Starting phenix.real_space_refine on Wed Feb 4 16:20:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qgr_53147/02_2026/9qgr_53147_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qgr_53147/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9qgr_53147/02_2026/9qgr_53147_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qgr_53147/02_2026/9qgr_53147_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qgr_53147/02_2026/9qgr_53147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qgr_53147/02_2026/9qgr_53147.map" } 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-2.0-5952/lib/python3.9/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: 2.56, 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: 0.92 Conformation dependent library (CDL) restraints added in 633.6 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: 0.32 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: 2.04 Time building geometry restraints manager: 1.28 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: 15380 2.55 - 5.11: 234 5.11 - 7.66: 19 7.66 - 10.21: 4 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: 6274 17.24 - 34.47: 561 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: 1492 0.063 - 0.126: 226 0.126 - 0.189: 13 0.189 - 0.253: 4 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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.870 Find NCS groups from input model: 0.070 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:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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= 0.221 Angle : 0.689 12.767 15639 Z= 0.389 Chirality : 0.045 0.316 1736 Planarity : 0.010 0.391 2037 Dihedral : 14.984 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 covalent geometry : bond 0.00504 (11553) covalent geometry : angle 0.68897 (15639) hydrogen bonds : bond 0.13911 ( 534) hydrogen bonds : angle 5.80100 ( 1506) Misc. bond : bond 0.00016 ( 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 : 0.474 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: 0.1179 time to fit residues: 20.2303 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 : 0.421 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3236 r_free = 0.3236 target = 0.072979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.055170 restraints weight = 30436.221| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.53 r_work: 0.2675 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0864 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 : 0.524 8.535 15639 Z= 0.269 Chirality : 0.042 0.167 1736 Planarity : 0.004 0.081 2037 Dihedral : 4.583 39.123 1554 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 1.79 (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 0.010 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 607 HIS 0.002 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00339 (11553) covalent geometry : angle 0.52395 (15639) hydrogen bonds : bond 0.03887 ( 534) hydrogen bonds : angle 4.59907 ( 1506) Misc. bond : bond 0.00082 ( 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 122 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.472 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: 0.8919 (pmm) REVERT: A 4791 TYR cc_start: 0.8061 (m-10) cc_final: 0.7510 (m-80) REVERT: B 391 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: B 418 TYR cc_start: 0.7632 (m-80) cc_final: 0.7276 (m-80) REVERT: B 519 LYS cc_start: 0.9323 (ttmm) cc_final: 0.8903 (tptp) REVERT: B 761 GLU cc_start: 0.7906 (tp30) cc_final: 0.7698 (tp30) REVERT: B 806 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7204 (pp30) REVERT: B 989 GLU cc_start: 0.8757 (tp30) cc_final: 0.8234 (tm-30) REVERT: B 998 MET cc_start: 0.8619 (mmm) cc_final: 0.8261 (mmm) REVERT: C 3 ILE cc_start: 0.9252 (pt) cc_final: 0.8962 (mm) REVERT: C 21 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8808 (t70) REVERT: C 74 ARG cc_start: 0.7691 (mmt-90) cc_final: 0.7352 (mmt180) REVERT: E 2 GLN cc_start: 0.9140 (tt0) cc_final: 0.8755 (tt0) REVERT: E 16 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8820 (mm-30) REVERT: E 18 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8733 (mm-30) REVERT: E 21 ASP cc_start: 0.8863 (m-30) cc_final: 0.8558 (m-30) REVERT: E 51 GLU cc_start: 0.9125 (pt0) cc_final: 0.8741 (pm20) REVERT: E 54 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8063 (mtp85) REVERT: E 64 GLU cc_start: 0.9102 (mp0) cc_final: 0.8806 (mp0) REVERT: E 65 SER cc_start: 0.8946 (m) cc_final: 0.8650 (p) outliers start: 15 