Starting phenix.real_space_refine on Fri Aug 22 18:52:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3h_29699/08_2025/8g3h_29699_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3h_29699/08_2025/8g3h_29699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3h_29699/08_2025/8g3h_29699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3h_29699/08_2025/8g3h_29699.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3h_29699/08_2025/8g3h_29699_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3h_29699/08_2025/8g3h_29699_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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: 7 Type Number sf(0) Gaussians Co 1 6.85 5 Zn 1 6.06 5 P 1 5.49 5 S 26 5.16 5 C 4159 2.51 5 N 1125 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6541 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6449 Classifications: {'peptide': 841} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 39, 'TRANS': 801} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {' ZN': 1, 'B12': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unsupported chir.volume_sign: {'cros': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1673 SG CYS A 256 34.318 42.889 80.873 1.00 12.37 S ATOM 2190 SG CYS A 323 34.049 43.743 84.392 1.00 19.07 S Time building chain proxies: 1.65, per 1000 atoms: 0.25 Number of scatterers: 6541 At special positions: 0 Unit cell: (64.146, 90.8735, 112.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Co 1 26.99 S 26 16.00 P 1 15.00 O 1228 8.00 N 1125 7.00 C 4159 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: 0.64 Conformation dependent library (CDL) restraints added in 367.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 256 " pdb="ZN ZN A1201 " - pdb=" SG CYS A 323 " 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 54.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.839A pdb=" N THR A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 100 removed outlier: 3.656A pdb=" N VAL A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 97 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 98 " --> pdb=" O HIS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 125 through 142 Processing helix chain 'A' and resid 165 through 183 removed outlier: 3.705A pdb=" N LEU A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 212 Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.682A pdb=" N LEU A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 6.119A pdb=" N ALA A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 4.352A pdb=" N THR A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.937A pdb=" N ILE A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.827A pdb=" N GLU A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 removed outlier: 3.551A pdb=" N ILE A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 436 removed outlier: 3.711A pdb=" N LYS A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 431 " --> pdb=" O ARG A 427 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N THR A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 455 removed outlier: 3.915A pdb=" N MET A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 454 " --> pdb=" O MET A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 485 removed outlier: 4.405A pdb=" N LYS A 474 " --> pdb=" O ASP A 470 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 522 removed outlier: 3.870A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 527 Processing helix chain 'A' and resid 546 through 560 removed outlier: 3.903A pdb=" N GLU A 550 " --> pdb=" O PRO A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 580 through 595 Processing helix chain 'A' and resid 605 through 609 removed outlier: 3.866A pdb=" N ILE A 609 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 629 Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 662 through 674 Processing helix chain 'A' and resid 678 through 690 Processing helix chain 'A' and resid 691 through 698 Processing helix chain 'A' and resid 698 through 713 removed outlier: 6.001A pdb=" N MET A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 736 removed outlier: 3.600A pdb=" N ALA A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 772 removed outlier: 3.786A pdb=" N ILE A 769 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU A 770 " --> pdb=" O