Starting phenix.real_space_refine on Wed Aug 5 06:51:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l8u_62891/08_2026/9l8u_62891_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l8u_62891/08_2026/9l8u_62891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l8u_62891/08_2026/9l8u_62891_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l8u_62891/08_2026/9l8u_62891_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l8u_62891/08_2026/9l8u_62891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l8u_62891/08_2026/9l8u_62891.map" } resolution = 2.53 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= -0.001 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 31 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 5441 2.51 5 N 1465 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8649 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 8042 Classifications: {'peptide': 986} Link IDs: {'PTRANS': 45, 'TRANS': 940} Chain breaks: 1 Chain: "B" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 342 Classifications: {'DNA': 16} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 15} Chain: "C" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 217 Classifications: {'DNA': 11} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' MG': 2, 'DCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.90, per 1000 atoms: 0.22 Number of scatterers: 8649 At special positions: 0 Unit cell: (81.046, 99.24, 102.548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 31 15.00 Mg 2 11.99 O 1659 8.00 N 1465 7.00 C 5441 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=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 287.4 milliseconds 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 8 sheets defined 50.7% alpha, 19.8% beta 11 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 6 through 15 Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 79 through 93 removed outlier: 4.166A pdb=" N GLN A 83 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 299 through 312 Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 366 through 374 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 410 through 435 Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 460 through 473 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'A' and resid 532 through 534 No H-bonds generated for 'chain 'A' and resid 532 through 534' Processing helix chain 'A' and resid 539 through 549 Processing helix chain 'A' and resid 580 through 608 Processing helix chain 'A' and resid 616 through 647 removed outlier: 3.561A pdb=" N LEU A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 642 " --> pdb=" O MET A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 679 Processing helix chain 'A' and resid 696 through 699 Processing helix chain 'A' and resid 700 through 710 Processing helix chain 'A' and resid 713 through 748 Processing helix chain 'A' and resid 792 through 796 Processing helix chain 'A' and resid 800 through 815 Processing helix chain 'A' and resid 826 through 841 Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 846 through 850 Processing helix chain 'A' and resid 862 through 883 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 928 through 935 Processing helix chain 'A' and resid 939 through 947 Processing helix chain 'A' and resid 947 through 957 Processing helix chain 'A' and resid 970 through 991 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 180 removed outlier: 6.560A pdb=" N SER A 54 " --> pdb=" O PRO A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 147 removed outlier: 4.283A pdb=" N VAL A 70 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ALA A 481 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG A 106 " --> pdb=" O ALA A 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 268 removed outlier: 9.183A pdb=" N THR A 265 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER A 250 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE A 267 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N CYS A 252 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 239 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER A 250 " --> pdb=" O MET A 237 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET A 237 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS A 252 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 235 " --> pdb=" O CYS A 252 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR A 254 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 233 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU A 213 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 235 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A 211 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET A 237 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 209 " --> pdb=" O MET A 237 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE A 239 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL A 207 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE A 206 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THR A 292 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N MET A 