639 GLN ** C 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.070183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.052247 restraints weight = 31010.524| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.53 r_work: 0.2612 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11554 Z= 0.194 Angle : 0.528 8.419 15639 Z= 0.270 Chirality : 0.042 0.149 1736 Planarity : 0.004 0.052 2037 Dihedral : 4.459 44.313 1542 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.53 % Allowed : 11.81 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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 (0.23), residues: 1412 helix: 1.95 (0.22), residues: 580 sheet: 0.91 (0.34), residues: 245 loop : 0.61 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 54 TYR 0.017 0.001 TYR B 901 PHE 0.012 0.001 PHE B1112 TRP 0.009 0.001 TRP B 607 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (11553) covalent geometry : angle 0.52840 / 0.27 (15639) hydrogen bonds : bond 0.03920 / 2.61 ( 534) hydrogen bonds : angle 4.29044 / 3.08 ( 1506) Misc. bond : bond 0.00092 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9240 (pmm) cc_final: 0.8903 (pmm) REVERT: A 4791 TYR cc_start: 0.8243 (m-10) cc_final: 0.7783 (m-80) REVERT: B 391 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: B 418 TYR cc_start: 0.7820 (m-80) cc_final: 0.7402 (m-80) REVERT: B 457 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8252 (pm20) REVERT: B 519 LYS cc_start: 0.9308 (ttmm) cc_final: 0.8967 (tmtt) REVERT: B 640 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8140 (pmt) REVERT: B 761 GLU cc_start: 0.7991 (tp30) cc_final: 0.7663 (tp30) REVERT: B 806 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7290 (pp30) REVERT: B 1057 ASP cc_start: 0.8620 (t0) cc_final: 0.8415 (t0) REVERT: C 1 MET cc_start: 0.7646 (ptp) cc_final: 0.7125 (ptp) REVERT: C 18 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8820 (mp0) REVERT: E 2 GLN cc_start: 0.9114 (tt0) cc_final: 0.8904 (tt0) REVERT: E 16 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8877 (mm-30) REVERT: E 21 ASP cc_start: 0.8648 (m-30) cc_final: 0.8360 (m-30) REVERT: E 51 GLU cc_start: 0.9113 (pt0) cc_final: 0.8545 (pm20) REVERT: E 64 GLU cc_start: 0.9154 (mp0) cc_final: 0.8789 (mp0) outliers start: 19 outliers final: 10 residues processed: 111 average time/residue: 0.1013 time to fit residues: 17.0195 Evaluate side-chains 104 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4756 SER Chi-restraints excluded: chain A residue 4794 CYS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain E residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 51 optimal weight: 0.0980 chunk 130 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 2 GLN C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.070881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.053062 restraints weight = 30617.902| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.52 r_work: 0.2630 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11554 Z= 0.134 Angle : 0.493 9.551 15639 Z= 0.251 Chirality : 0.041 0.151 1736 Planarity : 0.003 0.051 2037 Dihedral : 4.272 43.642 1540 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.29 % Allowed : 13.01 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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 (0.23), residues: 1412 helix: 2.03 (0.22), residues: 579 sheet: 0.84 (0.34), residues: 245 loop : 0.63 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.015 0.001 TYR B 901 PHE 0.013 0.001 PHE B1112 TRP 0.007 0.001 TRP A4732 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (11553) covalent geometry : angle 0.49345 / 0.25 (15639) hydrogen bonds : bond 0.03495 / 2.32 ( 534) hydrogen bonds : angle 4.18180 / 3.01 ( 1506) Misc. bond : bond 0.00049 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9237 (pmm) cc_final: 0.8853 (pmm) REVERT: A 4791 TYR cc_start: 0.8245 (m-10) cc_final: 0.7769 (m-80) REVERT: B 391 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: B 418 TYR cc_start: 0.7835 (m-80) cc_final: 0.7421 (m-80) REVERT: B 457 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: B 519 LYS cc_start: 0.9306 (ttmm) cc_final: 0.8966 (tmtt) REVERT: B 640 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8011 (pmt) REVERT: B 761 GLU cc_start: 0.8091 (tp30) cc_final: 0.7721 (tp30) REVERT: B 806 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7261 (pp30) REVERT: B 1057 ASP cc_start: 0.8589 (t0) cc_final: 0.8370 (t0) REVERT: C 1 MET cc_start: 0.7502 (ptp) cc_final: 0.6903 (ptp) REVERT: C 8 LEU cc_start: 0.9054 (mm) cc_final: 0.8666 (mm) REVERT: C 18 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8937 (mp0) REVERT: E 16 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8893 (mm-30) REVERT: E 21 ASP cc_start: 0.8673 (m-30) cc_final: 0.8374 (m-30) REVERT: E 34 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8617 (mm-30) REVERT: E 51 GLU cc_start: 0.9106 (pt0) cc_final: 0.8532 (pm20) REVERT: E 64 GLU cc_start: 0.9126 (mp0) cc_final: 0.8760 (mp0) outliers start: 16 outliers final: 8 residues processed: 105 average time/residue: 0.1081 time to fit residues: 17.0162 Evaluate side-chains 106 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4756 SER Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 83 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 40 optimal weight: 0.0470 chunk 120 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 793 GLN C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.069849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.052011 restraints weight = 31132.027| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.54 r_work: 0.2606 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11554 Z= 0.179 Angle : 0.508 9.431 15639 Z= 0.258 Chirality : 0.041 0.147 1736 Planarity : 0.004 0.051 2037 Dihedral : 4.289 44.299 1540 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.69 % Allowed : 12.69 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.77 (0.23), residues: 1412 helix: 2.01 (0.22), residues: 586 sheet: 0.79 (0.34), residues: 245 loop : 0.61 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.015 0.001 TYR B 901 PHE 0.012 0.001 PHE B1112 TRP 0.006 0.001 TRP B 607 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (11553) covalent geometry : angle 0.50834 / 0.26 (15639) hydrogen bonds : bond 0.03674 / 2.44 ( 534) hydrogen bonds : angle 4.17842 / 3.01 ( 1506) Misc. bond : bond 0.00056 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: B 418 TYR cc_start: 0.7901 (m-80) cc_final: 0.7487 (m-80) REVERT: B 457 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8305 (pm20) REVERT: B 519 LYS cc_start: 0.9301 (ttmm) cc_final: 0.8955 (tmtt) REVERT: B 640 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8077 (pmt) REVERT: B 806 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7296 (pp30) REVERT: B 1057 ASP cc_start: 0.8592 (t0) cc_final: 0.8354 (t0) REVERT: C 8 LEU cc_start: 0.9049 (mm) cc_final: 0.8694 (mm) REVERT: C 18 GLU cc_start: 0.9214 (mm-30) cc_final: 0.9005 (mp0) REVERT: E 2 GLN cc_start: 0.9221 (tt0) cc_final: 0.8906 (tt0) REVERT: E 16 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8685 (mm-30) REVERT: E 21 ASP cc_start: 0.8641 (m-30) cc_final: 0.8319 (m-30) REVERT: E 34 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8836 (tp30) REVERT: E 51 GLU cc_start: 0.9109 (pt0) cc_final: 0.8543 (pm20) REVERT: E 64 GLU cc_start: 0.9161 (mp0) cc_final: 0.8741 (mp0) outliers start: 21 outliers final: 14 residues processed: 101 average time/residue: 0.1107 time to fit residues: 16.4807 Evaluate side-chains 107 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4621 MET Chi-restraints excluded: chain A residue 4756 SER Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 73 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.052638 restraints weight = 30847.982| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.52 r_work: 0.2634 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11554 Z= 0.131 Angle : 0.484 10.220 15639 Z= 0.247 Chirality : 0.041 0.153 1736 Planarity : 0.003 0.051 2037 Dihedral : 4.242 44.049 1540 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.45 % Allowed : 12.93 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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 (0.23), residues: 1412 helix: 2.05 (0.22), residues: 584 sheet: 0.98 (0.36), residues: 224 loop : 0.64 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 74 TYR 0.014 0.001 TYR B 901 PHE 0.012 0.001 PHE B1112 TRP 0.005 0.001 TRP B 849 HIS 0.003 0.000 HIS A4817 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (11553) covalent geometry : angle 0.48427 / 0.25 (15639) hydrogen bonds : bond 0.03463 / 2.29 ( 534) hydrogen bonds : angle 4.12020 / 2.97 ( 1506) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9212 (pmm) cc_final: 0.8859 (pmm) REVERT: B 391 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: B 418 TYR cc_start: 0.7953 (m-80) cc_final: 0.7570 (m-80) REVERT: B 457 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: B 519 LYS cc_start: 0.9277 (ttmm) cc_final: 0.8935 (tmtt) REVERT: B 640 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8046 (pmt) REVERT: B 806 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7286 (pp30) REVERT: B 1057 ASP cc_start: 0.8613 (t0) cc_final: 0.8379 (t0) REVERT: C 1 MET cc_start: 0.7348 (ptp) cc_final: 0.6743 (ptp) REVERT: C 8 LEU cc_start: 0.9004 (mm) cc_final: 0.8677 (mm) REVERT: C 41 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8757 (mt0) REVERT: E 2 GLN cc_start: 0.9203 (tt0) cc_final: 0.8840 (tt0) REVERT: E 16 