VAL A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 797 removed outlier: 3.871A pdb=" N MET A 789 " --> pdb=" O PRO A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 824 removed outlier: 4.243A pdb=" N THR A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLN A 812 " --> pdb=" O VAL A 808 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 848 removed outlier: 5.300A pdb=" N GLU A 843 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU A 844 " --> pdb=" O TYR A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 869 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.138A pdb=" N LEU A 50 " --> pdb=" O VAL A 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.459A pdb=" N VAL A 148 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A 189 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLY A 150 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A 191 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 188 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N GLN A 222 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 190 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 253 Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 290 Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA6, first strand: chain 'A' and resid 440 through 442 removed outlier: 5.990A pdb=" N LEU A 410 " --> pdb=" O MET A 441 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 370 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASP A 411 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A 372 " --> pdb=" O ASP A 411 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER A 413 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N ARG A 374 " --> pdb=" O SER A 413 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A 373 " --> pdb=" O VAL A 604 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE A 567 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 603 " --> pdb=" O PHE A 567 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEU A 569 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N PHE A 530 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY A 570 " --> pdb=" O PHE A 530 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 491 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.701A pdb=" N LYS A 748 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY A 802 " --> pdb=" O LYS A 748 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL A 750 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU A 801 " --> pdb=" O ILE A 831 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.33: 1750 1.33 - 1.50: 2012 1.50 - 1.67: 2846 1.67 - 1.84: 47 1.84 - 2.01: 4 Bond restraints: 6659 Sorted by residual: bond pdb=" C3R B12 A1202 " pdb=" O2 B12 A1202 " ideal model delta sigma weight residual 1.426 1.651 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C15 B12 A1202 " pdb=" C53 B12 A1202 " ideal model delta sigma weight residual 1.500 1.685 -0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" C4 B12 A1202 " pdb=" N21 B12 A1202 " ideal model delta sigma weight residual 1.416 1.235 0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" C49 B12 A1202 " pdb=" C50 B12 A1202 " ideal model delta sigma weight residual 1.510 1.337 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" C5R B12 A1202 " pdb=" O8R B12 A1202 " ideal model delta sigma weight residual 1.432 1.267 0.165 2.00e-02 2.50e+03 6.84e+01 ... (remaining 6654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 8852 5.65 - 11.29: 161 11.29 - 16.94: 28 16.94 - 22.59: 5 22.59 - 28.23: 3 Bond angle restraints: 9049 Sorted by residual: angle pdb=" N ALA A 855 " pdb=" CA ALA A 855 " pdb=" C ALA A 855 " ideal model delta sigma weight residual 110.24 83.37 26.87 1.30e+00 5.92e-01 4.27e+02 angle pdb=" C ALA A 855 " pdb=" CA ALA A 855 " pdb=" CB ALA A 855 " ideal model delta sigma weight residual 109.64 137.87 -28.23 1.77e+00 3.19e-01 2.54e+02 angle pdb=" N VAL A 51 " pdb=" CA VAL A 51 " pdb=" C VAL A 51 " ideal model delta sigma weight residual 108.17 123.43 -15.26 1.40e+00 5.10e-01 1.19e+02 angle pdb=" C LEU A 562 " pdb=" N PRO A 563 " pdb=" CA PRO A 563 " ideal model delta sigma weight residual 120.03 111.29 8.74 9.90e-01 1.02e+00 7.79e+01 angle pdb=" C18 B12 A1202 " pdb=" C19 B12 A1202 " pdb=" N24 B12 A1202 " ideal model delta sigma weight residual 120.00 