208 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N CYS A 291 " --> pdb=" O ILE A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 346 removed outlier: 4.997A pdb=" N LYS A 339 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE A 355 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 500 through 501 removed outlier: 4.171A pdb=" N GLY A 686 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 692 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A 686 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 515 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU A 758 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP A 517 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR A 756 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 765 " --> pdb=" O GLY A 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 500 through 501 removed outlier: 4.171A pdb=" N GLY A 686 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 692 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A 686 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 515 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLU A 758 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP A 517 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N TYR A 756 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU A 760 " --> pdb=" O HIS A 776 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N HIS A 776 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS A 770 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA8, first strand: chain 'A' and resid 852 through 855 448 hydrogen bonds defined for protein. 1269 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1339 1.29 - 1.42: 2472 1.42 - 1.55: 4960 1.55 - 1.68: 60 1.68 - 1.81: 81 Bond restraints: 8912 Sorted by residual: bond pdb=" C2' DCP A1001 " pdb=" C3' DCP A1001 " ideal model delta sigma weight residual 1.522 1.287 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" O3B DCP A1001 " pdb=" PG DCP A1001 " ideal model delta sigma weight residual 1.746 1.596 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" C4 DCP A1001 " pdb=" N4 DCP A1001 " ideal model delta sigma weight residual 1.333 1.454 -0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" O5' DCP C 101 " pdb=" PA DCP C 101 " ideal model delta sigma weight residual 1.654 1.542 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C4' DCP A1001 " pdb=" O4' DCP A1001 " ideal model delta sigma weight residual 1.420 1.531 -0.111 2.00e-02 2.50e+03 3.07e+01 ... (remaining 8907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 11975 2.50 - 5.00: 171 5.00 - 7.50: 20 7.50 - 10.01: 6 10.01 - 12.51: 3 Bond angle restraints: 12175 Sorted by residual: angle pdb=" C4' DCP C 101 " pdb=" C5' DCP C 101 " pdb=" O5' DCP C 101 " ideal model delta sigma weight residual 112.56 100.05 12.51 3.00e+00 1.11e-01 1.74e+01 angle pdb=" O1A DCP A1001 " pdb=" PA DCP A1001 " pdb=" O2A DCP A1001 " ideal model delta sigma weight residual 121.40 109.05 12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C4' DG B 8 " pdb=" O4' DG B 8 " pdb=" C1' DG B 8 " ideal model delta sigma weight residual 110.10 106.10 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" O3A DCP A1001 " pdb=" PB DCP A1001 " pdb=" O3B DCP A1001 " ideal model delta sigma weight residual 98.91 109.81 -10.90 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C3' DG B 8 " pdb=" O3' DG B 8 " pdb=" P DG B 9 " ideal model delta sigma weight residual 119.70 123.82 -4.12 1.20e+00 6.94e-01 1.18e+01 ... (remaining 12170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 4893 23.10 - 46.20: 350 46.20 - 69.29: 71 69.29 - 92.39: 10 92.39 - 115.49: 1 Dihedral angle restraints: 5325 sinusoidal: 2400 harmonic: 2925 Sorted by residual: dihedral pdb=" C4' DT B 1 " pdb=" C3' DT B 1 " pdb=" O3' DT B 1 " pdb=" P DA B 2 " ideal model delta sinusoidal sigma weight residual -140.00 -24.51 -115.49 1 3.50e+01 8.16e-04 1.12e+01 dihedral pdb=" CA ASN A 862 " pdb=" C ASN A 862 " pdb=" N LYS A 863 " pdb=" CA LYS A 863 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CG ARG A 21 " pdb=" CD ARG A 21 " pdb=" NE ARG A 21 " pdb=" CZ ARG A 21 " ideal model delta sinusoidal sigma weight residual -90.00 -133.10 43.10 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 5322 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1034 0.050 - 0.101: 220 0.101 - 0.151: 56 0.151 - 0.202: 2 0.202 - 0.252: 3 Chirality restraints: 1315 Sorted by residual: chirality pdb=" C4' DCP A1001 " pdb=" C3' DCP A1001 " pdb=" C5' DCP A1001 " pdb=" O4' DCP A1001 " both_signs ideal model delta sigma weight residual False -2.49 -2.74 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA TRP A 403 " pdb=" N TRP A 403 " pdb=" C TRP A 403 " pdb=" CB TRP A 403 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE A 124 " pdb=" N ILE A 124 " pdb=" C ILE A 124 " pdb=" CB ILE A 124 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1312 not shown) Planarity restraints: 1453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 904 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C GLU A 904 " 0.063 2.00e-02 2.50e+03 pdb=" O