outliers final: 5 residues processed: 116 average time/residue: 0.1096 time to fit residues: 18.3604 Evaluate side-chains 108 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 62 optimal weight: 0.0000 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.073178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.055263 restraints weight = 30770.779| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.58 r_work: 0.2680 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11554 Z= 0.112 Angle : 0.490 9.070 15639 Z= 0.250 Chirality : 0.041 0.159 1736 Planarity : 0.003 0.048 2037 Dihedral : 4.169 38.409 1544 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.20 % Allowed : 11.97 % Favored : 86.83 % 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: 1.89 (0.22), residues: 585 sheet: 1.08 (0.34), residues: 243 loop : 0.61 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 54 TYR 0.013 0.001 TYR B 901 PHE 0.012 0.001 PHE B1108 TRP 0.006 0.001 TRP B 607 HIS 0.002 0.000 HIS B 778 Details of bonding type rmsd covalent geometry : bond 0.00244 (11553) covalent geometry : angle 0.49014 (15639) hydrogen bonds : bond 0.03453 ( 534) hydrogen bonds : angle 4.34420 ( 1506) Misc. bond : bond 0.00063 ( 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: 15 poor density : 110 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9248 (pmm) cc_final: 0.8904 (pmm) REVERT: A 4791 TYR cc_start: 0.8064 (m-10) cc_final: 0.7512 (m-80) REVERT: B 391 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: B 418 TYR cc_start: 0.7622 (m-80) cc_final: 0.7232 (m-80) REVERT: B 457 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: B 519 LYS cc_start: 0.9308 (ttmm) cc_final: 0.8988 (tmtt) REVERT: B 640 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.7992 (pmt) REVERT: B 761 GLU cc_start: 0.7926 (tp30) cc_final: 0.7639 (tp30) REVERT: B 806 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7222 (pp30) REVERT: B 989 GLU cc_start: 0.8745 (tp30) cc_final: 0.8211 (tm-30) REVERT: B 998 MET cc_start: 0.8578 (mmm) cc_final: 0.8062 (mmm) REVERT: C 3 ILE cc_start: 0.9187 (pt) cc_final: 0.8945 (mm) REVERT: C 24 GLU cc_start: 0.8900 (pm20) cc_final: 0.8134 (pm20) REVERT: C 74 ARG cc_start: 0.7854 (mmt-90) cc_final: 0.7466 (mmt180) REVERT: E 2 GLN cc_start: 0.9087 (tt0) cc_final: 0.8828 (tt0) REVERT: E 16 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8896 (mm-30) REVERT: E 21 ASP cc_start: 0.8715 (m-30) cc_final: 0.8461 (m-30) REVERT: E 51 GLU cc_start: 0.9111 (pt0) cc_final: 0.8703 (pm20) REVERT: E 64 GLU cc_start: 0.9117 (mp0) cc_final: 0.8809 (mp0) REVERT: E 65 SER cc_start: 0.8986 (m) cc_final: 0.8700 (p) outliers start: 15 outliers final: 5 residues processed: 120 average time/residue: 0.1129 time to fit residues: 19.3616 Evaluate side-chains 112 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 125 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 133 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4639 GLN C 2 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.054288 restraints weight = 30929.835| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 3.51 r_work: 0.2646 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11554 Z= 0.148 Angle : 0.501 8.564 15639 Z= 0.252 Chirality : 0.041 0.146 1736 Planarity : 0.003 0.051 2037 Dihedral : 4.065 38.183 1542 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.88 % Allowed : 12.45 % 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: 1.79 (0.23), residues: 1412 helix: 1.96 (0.22), residues: 585 sheet: 1.00 (0.34), residues: 244 loop : 0.60 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 54 TYR 0.015 0.001 TYR B 901 PHE 0.011 0.001 PHE B1112 TRP 0.006 0.001 TRP B 607 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00343 (11553) covalent geometry : angle 0.50054 (15639) hydrogen bonds : bond 0.03518 ( 534) hydrogen bonds : angle 4.22768 ( 1506) Misc. bond : bond 0.00090 ( 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 111 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9251 (pmm) cc_final: 0.8880 (pmm) REVERT: A 4791 TYR cc_start: 0.8162 (m-10) cc_final: 0.7663 (m-80) REVERT: B 391 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: B 418 TYR cc_start: 0.7795 (m-80) cc_final: 0.7363 (m-80) REVERT: B 457 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: B 519 LYS cc_start: 0.9311 (ttmm) cc_final: 0.8977 (tmtt) REVERT: B 640 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.7996 (pmt) REVERT: B 761 GLU cc_start: 0.7969 (tp30) cc_final: 0.7647 (tp30) REVERT: B 