94.26 25.74 3.00e+00 1.11e-01 7.36e+01 ... (remaining 9044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 3828 29.20 - 58.41: 191 58.41 - 87.61: 22 87.61 - 116.81: 1 116.81 - 146.02: 2 Dihedral angle restraints: 4044 sinusoidal: 1642 harmonic: 2402 Sorted by residual: dihedral pdb=" C ARG A 839 " pdb=" N ARG A 839 " pdb=" CA ARG A 839 " pdb=" CB ARG A 839 " ideal model delta harmonic sigma weight residual -122.60 -142.45 19.85 0 2.50e+00 1.60e-01 6.30e+01 dihedral pdb=" C ALA A 855 " pdb=" N ALA A 855 " pdb=" CA ALA A 855 " pdb=" CB ALA A 855 " ideal model delta harmonic sigma weight residual -122.60 -139.40 16.80 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" C3R B12 A1202 " pdb=" O2 B12 A1202 " pdb=" P B12 A1202 " pdb=" O4 B12 A1202 " ideal model delta sinusoidal sigma weight residual 60.00 -153.98 -146.02 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 4041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.110: 1034 1.110 - 2.220: 2 2.220 - 3.330: 2 3.330 - 4.441: 0 4.441 - 5.551: 1 Chirality restraints: 1039 Sorted by residual: chirality pdb=" C12 B12 A1202 " pdb=" C11 B12 A1202 " pdb=" C46 B12 A1202 " pdb=" C47 B12 A1202 " both_signs ideal model delta sigma weight residual False -2.64 2.91 -5.55 2.00e-01 2.50e+01 7.70e+02 chirality pdb=" N21 B12 A1202 " pdb=" C1 B12 A1202 " pdb=" C4 B12 A1202 " pdb="CO B12 A1202 " both_signs ideal model delta sigma weight residual False -3.05 0.08 -3.13 2.00e-01 2.50e+01 2.44e+02 chirality pdb=" N22 B12 A1202 " pdb=" C6 B12 A1202 " pdb=" C9 B12 A1202 " pdb="CO B12 A1202 " both_signs ideal model delta sigma weight residual False -2.93 -0.18 -2.75 2.00e-01 2.50e+01 1.89e+02 ... (remaining 1036 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C35 B12 A1202 " -0.186 2.00e-02 2.50e+03 1.40e-01 2.94e+02 pdb=" C4 B12 A1202 " 0.093 2.00e-02 2.50e+03 pdb=" C5 B12 A1202 " 0.145 2.00e-02 2.50e+03 pdb=" C6 B12 A1202 " 0.038 2.00e-02 2.50e+03 pdb=" C7 B12 A1202 " 0.110 2.00e-02 2.50e+03 pdb=" N22 B12 A1202 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1R B12 A1202 " 0.040 2.00e-02 2.50e+03 9.59e-02 2.76e+02 pdb=" C2B B12 A1202 " -0.137 2.00e-02 2.50e+03 pdb=" C4B B12 A1202 " -0.016 2.00e-02 2.50e+03 pdb=" C5B B12 A1202 " 0.036 2.00e-02 2.50e+03 pdb=" C5M B12 A1202 " 0.094 2.00e-02 2.50e+03 pdb=" C6B B12 A1202 " 0.060 2.00e-02 2.50e+03 pdb=" C6M B12 A1202 " -0.230 2.00e-02 2.50e+03 pdb=" C7B B12 A1202 " 0.088 2.00e-02 2.50e+03 pdb=" C8B B12 A1202 " 0.072 2.00e-02 2.50e+03 pdb=" C9B B12 A1202 " -0.006 2.00e-02 2.50e+03 pdb=" N1B B12 A1202 " 0.070 2.00e-02 2.50e+03 pdb=" N3B B12 A1202 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 B12 A1202 " 0.110 2.00e-02 2.50e+03 1.60e-01 2.55e+02 pdb=" C18 B12 A1202 " 0.094 2.00e-02 2.50e+03 pdb=" C19 B12 A1202 " -0.275 2.00e-02 2.50e+03 pdb=" N24 B12 A1202 " 0.071 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 684 2.76 - 3.30: 7130 3.30 - 3.83: 10904 3.83 - 4.37: 14047 4.37 - 4.90: 22381 Nonbonded interactions: 55146 Sorted by model distance: nonbonded pdb=" N ALA A 855 " pdb=" O ALA A 855 " model vdw 2.228 2.496 nonbonded pdb=" N GLY A 321 " pdb=" O GLY A 321 " model vdw 2.275 2.496 nonbonded pdb=" N MET A 803 " pdb=" O MET A 803 " model vdw 2.375 2.496 nonbonded pdb=" N ARG A 559 " pdb=" N GLU A 560 " model vdw 2.393 2.560 nonbonded pdb=" C TYR A 854 " pdb=" C ALA A 855 " model vdw 2.394 2.800 ... (remaining 55141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.590 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5129 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 : 0.017 0.569 6662 Z= 0.968 Angle : 2.317 28.234 9049 Z= 1.409 Chirality : 0.258 5.551 1039 Planarity : 0.017 0.160 1180 Dihedral : 17.251 146.016 2506 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.37 % Allowed : 14.61 % Favored : 81.02 % Cbeta Deviations : 1.