GLU A 904 " -0.024 2.00e-02 2.50e+03 pdb=" N LYS A 905 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 256 " -0.054 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO A 257 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 403 " -0.015 2.00e-02 2.50e+03 1.29e-02 4.16e+00 pdb=" CG TRP A 403 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP A 403 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 403 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 403 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 403 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 403 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 403 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 403 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 403 " -0.000 2.00e-02 2.50e+03 ... (remaining 1450 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 17 2.35 - 2.98: 4485 2.98 - 3.62: 14158 3.62 - 4.26: 21808 4.26 - 4.90: 35295 Nonbonded interactions: 75763 Sorted by model distance: nonbonded pdb=" OD2 ASP A 424 " pdb="MG MG A1003 " model vdw 1.708 2.170 nonbonded pdb=" OD1 ASP A 517 " pdb="MG MG A1002 " model vdw 1.839 2.170 nonbonded pdb=" OD2 ASP A 689 " pdb="MG MG A1002 " model vdw 2.129 2.170 nonbonded pdb=" O PHE A 518 " pdb="MG MG A1002 " model vdw 2.195 2.170 nonbonded pdb=" O2A DCP A1001 " pdb="MG MG A1002 " model vdw 2.208 2.170 ... (remaining 75758 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.970 Find NCS groups from input model: 0.030 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:7.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6285 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 : 0.006 0.235 8912 Z= 0.347 Angle : 0.721 12.508 12175 Z= 0.401 Chirality : 0.045 0.252 1315 Planarity : 0.005 0.082 1453 Dihedral : 15.643 115.490 3441 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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 are not related in a simple way. whole: 1.08 (0.27), residues: 982 helix: 1.23 (0.24), residues: 460 sheet: -0.10 (0.41), residues: 158 loop : 0.67 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 185 TYR 0.015 0.001 TYR A 144 PHE 0.023 0.002 PHE A 186 TRP 0.031 0.002 TRP A 856 HIS 0.011 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.35 ( 8912) covalent geometry : angle 0.72070 / 0.40 (12175) hydrogen bonds : bond 0.13797 / 9.30 ( 466) hydrogen bonds : angle 6.43931 / 4.33 ( 1325) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 20 GLN cc_start: 0.6906 (tp40) cc_final: 0.6099 (tm-30) REVERT: A 42 VAL cc_start: 0.7240 (t) cc_final: 0.6935 (m) REVERT: A 109 MET cc_start: 0.7470 (mmt) cc_final: 0.7140 (mmt) REVERT: A 122 ILE cc_start: 0.7005 (pt) cc_final: 0.6798 (mt) REVERT: A 178 GLU cc_start: 0.6770 (tt0) cc_final: 0.6547 (tt0) REVERT: A 180 ARG cc_start: 0.5805 (mtm110) cc_final: 0.4710 (ppt-90) REVERT: A 185 ARG cc_start: 0.6735 (mtp-110) cc_final: 0.6494 (mtm180) REVERT: A 191 GLU cc_start: 0.7462 (pt0) cc_final: 0.6973 (pm20) REVERT: A 285 ARG cc_start: 0.5297 (mtp85) cc_final: 0.4336 (mtm110) REVERT: A 296 ASP cc_start: 0.5972 (p0) cc_final: 0.5558 (p0) REVERT: A 316 GLU cc_start: 0.6235 (tt0) cc_final: 0.5241 (mp0) REVERT: A 320 LYS cc_start: 0.6842 (ttmm) cc_final: 0.6278 (tptp) REVERT: A 328 LYS cc_start: 0.6027 (mmmm) cc_final: 0.5678 (mppt) REVERT: A 334 LYS cc_start: 0.6721 (tttt) cc_final: 0.6198 (ttpt) REVERT: A 383 LYS cc_start: 0.6531 (ttpp) cc_final: 0.5634 (tttp) REVERT: A 511 LYS cc_start: 0.6165 (mtpt) cc_final: 0.5797 (mttt) REVERT: A 545 SER cc_start: 0.6924 (t) cc_final: 0.6689 (m) REVERT: A 552 SER cc_start: 0.7404 (m) cc_final: 0.7081 (p) REVERT: A 578 LYS cc_start: 0.6322 (mttt) cc_final: 0.6083 (mtmt) REVERT: A 591 ASN cc_start: 0.6425 (m-40) cc_final: 0.6077 (m-40) REVERT: A 592 LYS cc_start: 0.5690 (ttmm) cc_final: 0.5320 (mttp) REVERT: A 603 LEU cc_start: 0.4771 (tt) cc_final: 0.4450 (tp) REVERT: A 623 ARG cc_start: 0.5407 (ttp-110) cc_final: 0.4469 (tpt-90) REVERT: A 638 MET cc_start: 0.5549 (mtm) cc_final: 0.5242 (mtp) REVERT: A 722 HIS cc_start: 0.4542 (t-90) cc_final: 0.3990 (m-70) REVERT: A 730 LYS cc_start: 0.5104 (ptpp) cc_final: 0.4273 (pptt) REVERT: A 753 ARG cc_start: 0.6036 (mtm110) cc_final: 0.4968 (mtp-110) REVERT: A 801 LYS cc_start: 0.6242 (ttmm) cc_final: 0.5876 (ttmt) REVERT: A 846 ASN cc_start: 0.6131 (m-40) cc_final: 0.5515 (p0) REVERT: A 896 GLU cc_start: 0.6569 (pt0) cc_final: 0.5216 (mm-30) REVERT: A 934 LYS cc_start: 0.6578 (mtmm) cc_final: 0.6377 (mttt) REVERT: A 935 ASN cc_start: 0.6998 (m-40) cc_final: 0.6695 (m-40) REVERT: A 958 GLU cc_start: 0.5772 (pp20) cc_final: 0.5230 (pm20) REVERT: A 960 GLU cc_start: 0.6948 (tp30) cc_final: 0.6624 (pp20) REVERT: A 972 ASP cc_start: 0.6374 (t0) cc_final: 0.5951 (t70) REVERT: A 977 ARG cc_start: 0.5872 (mtm110) cc_final: 0.5138 (mtp180) REVERT: A 978 ARG cc_start: 0.6004 (tpp80) cc_final: 0.5414 (tpp-160) REVERT: A 981 SER cc_start: 0.6663 (m) cc_final: 0.6205 (m) REVERT: A 985 LYS cc_start: 0.6518 (mttp) cc_final: 0.6197 (mtmt) outliers start: 0 outliers final: 1 residues processed: 195 average time/residue: 0.5802 time to fit residues: 