806 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7195 (pp30) REVERT: C 1 MET cc_start: 0.7497 (ptp) cc_final: 0.7286 (ptp) REVERT: C 24 GLU cc_start: 0.8990 (pm20) cc_final: 0.8772 (pm20) REVERT: C 74 ARG cc_start: 0.7991 (mmt-90) cc_final: 0.7581 (mmt180) REVERT: E 2 GLN cc_start: 0.9121 (tt0) cc_final: 0.8833 (tt0) REVERT: E 16 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8802 (mm-30) REVERT: E 21 ASP cc_start: 0.8653 (m-30) cc_final: 0.8364 (m-30) REVERT: E 51 GLU cc_start: 0.9118 (pt0) cc_final: 0.8550 (pm20) REVERT: E 64 GLU cc_start: 0.9167 (mp0) cc_final: 0.8817 (mp0) outliers start: 11 outliers final: 5 residues processed: 106 average time/residue: 0.0945 time to fit residues: 15.0867 Evaluate side-chains 104 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4756 SER 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 C residue 17 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 51 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.069002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.051207 restraints weight = 30947.004| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.50 r_work: 0.2590 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 11554 Z= 0.249 Angle : 0.564 8.642 15639 Z= 0.285 Chirality : 0.043 0.201 1736 Planarity : 0.004 0.054 2037 Dihedral : 4.135 35.084 1540 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.61 % Allowed : 12.13 % Favored : 86.27 % 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: 1.72 (0.23), residues: 1412 helix: 1.94 (0.22), residues: 588 sheet: 0.84 (0.34), residues: 245 loop : 0.58 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 54 TYR 0.018 0.001 TYR B 901 PHE 0.014 0.001 PHE B1112 TRP 0.007 0.001 TRP A4732 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00586 (11553) covalent geometry : angle 0.56384 (15639) hydrogen bonds : bond 0.04052 ( 534) hydrogen bonds : angle 4.30975 ( 1506) Misc. bond : bond 0.00101 ( 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 114 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9224 (pmm) cc_final: 0.8872 (pmm) REVERT: B 212 MET cc_start: 0.8940 (mmm) cc_final: 0.8709 (mmm) REVERT: B 391 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: B 418 TYR cc_start: 0.7916 (m-80) cc_final: 0.7505 (m-80) REVERT: B 457 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8266 (pm20) REVERT: B 519 LYS cc_start: 0.9309 (ttmm) cc_final: 0.8959 (tmtt) REVERT: B 640 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8114 (pmt) REVERT: B 793 GLN cc_start: 0.9233 (tp40) cc_final: 0.8961 (mm-40) REVERT: B 796 GLU cc_start: 0.7988 (pt0) cc_final: 0.7727 (pt0) REVERT: B 806 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7287 (pp30) REVERT: C 8 LEU cc_start: 0.9047 (mm) cc_final: 0.8628 (mm) REVERT: C 24 GLU cc_start: 0.8943 (pm20) cc_final: 0.8671 (pm20) REVERT: C 74 ARG cc_start: 0.8111 (mmt-90) cc_final: 0.7688 (mmt180) REVERT: E 2 GLN cc_start: 0.9136 (tt0) cc_final: 0.8910 (tt0) REVERT: E 16 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8772 (mm-30) REVERT: E 21 ASP cc_start: 0.8698 (m-30) cc_final: 0.8401 (m-30) REVERT: E 34 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8863 (mm-30) REVERT: E 51 GLU cc_start: 0.9113 (pt0) cc_final: 0.8553 (pm20) REVERT: E 64 GLU cc_start: 0.9187 (mp0) cc_final: 0.8755 (mp0) outliers start: 20 outliers final: 11 residues processed: 107 average time/residue: 0.0956 time to fit residues: 15.2240 Evaluate side-chains 106 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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 C residue 17 VAL Chi-restraints excluded: chain C residue 18 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 83 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3173 r_free = 0.3173 target = 0.069610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.051797 restraints weight = 31072.078| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.53 r_work: 0.2601 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1944 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= 0.176 Angle : 0.519 9.822 15639 Z= 0.264 Chirality : 0.042 0.150 1736 Planarity : 0.004 0.053 2037 Dihedral : 4.055 34.792 1540 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.29 % Allowed : 12.85 % Favored : 85.86 % 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: 2.00 (0.22), residues: 585 sheet: 0.98 (0.36), residues: 227 loop : 0.57 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 54 TYR 0.014 0.001 TYR B 901 PHE 0.014 0.001 PHE B1112 TRP 0.005 