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.03 (0.24), residues: 839 helix: -2.85 (0.19), residues: 387 sheet: -1.65 (0.76), residues: 47 loop : -2.56 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 460 TYR 0.091 0.013 TYR A 854 PHE 0.096 0.018 PHE A 52 TRP 0.037 0.013 TRP A 166 HIS 0.013 0.004 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.01588 ( 6659) covalent geometry : angle 2.31674 ( 9049) hydrogen bonds : bond 0.17831 ( 282) hydrogen bonds : angle 9.55191 ( 807) metal coordination : bond 0.04934 ( 2) Misc. bond : bond 0.56853 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.5203 (mt) cc_final: 0.5002 (mt) REVERT: A 276 ARG cc_start: 0.4509 (mtm110) cc_final: 0.4093 (mmm160) REVERT: A 367 SER cc_start: 0.6095 (OUTLIER) cc_final: 0.5842 (t) REVERT: A 405 GLU cc_start: 0.6565 (OUTLIER) cc_final: 0.6037 (tt0) REVERT: A 464 ASN cc_start: 0.5844 (m-40) cc_final: 0.5216 (t0) REVERT: A 789 MET cc_start: 0.6153 (ttt) cc_final: 0.5770 (ttm) REVERT: A 820 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.3795 (p90) REVERT: A 865 MET cc_start: 0.3583 (mmm) cc_final: 0.3373 (mmt) outliers start: 29 outliers final: 6 residues processed: 168 average time/residue: 0.1103 time to fit residues: 23.0978 Evaluate side-chains 103 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.0470 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 198 GLN A 772 ASN ** A 817 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.230075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.209109 restraints weight = 8642.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.213391 restraints weight = 5419.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.216561 restraints weight = 3730.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.218668 restraints weight = 2742.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.220336 restraints weight = 2141.246| |-----------------------------------------------------------------------------| r_work (final): 0.4702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5260 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6662 Z= 0.197 Angle : 1.147 31.094 9049 Z= 0.503 Chirality : 0.094 2.404 1039 Planarity : 0.006 0.052 1180 Dihedral : 11.713 135.106 982 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.82 % Allowed : 16.42 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.26), residues: 839 helix: -1.20 (0.23), residues: 389 sheet: -2.19 (0.57), residues: 76 loop : -1.76 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 384 TYR 0.023 0.002 TYR A 820 PHE 0.017 0.002 PHE A 52 TRP 0.013 0.002 TRP A 166 HIS 0.010 0.002 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 6659) covalent geometry : angle 1.14724 ( 9049) hydrogen bonds : bond 0.04913 ( 282) hydrogen bonds : angle 6.02588 ( 807) metal coordination : bond 0.00291 ( 2) Misc. bond : bond 0.06253 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.3235 (OUTLIER) cc_final: 0.2120 (tt0) REVERT: A 81 VAL cc_start: 0.5807 (OUTLIER) cc_final: 0.5510 (t) REVERT: A 276 ARG cc_start: 0.5154 (mtm110) cc_final: 0.4255 (mmt180) REVERT: A 367 SER cc_start: 0.5163 (OUTLIER) cc_final: 0.4851 (t) REVERT: A 464 ASN cc_start: 0.6289 (m-40) cc_final: 0.5389 (t0) REVERT: A 513 MET cc_start: 0.1918 (ptp) cc_final: 0.1671 (ptm) REVERT: A 707 VAL cc_start: 0.6977 (t) cc_final: 0.6741 (t) REVERT: A 765 LEU cc_start: 0.5272 (OUTLIER) cc_final: 0.5038 (mm) outliers start: 32 outliers final: 15 residues processed: 129 average time/residue: 0.0907 time to fit residues: 15.4057 Evaluate side-chains 105 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 68 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 chunk 73 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.230796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.209177 restraints weight = 8541.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.213436 restraints weight = 5474.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.216337 restraints weight = 3795.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.218570 restraints weight = 2865.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.219974 restraints weight = 2261.502| |-----------------------------------------------------------------------------| r_work (final): 0.4710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6662 Z= 0.168 Angle : 1.057 30.929 9049 Z= 0.451 Chirality : 0.092 2.405 1039 Planarity : 0.006 0.059 1180 Dihedral : 10.767 130.694 978 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.92 % Allowed : 19.13 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.88 (0.27), residues: 839 helix: -0.64 (0.24), residues: 389 sheet: -2.14 (0.57), residues: 76 loop : -1.61 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 384 TYR 0.018 0.002 TYR A 820 PHE 0.019 0.002 PHE A 643 TRP 0.011 0.001 TRP A 166 HIS 0.009 