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8591 (mm-30) REVERT: E 21 ASP cc_start: 0.8683 (m-30) cc_final: 0.8378 (m-30) REVERT: E 34 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8535 (mm-30) REVERT: E 51 GLU cc_start: 0.9113 (pt0) cc_final: 0.8558 (pm20) REVERT: E 64 GLU cc_start: 0.9180 (mp0) cc_final: 0.8750 (mp0) outliers start: 18 outliers final: 11 residues processed: 95 average time/residue: 0.1060 time to fit residues: 15.1170 Evaluate side-chains 103 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4621 MET Chi-restraints excluded: chain A residue 4756 SER Chi-restraints excluded: chain A residue 4760 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 GLN Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 27 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.0010 chunk 63 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.069756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.051977 restraints weight = 30799.277| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 3.51 r_work: 0.2620 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11554 Z= 0.171 Angle : 0.503 10.245 15639 Z= 0.256 Chirality : 0.041 0.146 1736 Planarity : 0.003 0.053 2037 Dihedral : 4.246 44.239 1540 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.53 % Allowed : 12.69 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.78 (0.23), residues: 1412 helix: 2.06 (0.22), residues: 584 sheet: 0.79 (0.36), residues: 218 loop : 0.58 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 42 TYR 0.014 0.001 TYR B 901 PHE 0.012 0.001 PHE B1112 TRP 0.005 0.001 TRP A4797 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (11553) covalent geometry : angle 0.50332 / 0.26 (15639) hydrogen bonds : bond 0.03573 / 2.37 ( 534) hydrogen bonds : angle 4.14188 / 2.98 ( 1506) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 391 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: B 418 TYR cc_start: 0.8014 (m-80) cc_final: 0.7631 (m-80) REVERT: B 457 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: B 519 LYS cc_start: 0.9283 (ttmm) cc_final: 0.8936 (tmtt) REVERT: B 640 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8066 (pmt) REVERT: B 806 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7312 (pp30) REVERT: B 1057 ASP cc_start: 0.8614 (t0) cc_final: 0.8369 (t0) REVERT: C 8 LEU cc_start: 0.9039 (mm) cc_final: 0.8728 (mm) REVERT: E 2 GLN cc_start: 0.9196 (tt0) cc_final: 0.8837 (tt0) REVERT: E 16 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8506 (mm-30) REVERT: E 21 ASP cc_start: 0.8696 (m-30) cc_final: 0.8386 (m-30) REVERT: E 34 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8513 (mm-30) REVERT: E 51 GLU cc_start: 0.9114 (pt0) cc_final: 0.8553 (pm20) REVERT: E 64 GLU cc_start: 0.9186 (mp0) cc_final: 0.8756 (mp0) outliers start: 19 outliers final: 11 residues processed: 96 average time/residue: 0.1185 time to fit residues: 16.8437 Evaluate side-chains 102 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4621 MET Chi-restraints excluded: chain A residue 4756 SER Chi-restraints excluded: chain A residue 4760 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.071877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.054138 restraints weight = 30883.868| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.49 r_work: 0.2644 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11554 Z= 0.102 Angle : 0.474 11.059 15639 Z= 0.241 Chirality : 0.040 0.143 1736 Planarity : 0.003 0.051 2037 Dihedral : 4.135 44.497 1540 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.12 % Allowed : 13.09 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.82 (0.23), residues: 1412 helix: 2.05 (0.22), residues: 590 sheet: 0.80 (0.37), residues: 212 loop : 0.66 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 74 TYR 0.012 0.001 TYR B 901 PHE 0.011 0.001 PHE B1108 TRP 0.007 0.001 TRP B 849 HIS 0.003 0.000 HIS A4817 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (11553) covalent geometry : angle 0.47391 / 0.24 (15639) hydrogen bonds : bond 0.03154 / 2.07 ( 534) hydrogen bonds : angle 4.02773 / 2.91 ( 1506) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9250 (pmm) cc_final: 0.9012 (pmm) REVERT: B 391 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7739 (m-30) REVERT: B 418 TYR cc_start: 0.7972 (m-80) cc_final: 0.7630 (m-80) REVERT: B 457 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8365 (pm20) REVERT: B 519 LYS cc_start: 0.9252 (ttmm) cc_final: 0.8910 (tmtt) REVERT: B 640 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.7948 (pmt) REVERT: B 806 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7295 (pp30) REVERT: B 1057 ASP cc_start: 0.8647 (t0) cc_final: 0.8393 (t0) REVERT: C 1 MET cc_start: 0.7354 (ptp) cc_final: 0.6827 (ptp) REVERT: C 8 LEU cc_start: 0.9021 (mm) cc_final: 0.8730 (mm) REVERT: C 41 GLN cc_start: 0.8785 (mt0) cc_final: 0.8545 (pt0) REVERT: E 21 ASP cc_start: 0.8686 (m-30) cc_final: 0.8398 (m-30) REVERT: E 51 GLU cc_start: 0.9094 (pt0) cc_final: 0.8531 (pm20) REVERT: E 62 GLN cc_start: 0.9178 (mt0) cc_final: 0.8774 (mp10) REVERT: E 64 GLU cc_start: 0.9183 (mp0) cc_final: 0.8766 (mp0) outliers start: 14 outliers final: 8 residues processed: 103 average time/residue: 0.1031 time to fit residues: 16.0996 Evaluate side-chains 98 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4756 SER Chi-restraints excluded: chain A residue 4760 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 17 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 42 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.070484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.052731 restraints weight = 31095.011| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 3.53 r_work: 0.2621 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11554 Z= 0.144 Angle : 0.507 10.877 15639 Z= 0.257 Chirality : 0.041 0.151 1736 Planarity : 0.003 0.051 2037 Dihedral : 4.185 44.997 1540 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.20 % Allowed : 13.09 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.81 (0.23), residues: 1412 helix: 2.07 (0.22), residues: 590 sheet: 0.79 (0.36), residues: 218 loop : 0.61 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 72 TYR 0.013 0.001 TYR B 901 PHE 0.011 0.001 PHE B1108 TRP 0.005 0.001 TRP B 607 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (11553) covalent geometry : angle 0.50670 / 0.26 (15639) hydrogen bonds : bond 0.03360 / 2.22 ( 534) hydrogen bonds : angle 4.05386 / 2.92 ( 1506) Misc. bond : bond 0.00028 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2824 Ramachandran restraints generated. 1412 Oldfield, 0 Emsley, 1412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9213 (pmm) cc_final: 0.8946 (pmm) REVERT: B 391 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: B 418 TYR cc_start: 0.8037 (m-80) cc_final: 0.7678 (m-80) REVERT: B 457 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8376 (pm20) REVERT: B 519 LYS cc_start: 0.9270 (ttmm) cc_final: 0.8926 (tmtt) REVERT: B 640 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8001 (pmt) REVERT: B 806 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7314 (pp30) REVERT: B 1057 ASP cc_start: 0.8636 (t0) cc_final: 0.8376 (t0) REVERT: C 8 LEU cc_start: 0.8994 (mm) cc_final: 0.8673 (mm) REVERT: C 41 GLN cc_start: 0.8862 (mt0) cc_final: 0.8604 (pt0) REVERT: C 63 LYS cc_start: 0.9229 (ttpp) cc_final: 0.8788 (tptm) REVERT: E 2 GLN cc_start: 0.9120 (tt0) cc_final: 0.8816 (tt0) REVERT: E 21 ASP cc_start: 0.8680 (m-30) cc_final: 0.8386 (m-30) REVERT: E 51 GLU cc_start: 0.9091 (pt0) cc_final: 0.8517 (pm20) REVERT: E 62 GLN cc_start: 0.9158 (mt0) cc_final: 0.8769 (mp10) REVERT: E 64 GLU cc_start: 0.9177 (mp0) cc_final: 0.8761 (mp0) outliers start: 15 outliers final: 9 residues processed: 95 average time/residue: 0.1061 time to fit residues: 15.2643 Evaluate side-chains 99 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4756 SER Chi-restraints excluded: chain A residue 4760 VAL Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 806 GLN Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 1135 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain E residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 65 optimal weight: 3.9990 chunk 78 optimal weight: 0.0170 chunk 93 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 235 ASN ** C 41 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 = 0.3212 r_free = 0.3212 target = 0.071461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.053888 restraints weight = 30731.716| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.50 r_work: 0.2649 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11554 Z= 0.100 Angle : 0.484 10.891 15639 Z= 0.245 Chirality : 0.040 0.145 1736 Planarity : 0.003 0.050 2037 Dihedral : 4.117 44.946 1540 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.04 % Allowed : 13.25 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.07 % 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: 1.86 (0.23), residues: 1412 helix: 2.11 (0.22), residues: 590 sheet: 0.84 (0.37), residues: 215 loop : 0.63 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 72 TYR 0.011 0.001 TYR B 901 PHE 0.010 0.001 PHE B1108 TRP 0.006 0.001 TRP B 849 HIS 0.003 0.000 HIS A4817 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (11553) covalent geometry : angle 0.48364 / 0.24 (15639) hydrogen bonds : bond 0.03086 / 2.03 ( 534) hydrogen bonds : angle 3.98487 / 2.88 ( 1506) Misc. bond : bond 0.00022 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2596.04 seconds wall clock time: 45 minutes 32.82 seconds (2732.82 seconds total)