0.001 TRP B 607 HIS 0.003 0.001 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00410 (11553) covalent geometry : angle 0.51913 (15639) hydrogen bonds : bond 0.03733 ( 534) hydrogen bonds : angle 4.22901 ( 1506) Misc. bond : bond 0.00083 ( 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 107 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9227 (pmm) cc_final: 0.8867 (pmm) REVERT: B 391 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: B 418 TYR cc_start: 0.7895 (m-80) cc_final: 0.7486 (m-80) REVERT: B 457 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: B 519 LYS cc_start: 0.9305 (ttmm) cc_final: 0.8952 (tmtt) REVERT: B 640 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8032 (pmt) REVERT: B 793 GLN cc_start: 0.9221 (tp40) cc_final: 0.8994 (mm-40) REVERT: B 796 GLU cc_start: 0.7999 (pt0) cc_final: 0.7786 (pt0) REVERT: B 806 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7299 (pp30) REVERT: C 1 MET cc_start: 0.7508 (ptp) cc_final: 0.6908 (ptp) REVERT: C 8 LEU cc_start: 0.9069 (mm) cc_final: 0.8700 (mm) REVERT: C 24 GLU cc_start: 0.8954 (pm20) cc_final: 0.8651 (pm20) REVERT: C 27 LYS cc_start: 0.9636 (mttm) cc_final: 0.9385 (mttm) REVERT: C 74 ARG cc_start: 0.8135 (mmt-90) cc_final: 0.7703 (mmt180) REVERT: E 2 GLN cc_start: 0.9103 (tt0) cc_final: 0.8882 (tt0) REVERT: E 16 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8778 (mm-30) REVERT: E 21 ASP cc_start: 0.8698 (m-30) cc_final: 0.8379 (m-30) REVERT: E 51 GLU cc_start: 0.9106 (pt0) cc_final: 0.8528 (pm20) REVERT: E 64 GLU cc_start: 0.9175 (mp0) cc_final: 0.8737 (mp0) outliers start: 16 outliers final: 10 residues processed: 98 average time/residue: 0.0991 time to fit residues: 14.6423 Evaluate side-chains 102 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 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 B residue 1181 VAL Chi-restraints excluded: chain C residue 17 VAL 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: 0.8980 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3182 r_free = 0.3182 target = 0.070185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.052681 restraints weight = 30762.234| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.41 r_work: 0.2620 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2035 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= 0.138 Angle : 0.498 10.233 15639 Z= 0.251 Chirality : 0.041 0.156 1736 Planarity : 0.003 0.052 2037 Dihedral : 3.941 34.174 1540 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.45 % Allowed : 13.09 % Favored : 85.46 % 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: 1.80 (0.23), residues: 1412 helix: 2.07 (0.22), residues: 584 sheet: 0.86 (0.38), residues: 201 loop : 0.58 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 54 TYR 0.013 0.001 TYR B 901 PHE 0.012 0.001 PHE B1112 TRP 0.006 0.001 TRP B 849 HIS 0.003 0.000 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00321 (11553) covalent geometry : angle 0.49771 (15639) hydrogen bonds : bond 0.03446 ( 534) hydrogen bonds : angle 4.13175 ( 1506) Misc. bond : bond 0.00060 ( 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 111 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9289 (pmm) cc_final: 0.8923 (pmm) REVERT: B 391 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: B 418 TYR cc_start: 0.7913 (m-80) cc_final: 0.7540 (m-80) REVERT: B 457 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: B 519 LYS cc_start: 0.9257 (ttmm) cc_final: 0.8929 (tmtt) REVERT: B 640 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8068 (pmt) REVERT: B 796 GLU cc_start: 0.8031 (pt0) cc_final: 0.7824 (pt0) REVERT: B 806 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7295 (pp30) REVERT: C 1 MET cc_start: 0.7407 (ptp) cc_final: 0.6909 (ptp) REVERT: C 24 GLU cc_start: 0.8934 (pm20) cc_final: 0.8655 (pm20) REVERT: C 74 ARG cc_start: 0.8189 (mmt-90) cc_final: 0.7779 (mmt180) REVERT: E 2 GLN cc_start: 0.9103 (tt0) cc_final: 0.8899 (tt0) REVERT: E 16 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8782 (mm-30) REVERT: E 21 ASP cc_start: 0.8712 (m-30) cc_final: 0.8413 (m-30) REVERT: E 51 GLU cc_start: 0.9119 (pt0) cc_final: 0.8576 (pm20) REVERT: E 64 GLU cc_start: 0.9162 (mp0) cc_final: 0.8759 (mp0) outliers start: 18 outliers final: 10 residues processed: 104 average time/residue: 0.1095 time to fit residues: 16.4974 Evaluate side-chains 101 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 C residue 17 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 27 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 