0.001 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6659) covalent geometry : angle 1.05661 ( 9049) hydrogen bonds : bond 0.04313 ( 282) hydrogen bonds : angle 5.58545 ( 807) metal coordination : bond 0.00141 ( 2) Misc. bond : bond 0.06914 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 ARG cc_start: 0.5098 (mtm110) cc_final: 0.4230 (mmt180) REVERT: A 464 ASN cc_start: 0.6093 (m-40) cc_final: 0.5478 (t0) REVERT: A 513 MET cc_start: 0.2209 (ptp) cc_final: 0.1624 (ptm) REVERT: A 765 LEU cc_start: 0.5417 (OUTLIER) cc_final: 0.5102 (mm) REVERT: A 783 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.7011 (mtmm) REVERT: A 820 TYR cc_start: 0.6293 (OUTLIER) cc_final: 0.4038 (p90) outliers start: 26 outliers final: 12 residues processed: 119 average time/residue: 0.0765 time to fit residues: 12.3014 Evaluate side-chains 105 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.0470 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 799 HIS ** 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 = 0.4799 r_free = 0.4799 target = 0.229327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.207097 restraints weight = 8634.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.211236 restraints weight = 5570.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.214339 restraints weight = 3919.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.216575 restraints weight = 2949.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.217998 restraints weight = 2334.310| |-----------------------------------------------------------------------------| r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5336 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 6662 Z= 0.162 Angle : 1.032 31.144 9049 Z= 0.435 Chirality : 0.090 2.387 1039 Planarity : 0.005 0.059 1180 Dihedral : 10.336 127.876 976 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.52 % Allowed : 19.58 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.27), residues: 839 helix: -0.37 (0.25), residues: 392 sheet: -2.21 (0.58), residues: 78 loop : -1.50 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.018 0.002 TYR A 820 PHE 0.012 0.002 PHE A 52 TRP 0.015 0.002 TRP A 166 HIS 0.017 0.002 HIS A 799 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6659) covalent geometry : angle 1.03218 ( 9049) hydrogen bonds : bond 0.03988 ( 282) hydrogen bonds : angle 5.33918 ( 807) metal coordination : bond 0.00118 ( 2) Misc. bond : bond 0.08039 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.6638 (mtt) cc_final: 0.6218 (mtt) REVERT: A 276 ARG cc_start: 0.5289 (mtm110) cc_final: 0.4252 (mmt180) REVERT: A 513 MET cc_start: 0.2277 (ptp) cc_final: 0.1739 (ptm) REVERT: A 610 LEU cc_start: 0.5870 (pt) cc_final: 0.5360 (mt) REVERT: A 820 TYR cc_start: 0.6493 (OUTLIER) cc_final: 0.4025 (p90) outliers start: 30 outliers final: 16 residues processed: 113 average time/residue: 0.0634 time to fit residues: 10.3113 Evaluate side-chains 98 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** 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 = 0.4759 r_free = 0.4759 target = 0.224582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.202372 restraints weight = 8682.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.206569 restraints weight = 5558.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.209585 restraints weight = 3892.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.211832 restraints weight = 2926.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.213419 restraints weight = 2313.493| |-----------------------------------------------------------------------------| r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 6662 Z= 0.183 Angle : 1.052 31.416 9049 Z= 0.444 Chirality : 0.091 2.382 1039 Planarity : 0.006 0.063 1180 Dihedral : 10.274 125.561 976 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.52 % Allowed : 20.48 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.28), residues: 839 helix: -0.41 (0.25), residues: 395 sheet: -2.25 (0.59), residues: 78 loop : -1.44 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 559 TYR 0.018 0.002 TYR A 820 PHE 0.031 0.002 PHE A 711 TRP 0.011 0.002 TRP A 166 HIS 0.006 0.002 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 6659) covalent geometry : angle 1.05193 ( 9049) hydrogen bonds : bond 0.04131 ( 282) hydrogen bonds : angle 5.45337 ( 807) metal coordination : bond 0.00173 ( 2) Misc. bond : bond 0.10620 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 MET cc_start: 0.2461 (ptp) cc_final: 0.2070 (ptm) REVERT: A 820 TYR cc_start: 0.6675 (OUTLIER) cc_final: 0.4292 (p90) outliers start: 30 outliers final: 21 residues processed: 110 average time/residue: 0.0625 time to fit residues: 9.9908 Evaluate side-chains 104 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 65 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4864 r_free = 0.4864 target = 0.234566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.218703 restraints weight = 8423.