119.4964 Evaluate side-chains 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 648 ASN ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.197245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165850 restraints weight = 8675.302| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.18 r_work: 0.3708 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8912 Z= 0.148 Angle : 0.585 7.186 12175 Z= 0.315 Chirality : 0.043 0.152 1315 Planarity : 0.004 0.042 1453 Dihedral : 15.610 115.162 1436 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.69 % Allowed : 9.03 % Favored : 89.28 % 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 are not related in a simple way. whole: 1.32 (0.26), residues: 982 helix: 1.59 (0.23), residues: 458 sheet: 0.08 (0.40), residues: 156 loop : 0.51 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 13 TYR 0.017 0.001 TYR A 522 PHE 0.016 0.002 PHE A 637 TRP 0.015 0.001 TRP A 856 HIS 0.008 0.001 HIS A 462 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 8912) covalent geometry : angle 0.58502 / 0.32 (12175) hydrogen bonds : bond 0.04911 / 3.33 ( 466) hydrogen bonds : angle 4.97298 / 3.36 ( 1325) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.192 Fit side-chains REVERT: A 20 GLN cc_start: 0.7572 (tp40) cc_final: 0.7141 (tm-30) REVERT: A 109 MET cc_start: 0.8326 (mmt) cc_final: 0.8002 (mmt) REVERT: A 116 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8151 (mtmp) REVERT: A 122 ILE cc_start: 0.8522 (pt) cc_final: 0.8306 (mt) REVERT: A 142 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.6063 (mmp) REVERT: A 180 ARG cc_start: 0.6798 (mtm110) cc_final: 0.6257 (ppt-90) REVERT: A 237 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8817 (ptm) REVERT: A 281 GLU cc_start: 0.7863 (tp30) cc_final: 0.7577 (tm-30) REVERT: A 316 GLU cc_start: 0.7088 (tt0) cc_final: 0.6860 (mp0) REVERT: A 383 LYS cc_start: 0.8389 (ttpp) cc_final: 0.7870 (tttp) REVERT: A 722 HIS cc_start: 0.6395 (t-90) cc_final: 0.5940 (m-70) REVERT: A 801 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7912 (tttp) REVERT: A 896 GLU cc_start: 0.6723 (pt0) cc_final: 0.6375 (mm-30) REVERT: A 977 ARG cc_start: 0.7918 (mtm110) cc_final: 0.7635 (mtp180) REVERT: A 985 LYS cc_start: 0.8003 (mttp) cc_final: 0.7771 (mtmt) outliers start: 15 outliers final: 5 residues processed: 163 average time/residue: 0.6093 time to fit residues: 104.6595 Evaluate side-chains 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 949 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.0050 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 HIS ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.189675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.158509 restraints weight = 8418.101| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.15 r_work: 0.3589 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8912 Z= 0.190 Angle : 0.612 6.555 12175 Z= 0.326 Chirality : 0.044 0.179 1315 Planarity : 0.004 0.036 1453 Dihedral : 15.792 115.829 1433 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.93 % Allowed : 11.96 % Favored : 85.10 % 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 are not related in a simple way. whole: 1.15 (0.26), residues: 982 helix: 1.53 (0.23), residues: 467 sheet: -0.24 (0.37), residues: 170 loop : 0.41 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 185 TYR 0.021 0.002 TYR A 692 PHE 0.013 0.002 PHE A 850 TRP 0.011 0.002 TRP A 856 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 8912) covalent geometry : angle 0.61193 / 0.33 (12175) hydrogen bonds : bond 0.05067 / 3.47 ( 466) hydrogen bonds : angle 4.84404 / 3.25 ( 1325) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.322 Fit side-chains REVERT: A 20 GLN cc_start: 0.7534 (tp40) cc_final: 0.7176 (tm-30) REVERT: A 109 MET cc_start: 0.8533 (mmt) cc_final: 0.8279 (mmt) REVERT: A 116 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8089 (mtmp) REVERT: A 122 ILE cc_start: 0.8570 (pt) cc_final: 0.8307 (mt) REVERT: A 142 MET cc_start: 0.6646 (OUTLIER) cc_final: 0.6381 (mmp) REVERT: A 145 ASN cc_start: 0.5957 (m-40) cc_final: 0.5659 (t0) REVERT: A 180 ARG cc_start: 0.6869 (mtm110) cc_final: 0.6583 (ppt-90) REVERT: A 215 TYR cc_start: 0.7543 (t80) cc_final: 0.7228 (t80) REVERT: A 285 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7458 (mtm110) REVERT: A 316 GLU cc_start: 0.7458 (tt0) cc_final: 0.7184 (mp0) REVERT: A 342 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6560 (ttm170) REVERT: A 383 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8025 (tttp) REVERT: A 801 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7965 (tttp) REVERT: A 896 GLU cc_start: 0.6954 (pt0) cc_final: 0.6688 (mm-30) REVERT: A 949 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 977 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7636 (mtp180) REVERT: A 985 LYS cc_start: 0.8237 (mttp) cc_final: 0.7989 (mttt) outliers start: 26 outliers final: 7 residues processed: 146 average time/residue: 0.5551 time to fit residues: 85.7982 Evaluate side-chains 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 989 