793 GLN ** 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 = 0.3196 r_free = 0.3196 target = 0.070940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.053541 restraints weight = 30627.848| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.40 r_work: 0.2640 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2106 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= 0.107 Angle : 0.487 10.418 15639 Z= 0.247 Chirality : 0.041 0.162 1736 Planarity : 0.003 0.051 2037 Dihedral : 3.851 33.506 1540 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.20 % Allowed : 13.25 % Favored : 85.54 % 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: 2.07 (0.22), residues: 590 sheet: 0.86 (0.38), residues: 201 loop : 0.61 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 54 TYR 0.012 0.001 TYR B 901 PHE 0.011 0.001 PHE B1108 TRP 0.006 0.001 TRP B 849 HIS 0.003 0.000 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00243 (11553) covalent geometry : angle 0.48688 (15639) hydrogen bonds : bond 0.03259 ( 534) hydrogen bonds : angle 4.07721 ( 1506) Misc. bond : bond 0.00051 ( 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 105 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9308 (pmm) cc_final: 0.9004 (pmm) REVERT: B 391 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: B 418 TYR cc_start: 0.7945 (m-80) cc_final: 0.7604 (m-80) REVERT: B 457 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: B 519 LYS cc_start: 0.9244 (ttmm) cc_final: 0.8922 (tmtt) REVERT: B 640 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8014 (pmt) REVERT: B 806 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7287 (pp30) REVERT: C 24 GLU cc_start: 0.8951 (pm20) cc_final: 0.8654 (pm20) REVERT: C 74 ARG cc_start: 0.8198 (mmt-90) cc_final: 0.7785 (mmt180) REVERT: E 2 GLN cc_start: 0.9089 (tt0) cc_final: 0.8882 (tt0) REVERT: E 16 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8802 (mm-30) REVERT: E 21 ASP cc_start: 0.8705 (m-30) cc_final: 0.8407 (m-30) REVERT: E 51 GLU cc_start: 0.9099 (pt0) cc_final: 0.8548 (pm20) REVERT: E 64 GLU cc_start: 0.9153 (mp0) cc_final: 0.8763 (mp0) outliers start: 15 outliers final: 10 residues processed: 99 average time/residue: 0.1077 time to fit residues: 15.7858 Evaluate side-chains 103 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.0050 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 93 optimal weight: 0.0010 chunk 77 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3223 r_free = 0.3223 target = 0.072165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.054362 restraints weight = 30792.351| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.51 r_work: 0.2659 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11554 Z= 0.094 Angle : 0.481 10.857 15639 Z= 0.242 Chirality : 0.040 0.152 1736 Planarity : 0.003 0.052 2037 Dihedral : 3.729 32.425 1540 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.29 % Allowed : 13.17 % Favored : 85.54 % 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: 1.84 (0.23), residues: 1412 helix: 2.13 (0.22), residues: 590 sheet: 0.97 (0.38), residues: 196 loop : 0.54 (0.25), residues: 626 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 0.011 0.001 PHE B1108 TRP 0.006 0.001 TRP B 849 HIS 0.003 0.000 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00209 (11553) covalent geometry : angle 0.48139 (15639) hydrogen bonds : bond 0.03045 ( 534) hydrogen bonds : angle 3.98896 ( 1506) Misc. bond : bond 0.00044 ( 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 114 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4700 MET cc_start: 0.9258 (pmm) cc_final: 0.8959 (pmm) REVERT: A 4791 TYR cc_start: 0.8335 (m-10) cc_final: 0.7886 (m-80) REVERT: B 391 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: B 418 TYR cc_start: 0.8022 (m-80) cc_final: 0.7682 (m-80) REVERT: B 457 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: B 519 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8928 (tmtt) REVERT: B 640 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.7840 (pmt) REVERT: B 806 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7298 (pp30) REVERT: C 1 MET cc_start: 0.7417 (ptp) cc_final: 0.6901 (ptp) REVERT: C 8 LEU cc_start: 0.8887 (mm) cc_final: 0.8605 (mm) REVERT: C 24 GLU cc_start: 0.9001 (pm20) cc_final: 0.8718 (pm20) REVERT: C 74 ARG cc_start: 0.8253 (mmt-90) cc_final: 0.7819 (mmt180) REVERT: E 2 GLN cc_start: 0.9099 (tt0) cc_final: 0.8798 (tt0) REVERT: E 16 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8701 (mm-30) REVERT: E 21 ASP cc_start: 0.8680 (m-30) cc_final: 0.8408 (m-30) REVERT: E 51 GLU cc_start: 0.9097 (pt0) cc_final: 0.8651 (pm20) REVERT: E 62 GLN cc_start: 0.9093 (mt0) cc_final: 0.8679 (mp10) REVERT: E 64 GLU cc_start: 0.9163 (mp0) cc_final: 0.8768 (mp0) outliers start: 16 outliers final: 8 residues processed: 107 average time/residue: 0.1007 time to fit residues: 15.9465 Evaluate side-chains 101 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4756 SER 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 B residue 1181 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 GLN 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: 4.