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.220637 restraints weight = 6407.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.222104 restraints weight = 5216.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.223052 restraints weight = 3910.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.223207 restraints weight = 3453.382| |-----------------------------------------------------------------------------| r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 6662 Z= 0.184 Angle : 1.046 31.408 9049 Z= 0.441 Chirality : 0.090 2.384 1039 Planarity : 0.006 0.061 1180 Dihedral : 10.205 123.595 976 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.22 % Allowed : 22.44 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.27), residues: 839 helix: -0.49 (0.24), residues: 398 sheet: -2.57 (0.64), residues: 65 loop : -1.60 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 559 TYR 0.018 0.002 TYR A 820 PHE 0.031 0.002 PHE A 711 TRP 0.009 0.001 TRP A 166 HIS 0.005 0.002 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 6659) covalent geometry : angle 1.04599 ( 9049) hydrogen bonds : bond 0.04053 ( 282) hydrogen bonds : angle 5.33799 ( 807) metal coordination : bond 0.00220 ( 2) Misc. bond : bond 0.11229 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 513 MET cc_start: 0.2423 (ptp) cc_final: 0.2204 (ptm) REVERT: A 820 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.4504 (p90) outliers start: 28 outliers final: 22 residues processed: 112 average time/residue: 0.0746 time to fit residues: 11.7133 Evaluate side-chains 105 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4744 r_free = 0.4744 target = 0.222591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.200516 restraints weight = 8562.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.204583 restraints weight = 5423.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.207602 restraints weight = 3798.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.209708 restraints weight = 2853.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.211365 restraints weight = 2279.537| |-----------------------------------------------------------------------------| r_work (final): 0.4642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5441 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 6662 Z= 0.179 Angle : 1.055 31.398 9049 Z= 0.444 Chirality : 0.090 2.386 1039 Planarity : 0.005 0.066 1180 Dihedral : 10.142 121.711 976 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.37 % Allowed : 22.59 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.27), residues: 839 helix: -0.54 (0.24), residues: 396 sheet: -2.30 (0.62), residues: 70 loop : -1.67 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.018 0.002 TYR A 820 PHE 0.030 0.002 PHE A 711 TRP 0.009 0.001 TRP A 166 HIS 0.006 0.002 HIS A 759 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6659) covalent geometry : angle 1.05495 ( 9049) hydrogen bonds : bond 0.03991 ( 282) hydrogen bonds : angle 5.40984 ( 807) metal coordination : bond 0.00221 ( 2) Misc. bond : bond 0.10758 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7523 (pt) REVERT: A 728 MET cc_start: 0.6301 (mtt) cc_final: 0.5890 (mtt) REVERT: A 765 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5498 (mm) REVERT: A 820 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.4193 (p90) outliers start: 29 outliers final: 19 residues processed: 104 average time/residue: 0.0659 time to fit residues: 10.0121 Evaluate side-chains 100 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 80 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.223351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.200949 restraints weight = 8807.