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 20 GLN A 24 ASN A 573 ASN A 959 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.188426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158810 restraints weight = 8591.694| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.08 r_work: 0.3572 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8912 Z= 0.175 Angle : 0.586 6.255 12175 Z= 0.311 Chirality : 0.044 0.248 1315 Planarity : 0.004 0.030 1453 Dihedral : 15.904 117.176 1433 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.61 % Allowed : 14.00 % Favored : 82.39 % 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 are not related in a simple way. whole: 1.17 (0.26), residues: 982 helix: 1.59 (0.23), residues: 464 sheet: -0.30 (0.38), residues: 170 loop : 0.43 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 13 TYR 0.016 0.002 TYR A 692 PHE 0.012 0.002 PHE A 283 TRP 0.009 0.001 TRP A 856 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 ( 8912) covalent geometry : angle 0.58637 / 0.31 (12175) hydrogen bonds : bond 0.04693 / 3.21 ( 466) hydrogen bonds : angle 4.76308 / 3.21 ( 1325) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.197 Fit side-chains REVERT: A 20 GLN cc_start: 0.7530 (tp-100) cc_final: 0.7220 (tm-30) REVERT: A 109 MET cc_start: 0.8642 (mmt) cc_final: 0.8220 (mmt) REVERT: A 116 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8111 (mtmp) REVERT: A 122 ILE cc_start: 0.8547 (pt) cc_final: 0.8285 (mt) REVERT: A 145 ASN cc_start: 0.5973 (m-40) cc_final: 0.5688 (t0) REVERT: A 191 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7154 (pm20) REVERT: A 215 TYR cc_start: 0.7515 (t80) cc_final: 0.7221 (t80) REVERT: A 237 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8853 (ptm) REVERT: A 285 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7508 (mtm110) REVERT: A 316 GLU cc_start: 0.7441 (tt0) cc_final: 0.7176 (mp0) REVERT: A 342 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6624 (ttm170) REVERT: A 383 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8099 (tttp) REVERT: A 598 GLN cc_start: 0.7121 (pp30) cc_final: 0.6678 (mt0) REVERT: A 730 LYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6474 (tmmt) REVERT: A 801 LYS cc_start: 0.8397 (ttmm) cc_final: 0.7981 (tttp) REVERT: A 896 GLU cc_start: 0.6971 (pt0) cc_final: 0.6723 (mm-30) REVERT: A 949 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8092 (mp) REVERT: A 985 LYS cc_start: 0.8246 (mttp) cc_final: 0.7995 (mttt) outliers start: 32 outliers final: 8 residues processed: 146 average time/residue: 0.5253 time to fit residues: 81.3348 Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 949 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.189262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.159271 restraints weight = 8493.167| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.12 r_work: 0.3581 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8912 Z= 0.147 Angle : 0.559 7.686 12175 Z= 0.296 Chirality : 0.042 0.179 1315 Planarity : 0.004 0.029 1453 Dihedral : 15.817 116.658 1433 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.50 % Allowed : 15.01 % Favored : 81.49 % 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 are not related in a simple way. whole: 1.19 (0.26), residues: 982 helix: 1.62 (0.23), residues: 462 sheet: -0.31 (0.38), residues: 170 loop : 0.43 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 180 TYR 0.016 0.001 TYR A 756 PHE 0.010 0.001 PHE A 294 TRP 0.004 0.001 TRP A 325 HIS 0.006 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 8912) covalent geometry : angle 0.55892 / 0.30 (12175) hydrogen bonds : bond 0.04425 / 3.05 ( 466) hydrogen bonds : angle 4.65917 / 3.14 ( 1325) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.238 Fit side-chains REVERT: A 20 GLN cc_start: 0.7497 (tp-100) cc_final: 0.7197 (tm-30) REVERT: A 109 MET cc_start: 0.8656 (mmt) cc_final: 0.8278 (mmt) REVERT: A 116 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8123 (mtmp) REVERT: A 122 ILE cc_start: 0.8517 (pt) cc_final: 0.8253 (mt) REVERT: A 145 ASN cc_start: 0.5925 (m-40) cc_final: 0.5592 (t0) REVERT: A 191 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7110 (pm20) REVERT: A 237 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8996 (ptm) REVERT: A 255 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6716 (mmt) REVERT: A 285 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7519 (mtm110) REVERT: A 316 GLU cc_start: 0.7428 (tt0) cc_final: 0.7178 (mp0) REVERT: A 342 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6597 (ttm170) REVERT: A 383 LYS cc_start: 0.8346 (ttpp) cc_final: 0.7990 (tttp) REVERT: A 547 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.5470 (mpp) REVERT: A 598 GLN cc_start: 0.7176 (pp30) cc_final: 0.6684 (mt0) REVERT: A 619 GLU cc_start: 0.6778 (tm-30) cc_final: 0.6442 (tp30) REVERT: A 730 LYS cc_start: 0.7024 (tttm) cc_final: 0.6431 (tmmt) REVERT: A 801 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7949 (tttp) REVERT: A 896 GLU cc_start: 0.6946 (pt0) cc_final: 0.6669 (mm-30) REVERT: A 949 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 