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.053182 restraints weight = 31145.492| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.54 r_work: 0.2629 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11554 Z= 0.138 Angle : 0.511 10.805 15639 Z= 0.257 Chirality : 0.041 0.202 1736 Planarity : 0.003 0.053 2037 Dihedral : 3.781 32.526 1540 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.96 % Allowed : 13.73 % Favored : 85.30 % 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: 1.84 (0.23), residues: 1412 helix: 2.13 (0.22), residues: 591 sheet: 0.90 (0.37), residues: 198 loop : 0.55 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 42 TYR 0.013 0.001 TYR B 901 PHE 0.011 0.001 PHE B1108 TRP 0.006 0.001 TRP B 607 HIS 0.003 0.000 HIS A4817 Details of bonding type rmsd covalent geometry : bond 0.00324 (11553) covalent geometry : angle 0.51052 (15639) hydrogen bonds : bond 0.03316 ( 534) hydrogen bonds : angle 4.03669 ( 1506) Misc. bond : bond 0.00048 ( 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 101 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4601 MET cc_start: 0.9097 (mtm) cc_final: 0.8424 (mtm) REVERT: A 4700 MET cc_start: 0.9258 (pmm) cc_final: 0.8943 (pmm) REVERT: B 391 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7738 (m-30) REVERT: B 418 TYR cc_start: 0.8048 (m-80) cc_final: 0.7713 (m-80) REVERT: B 457 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: B 519 LYS cc_start: 0.9270 (ttmm) cc_final: 0.8939 (tmtt) REVERT: B 640 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.7963 (pmt) REVERT: B 806 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7325 (pp30) REVERT: C 8 LEU cc_start: 0.8966 (mm) cc_final: 0.8704 (mm) REVERT: C 24 GLU cc_start: 0.9004 (pm20) cc_final: 0.8730 (pm20) REVERT: C 41 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8662 (pt0) REVERT: C 74 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.7861 (mmt180) REVERT: E 2 GLN cc_start: 0.9093 (tt0) cc_final: 0.8861 (tt0) REVERT: E 16 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8744 (mm-30) REVERT: E 21 ASP cc_start: 0.8681 (m-30) cc_final: 0.8397 (m-30) REVERT: E 51 GLU cc_start: 0.9058 (pt0) cc_final: 0.8508 (pm20) REVERT: E 62 GLN cc_start: 0.9118 (mt0) cc_final: 0.8715 (mp10) REVERT: E 64 GLU cc_start: 0.9170 (mp0) cc_final: 0.8773 (mp0) outliers start: 12 outliers final: 7 residues processed: 95 average time/residue: 0.1004 time to fit residues: 14.3063 Evaluate side-chains 99 residues out of total 1245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4756 SER 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 B residue 1181 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 41 GLN 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: 0.0270 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.071828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.054222 restraints weight = 30822.664| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.49 r_work: 0.2650 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2316 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= 0.102 Angle : 0.494 10.826 15639 Z= 0.248 Chirality : 0.041 0.197 1736 Planarity : 0.003 0.052 2037 Dihedral : 3.723 32.354 1540 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.12 % Allowed : 13.57 % Favored : 85.30 % 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: 2.14 (0.22), residues: 591 sheet: 0.89 (0.37), residues: 198 loop : 0.57 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 54 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 covalent geometry : bond 0.00230 (11553) covalent geometry : angle 0.49357 (15639) hydrogen bonds : bond 0.03101 ( 534) hydrogen bonds : angle 3.97891 ( 1506) Misc. bond : bond 0.00039 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2354.46 seconds wall clock time: 41 minutes 25.32 seconds (2485.32 seconds total)