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.205093 restraints weight = 5650.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.208152 restraints weight = 3980.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.210220 restraints weight = 3001.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.211896 restraints weight = 2406.699| |-----------------------------------------------------------------------------| r_work (final): 0.4643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 6662 Z= 0.166 Angle : 1.031 31.281 9049 Z= 0.432 Chirality : 0.089 2.389 1039 Planarity : 0.005 0.066 1180 Dihedral : 9.996 119.292 976 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.77 % Allowed : 23.19 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.28), residues: 839 helix: -0.43 (0.25), residues: 391 sheet: -2.06 (0.62), residues: 72 loop : -1.44 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 559 TYR 0.017 0.001 TYR A 820 PHE 0.030 0.002 PHE A 711 TRP 0.009 0.001 TRP A 166 HIS 0.006 0.002 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 6659) covalent geometry : angle 1.03125 ( 9049) hydrogen bonds : bond 0.03794 ( 282) hydrogen bonds : angle 5.35563 ( 807) metal coordination : bond 0.00192 ( 2) Misc. bond : bond 0.09367 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.6586 (mtt) cc_final: 0.6027 (mtt) REVERT: A 412 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7570 (pt) REVERT: A 728 MET cc_start: 0.6426 (mtt) cc_final: 0.6134 (mtt) REVERT: A 765 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5448 (mm) REVERT: A 820 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.4157 (p90) outliers start: 25 outliers final: 18 residues processed: 103 average time/residue: 0.0649 time to fit residues: 9.4884 Evaluate side-chains 105 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 68 optimal weight: 0.1980 chunk 14 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 64 optimal weight: 0.0670 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 overall best weight: 0.2718 ------------------------------------------------------------------------------- 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 = 0.4771 r_free = 0.4771 target = 0.226860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.205203 restraints weight = 8752.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.209380 restraints weight = 5479.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.212398 restraints weight = 3793.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.214386 restraints weight = 2828.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.216069 restraints weight = 2258.745| |-----------------------------------------------------------------------------| r_work (final): 0.4676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5325 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6662 Z= 0.145 Angle : 1.014 31.017 9049 Z= 0.421 Chirality : 0.089 2.400 1039 Planarity : 0.005 0.068 1180 Dihedral : 9.739 116.435 976 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.61 % Allowed : 23.04 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.28), residues: 839 helix: -0.23 (0.25), residues: 391 sheet: -2.19 (0.62), residues: 70 loop : -1.40 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 559 TYR 0.016 0.001 TYR A 820 PHE 0.028 0.002 PHE A 711 TRP 0.010 0.001 TRP A 166 HIS 0.006 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6659) covalent geometry : angle 1.01404 ( 9049) hydrogen bonds : bond 0.03677 ( 282) hydrogen bonds : angle 5.18822 ( 807) metal coordination : bond 0.00152 ( 2) Misc. bond : bond 0.06080 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.3232 (mtt) cc_final: 0.2574 (mtp) REVERT: A 412 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7408 (pt) REVERT: A 610 LEU cc_start: 0.5830 (pt) cc_final: 0.5349 (mt) REVERT: A 726 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7562 (mt-10) REVERT: A 728 MET cc_start: 0.6398 (mtt) cc_final: 0.5977 (mtt) REVERT: A 765 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5646 (mm) REVERT: A 803 MET cc_start: 0.6508 (tpp) cc_final: 0.6301 (tpp) REVERT: A 820 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.4038 (p90) outliers start: 24 outliers final: 16 residues processed: 105 average time/residue: 0.0640 time to fit residues: 9.6899 Evaluate side-chains 99 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 70 optimal weight: 0.0470 chunk 32 optimal weight: 0.0970 overall best weight: 0.3076 ------------------------------------------------------------------------------- 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 = 0.4767 r_free = 0.4767 target = 0.226332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.204504 restraints weight = 8848.