985 LYS cc_start: 0.8235 (mttp) cc_final: 0.7977 (mttt) outliers start: 31 outliers final: 10 residues processed: 146 average time/residue: 0.4864 time to fit residues: 75.3542 Evaluate side-chains 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 980 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.189776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.159929 restraints weight = 8520.096| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.13 r_work: 0.3594 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8912 Z= 0.134 Angle : 0.546 7.891 12175 Z= 0.290 Chirality : 0.041 0.186 1315 Planarity : 0.003 0.028 1453 Dihedral : 15.737 116.226 1433 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.61 % Allowed : 16.14 % Favored : 80.25 % 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 are not related in a simple way. whole: 1.18 (0.26), residues: 982 helix: 1.62 (0.23), residues: 466 sheet: -0.36 (0.38), residues: 170 loop : 0.41 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 13 TYR 0.014 0.001 TYR A 692 PHE 0.010 0.001 PHE A 294 TRP 0.006 0.001 TRP A 845 HIS 0.006 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8912) covalent geometry : angle 0.54618 / 0.29 (12175) hydrogen bonds : bond 0.04252 / 2.93 ( 466) hydrogen bonds : angle 4.59365 / 3.11 ( 1325) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.190 Fit side-chains REVERT: A 109 MET cc_start: 0.8656 (mmt) cc_final: 0.8301 (mmt) REVERT: A 122 ILE cc_start: 0.8498 (pt) cc_final: 0.8244 (mt) REVERT: A 145 ASN cc_start: 0.5915 (m-40) cc_final: 0.5588 (t0) REVERT: A 191 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7168 (pm20) REVERT: A 237 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.8992 (ptm) REVERT: A 285 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7554 (mtm110) REVERT: A 316 GLU cc_start: 0.7438 (tt0) cc_final: 0.7169 (mp0) REVERT: A 342 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6586 (ttm170) REVERT: A 383 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8084 (tttp) REVERT: A 547 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.5533 (mpp) REVERT: A 598 GLN cc_start: 0.7222 (pp30) cc_final: 0.6712 (mt0) REVERT: A 619 GLU cc_start: 0.6811 (tm-30) cc_final: 0.6484 (tp30) REVERT: A 730 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6488 (tmmt) REVERT: A 896 GLU cc_start: 0.6832 (pt0) cc_final: 0.6569 (mm-30) REVERT: A 949 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8049 (mp) REVERT: A 959 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7704 (m110) REVERT: A 985 LYS cc_start: 0.8198 (mttp) cc_final: 0.7946 (mttt) outliers start: 32 outliers final: 10 residues processed: 143 average time/residue: 0.5108 time to fit residues: 77.3245 Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 980 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 chunk 94 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.189814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.159863 restraints weight = 8553.552| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.13 r_work: 0.3594 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8912 Z= 0.131 Angle : 0.540 7.094 12175 Z= 0.288 Chirality : 0.041 0.181 1315 Planarity : 0.003 0.033 1453 Dihedral : 15.686 115.763 1433 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.39 % Allowed : 16.59 % Favored : 80.02 % 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 are not related in a simple way. whole: 1.22 (0.26), residues: 982 helix: 1.68 (0.23), residues: 464 sheet: -0.36 (0.38), residues: 170 loop : 0.41 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 13 TYR 0.014 0.001 TYR A 692 PHE 0.010 0.001 PHE A 942 TRP 0.018 0.001 TRP A 856 HIS 0.006 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 ( 8912) covalent geometry : angle 0.54042 / 0.29 (12175) hydrogen bonds : bond 0.04168 / 2.87 ( 466) hydrogen bonds : angle 4.55689 / 3.08 ( 1325) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.218 Fit side-chains REVERT: A 20 GLN cc_start: 0.7593 (tp-100) cc_final: 0.7266 (tm-30) REVERT: A 109 MET cc_start: 0.8648 (mmt) cc_final: 0.8211 (mmt) REVERT: A 122 ILE cc_start: 0.8472 (pt) cc_final: 0.8215 (mt) REVERT: A 145 ASN cc_start: 0.5931 (m-40) cc_final: 0.5652 (t0) REVERT: A 191 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7162 (pm20) REVERT: A 237 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8674 (ptm) REVERT: A 285 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7550 (mtm110) REVERT: A 316 GLU cc_start: 0.7451 (tt0) cc_final: 0.7202 (mp0) REVERT: A 342 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6588 (ttm170) REVERT: A 383 LYS cc_start: 0.8297 (ttpp) cc_final: 0.7968 (tttp) REVERT: A 547 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.5653 (mpp) REVERT: A 598 GLN cc_start: 0.7238 (pp30) cc_final: 0.6716 (mt0) REVERT: A 619 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6487 (tp30) REVERT: A 730 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6475 (tmmt) REVERT: A 854 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7864 (t0) REVERT: A 896 GLU cc_start: 0.6812 (pt0) cc_final: 0.6512 (mm-30) REVERT: A 949 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8072 (mp) REVERT: A 960 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6654 (pp20) REVERT: A 985 LYS cc_start: 0.8206 (mttp) cc_final: 0.7939 (mttt) outliers start: 30 outliers final: 14 residues processed: 145 average time/residue: 0.5129 time to fit residues: 78.7819 Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 980 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 GLN A 573 ASN A 959 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.188955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159191 restraints weight = 8469.955| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.10 r_work: 0.3587 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8912 Z= 0.143 Angle : 0.554 8.747 12175 Z= 0.294 Chirality : 0.042 0.187 1315 Planarity : 0.003 0.030 1453 Dihedral : 15.704 115.239 1433 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.84 % Allowed : 16.59 % Favored : 79.57 % 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 are not related in a simple way. whole: 1.20 (0.26), residues: 982 helix: 1.67 (0.23), residues: 464 sheet: -0.38 (0.38), residues: 170 loop : 0.40 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 13 TYR 0.015 0.001 TYR A 692 PHE 0.010 0.001 PHE A 942 TRP 0.026 0.001 TRP A 856 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 8912) covalent geometry : angle 0.55400 / 0.29 (12175) hydrogen bonds : bond 0.04250 / 2.92 ( 466) hydrogen bonds : angle 4.54379 / 3.07 ( 1325) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 123 time to evaluate : 0.258 Fit side-chains REVERT: A 20 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7329 (tm-30) REVERT: A 109 MET cc_start: 0.8652 (mmt) cc_final: 0.8202 (mmt) REVERT: A 122 ILE cc_start: 0.8510 (pt) cc_final: 0.8257 (mt) REVERT: A 145 ASN cc_start: 0.6015 (m-40) cc_final: 0.5673 (t0) REVERT: A 191 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: A 215 TYR cc_start: 0.7338 (t80) cc_final: 0.6961 (t80) REVERT: A 237 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8927 (ptm) REVERT: A 285 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7544 (mtm110) REVERT: A 316 GLU cc_start: 0.7465 (tt0) cc_final: 0.7200 (mp0) REVERT: A 342 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6586 (ttm170) REVERT: A 383 LYS cc_start: 0.8304 (ttpp) cc_final: 0.8055 (tttp) REVERT: A 547 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.5752 (mpp) REVERT: A 598 GLN cc_start: 0.7233 (pp30) cc_final: 0.6720 (mt0) REVERT: A 619 GLU cc_start: 0.6780 (OUTLIER) cc_final: 0.6530 (tp30) REVERT: A 722 HIS cc_start: 0.6887 (t70) cc_final: 0.6440 (m-70) REVERT: A 730 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6477 (tmmt) REVERT: A 854 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7782 (t0) REVERT: A 896 GLU cc_start: 0.6824 (pt0) cc_final: 0.6520 (mm-30) REVERT: A 949 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8093 (mp) REVERT: A 959 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.7857 (m110) REVERT: A 960 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6662 (pp20) REVERT: A 985 LYS cc_start: 0.8208 (mttp) cc_final: 0.7907 (mttt) outliers start: 34 outliers final: 14 residues processed: 142 average time/residue: 0.5048 time to fit residues: 76.0661 Evaluate side-chains 141 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 980 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 96 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 75 GLN A 573 ASN A 959 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.189546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.159618 restraints weight = 8563.189| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.13 r_work: 0.3592 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 0.003 0.062 8912 Z= 0.136 Angle : 0.552 8.489 12175 Z= 0.293 Chirality : 0.042 0.187 1315 Planarity : 0.003 0.032 1453 Dihedral : 15.692 115.006 1433 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.16 % Allowed : 16.82 % Favored : 80.02 % 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 are not related in a simple way. whole: 1.22 (0.26), residues: 982 helix: 1.68 (0.23), residues: 464 sheet: -0.37 (0.38), residues: 170 loop : 0.41 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 13 TYR 0.014 0.001 TYR A 692 PHE 0.010 0.001 PHE A 942 TRP 0.029 0.002 TRP A 856 HIS 0.006 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 8912) covalent geometry : angle 0.55166 / 0.29 (12175) hydrogen bonds : bond 0.04167 / 2.86 ( 466) hydrogen bonds : angle 4.52026 / 3.06 ( 1325) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.233 Fit side-chains REVERT: A 20 GLN cc_start: 0.7583 (tp-100) cc_final: 0.7278 (tm-30) REVERT: A 109 MET cc_start: 0.8653 (mmt) cc_final: 0.8192 (mmt) REVERT: A 122 ILE cc_start: 0.8529 (pt) cc_final: 0.8294 (mt) REVERT: A 145 ASN cc_start: 0.6015 (m-40) cc_final: 0.5662 (t0) REVERT: A 191 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7132 (pm20) REVERT: A 215 TYR cc_start: 0.7306 (t80) cc_final: 0.6914 (t80) REVERT: A 285 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7541 (mtm110) REVERT: A 316 GLU cc_start: 0.7454 (tt0) cc_final: 0.7203 (mp0) REVERT: A 342 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6599 (ttm170) REVERT: A 383 LYS cc_start: 0.8283 (ttpp) cc_final: 0.8035 (tttp) REVERT: A 547 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.5759 (mpp) REVERT: A 598 GLN cc_start: 0.7239 (pp30) cc_final: 0.6729 (mt0) REVERT: A 619 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6530 (tp30) REVERT: A 722 HIS cc_start: 0.6795 (t70) cc_final: 0.6407 (m-70) REVERT: A 730 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6459 (tmmt) REVERT: A 896 GLU cc_start: 0.6789 (pt0) cc_final: 0.6483 (mm-30) REVERT: A 949 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8083 (mp) REVERT: A 985 LYS cc_start: 0.8184 (mttp) cc_final: 0.7884 (mttt) outliers start: 28 outliers final: 14 residues processed: 137 average time/residue: 0.5363 time to fit residues: 77.6007 Evaluate side-chains 140 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 959 ASN Chi-restraints excluded: chain A residue 980 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 75 GLN A 573 ASN A 957 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.185672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.162812 restraints weight = 8062.357| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.67 r_work: 0.3462 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8912 Z= 0.143 Angle : 0.563 9.373 12175 Z= 0.299 Chirality : 0.042 0.189 1315 Planarity : 0.004 0.029 1453 Dihedral : 15.687 114.660 1433 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.71 % Allowed : 17.27 % Favored : 80.02 % 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 are not related in a simple way. whole: 1.21 (0.26), residues: 982 helix: 1.66 (0.23), residues: 464 sheet: -0.35 (0.38), residues: 170 loop : 0.43 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 13 TYR 0.014 0.001 TYR A 692 PHE 0.010 0.001 PHE A 942 TRP 0.037 0.002 TRP A 856 HIS 0.006 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8912) covalent geometry : angle 0.56270 / 0.30 (12175) hydrogen bonds : bond 0.04197 / 2.88 ( 466) hydrogen bonds : angle 4.52780 / 3.07 ( 1325) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.214 Fit side-chains REVERT: A 20 GLN cc_start: 0.7527 (tp-100) cc_final: 0.7238 (tm-30) REVERT: A 109 MET cc_start: 0.8636 (mmt) cc_final: 0.8169 (mmt) REVERT: A 122 ILE cc_start: 0.8500 (pt) cc_final: 0.8247 (mt) REVERT: A 133 ARG cc_start: 0.7480 (ttt90) cc_final: 0.7267 (ttt180) REVERT: A 145 ASN cc_start: 0.5980 (m-40) cc_final: 0.5583 (t0) REVERT: A 191 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: A 215 TYR cc_start: 0.7292 (t80) cc_final: 0.6937 (t80) REVERT: A 285 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7452 (mtm110) REVERT: A 316 GLU cc_start: 0.7426 (tt0) cc_final: 0.7086 (mp0) REVERT: A 342 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6585 (ttm170) REVERT: A 383 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7957 (tttp) REVERT: A 547 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.5689 (mpp) REVERT: A 598 GLN cc_start: 0.7214 (pp30) cc_final: 0.6665 (mt0) REVERT: A 619 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6570 (tp30) REVERT: A 730 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6410 (tmmt) REVERT: A 896 GLU cc_start: 0.6779 (pt0) cc_final: 0.6468 (mm-30) REVERT: A 949 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 985 LYS cc_start: 0.8210 (mttp) cc_final: 0.7893 (mttt) outliers start: 24 outliers final: 14 residues processed: 132 average time/residue: 0.5326 time to fit residues: 74.3883 Evaluate side-chains 137 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 957 ASN Chi-restraints excluded: chain A residue 980 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0770 chunk 9 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 chunk 86 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 ASN A 75 GLN A 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.185304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153018 restraints weight = 8055.105| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.12 r_work: 0.3449 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.260 8912 Z= 0.286 Angle : 0.894 59.106 12175 Z= 0.535 Chirality : 0.044 0.555 1315 Planarity : 0.004 0.027 1453 Dihedral : 15.707 114.658 1433 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.60 % Allowed : 17.27 % Favored : 80.14 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.23 (0.26), residues: 982 helix: 1.66 (0.23), residues: 464 sheet: -0.35 (0.38), residues: 170 loop : 0.45 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 13 TYR 0.014 0.001 TYR A 692 PHE 0.010 0.001 PHE A 942 TRP 0.032 0.002 TRP A 856 HIS 0.006 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.29 ( 8912) covalent geometry : angle 0.89432 / 0.54 (12175) hydrogen bonds : bond 0.04262 / 2.90 ( 466) hydrogen bonds : angle 4.60729 / 3.11 ( 1325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2578.01 seconds wall clock time: 44 minutes 35.69 seconds (2675.69 seconds total)