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.208589 restraints weight = 5695.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.211661 restraints weight = 3997.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.213552 restraints weight = 2995.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.215429 restraints weight = 2412.350| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5336 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6662 Z= 0.150 Angle : 1.020 31.089 9049 Z= 0.425 Chirality : 0.089 2.394 1039 Planarity : 0.005 0.067 1180 Dihedral : 9.673 115.536 976 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.86 % Allowed : 23.34 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.28), residues: 839 helix: -0.23 (0.25), residues: 399 sheet: -2.22 (0.59), residues: 75 loop : -1.36 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 559 TYR 0.016 0.001 TYR A 820 PHE 0.020 0.002 PHE A 643 TRP 0.009 0.001 TRP A 166 HIS 0.007 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6659) covalent geometry : angle 1.02049 ( 9049) hydrogen bonds : bond 0.03602 ( 282) hydrogen bonds : angle 5.12805 ( 807) metal coordination : bond 0.00133 ( 2) Misc. bond : bond 0.06207 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.7935 (mp) cc_final: 0.7665 (mp) REVERT: A 210 MET cc_start: 0.3246 (mtt) cc_final: 0.2604 (mtp) REVERT: A 412 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7396 (pt) REVERT: A 704 MET cc_start: 0.6792 (mmt) cc_final: 0.6584 (mpp) REVERT: A 726 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7171 (mp0) REVERT: A 728 MET cc_start: 0.6302 (mtt) cc_final: 0.6002 (mtt) REVERT: A 765 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5673 (mm) REVERT: A 803 MET cc_start: 0.6301 (tpp) cc_final: 0.6086 (tpp) REVERT: A 820 TYR cc_start: 0.6574 (OUTLIER) cc_final: 0.4021 (p90) outliers start: 19 outliers final: 16 residues processed: 99 average time/residue: 0.0639 time to fit residues: 8.9309 Evaluate side-chains 102 residues out of total 675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 405 GLU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 535 PHE Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 820 TYR Chi-restraints excluded: chain A residue 841 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 72 optimal weight: 0.0070 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.4754 r_free = 0.4754 target = 0.224763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.203323 restraints weight = 8876.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.207221 restraints weight = 5714.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.210118 restraints weight = 4050.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.211932 restraints weight = 3056.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.213762 restraints weight = 2475.577| |-----------------------------------------------------------------------------| r_work (final): 0.4654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6662 Z= 0.157 Angle : 1.026 31.156 9049 Z= 0.428 Chirality : 0.089 2.390 1039 Planarity : 0.005 0.066 1180 Dihedral : 9.695 114.785 976 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.31 % Allowed : 23.34 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.28), residues: 839 helix: -0.24 (0.25), residues: 399 sheet: -2.05 (0.61), residues: 72 loop : -1.32 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 559 TYR 0.017 0.001 TYR A 820 PHE 0.020 0.002 PHE A 643 TRP 0.008 0.001 TRP A 166 HIS 0.007 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6659) covalent geometry : angle 1.02626 ( 9049) hydrogen bonds : bond 0.03698 ( 282) hydrogen bonds : angle 5.16986 ( 807) metal coordination : bond 0.00206 ( 2) Misc. bond : bond 0.07778 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1273.69 seconds wall clock time: 22 minutes 39.56 seconds (1359.56 seconds total)