Starting phenix.real_space_refine on Wed Feb 4 04:34:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l8u_62891/02_2026/9l8u_62891_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l8u_62891/02_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_62891/02_2026/9l8u_62891_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l8u_62891/02_2026/9l8u_62891_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l8u_62891/02_2026/9l8u_62891.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l8u_62891/02_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-2.0-5952/lib/python3.9/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: 11 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.89, 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: 0.80 Conformation dependent library (CDL) restraints added in 205.0 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: 0.90 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: 1.32 Time building geometry restraints manager: 0.92 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 1.523 1.287 0.236 1.30e-02 5.92e+03 3.30e+02 bond pdb=" C4 DCP A1001 " pdb=" N4 DCP A1001 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.20e-02 6.94e+03 9.97e+01 bond pdb=" C1' DCP A1001 " pdb=" O4' DCP A1001 " ideal model delta sigma weight residual 1.418 1.313 0.105 1.20e-02 6.94e+03 7.70e+01 bond pdb=" C4' DCP A1001 " pdb=" O4' DCP A1001 " ideal model delta sigma weight residual 1.444 1.531 -0.087 1.00e-02 1.00e+04 7.53e+01 bond pdb=" C4' DCP A1001 " pdb=" C5' DCP A1001 " ideal model delta sigma weight residual 1.508 1.424 0.084 1.10e-02 8.26e+03 5.84e+01 ... (remaining 8907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 12101 3.55 - 7.11: 67 7.11 - 10.66: 5 10.66 - 14.21: 1 14.21 - 17.77: 1 Bond angle restraints: 12175 Sorted by residual: angle pdb=" PB DCP A1001 " pdb=" O3B DCP A1001 " pdb=" PG DCP A1001 " ideal model delta sigma weight residual 139.87 122.10 17.77 1.00e+00 1.00e+00 3.16e+02 angle pdb=" PA DCP A1001 " pdb=" O3A DCP A1001 " pdb=" PB DCP A1001 " ideal model delta sigma weight residual 136.83 123.90 12.93 1.00e+00 1.00e+00 1.67e+02 angle pdb=" C2' DCP A1001 " pdb=" C1' DCP A1001 " pdb=" N1 DCP A1001 " ideal model delta sigma weight residual 113.92 105.92 8.00 1.28e+00 6.12e-01 3.92e+01 angle pdb=" O3A DCP A1001 " pdb=" PB DCP A1001 " pdb=" O3B DCP A1001 " ideal model delta sigma weight residual 101.57 109.81 -8.24 1.54e+00 4.24e-01 2.88e+01 angle pdb=" C3' DCP A1001 " pdb=" C4' DCP A1001 " pdb=" O4' DCP A1001 " ideal model delta sigma weight residual 105.64 100.30 5.34 1.08e+00 8.51e-01 2.43e+01 ... (remaining 12170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 4889 23.10 - 46.20: 345 46.20 - 69.29: 70 69.29 - 92.39: 11 92.39 - 115.49: 1 Dihedral angle restraints: 5316 sinusoidal: 2391 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 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1113 0.056 - 0.112: 169 0.112 - 0.168: 29 0.168 - 0.225: 1 0.225 - 0.281: 3 Chirality restraints: 1315 Sorted by residual: chirality pdb=" C3' DCP A1001 " pdb=" C2' DCP A1001 " pdb=" C4' DCP A1001 " pdb=" O3' DCP A1001 " both_signs ideal model delta sigma weight residual False -2.68 -2.40 -0.28 2.00e-01 2.50e+01 1.97e+00 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 -2.50 -2.74 0.24 2.00e-01 2.50e+01 1.50e+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 ... (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: 1.510 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.820 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:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5951 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 0.236 8912 Z= 0.409 Angle : 0.718 17.768 12175 Z= 0.453 Chirality : 0.043 0.281 1315 Planarity : 0.005 0.082 1453 Dihedral : 15.666 115.490 3432 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 covalent geometry : bond 0.00586 ( 8912) covalent geometry : angle 0.71772 (12175) hydrogen bonds : bond 0.13797 ( 466) hydrogen bonds : angle 6.43931 ( 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 : 0.323 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: 0.5923 time to fit residues: 121.7933 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 : 0.202 ------------------------------------------------------------------------------- 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: 4.9990 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: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4211 r_free = 0.4211 target = 0.193621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.161187 restraints weight = 8631.325| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.26 r_work: 0.3647 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8912 Z= 0.159 Angle : 0.559 6.659 12175 Z= 0.303 Chirality : 0.042 0.144 1315 Planarity : 0.004 0.043 1453 Dihedral : 15.827 115.853 1427 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.81 % Allowed : 9.37 % Favored : 88.83 % 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: 1.38 (0.26), residues: 982 helix: 1.66 (0.23), residues: 460 sheet: 0.10 (0.40), residues: 156 loop : 0.50 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 13 TYR 0.019 0.001 TYR A 522 PHE 0.012 0.002 PHE A 675 TRP 0.013 0.001 TRP A 856 HIS 0.007 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8912) covalent geometry : angle 0.55912 (12175) hydrogen bonds : bond 0.04621 ( 466) hydrogen bonds : angle 4.82508 ( 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 164 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.215 Fit side-chains REVERT: A 20 GLN cc_start: 0.7560 (tp40) cc_final: 0.7122 (tm-30) REVERT: A 99 ARG cc_start: 0.7219 (ptt-90) cc_final: 0.6994 (pmt170) REVERT: A 109 MET cc_start: 0.8404 (mmt) cc_final: 0.8098 (mmt) REVERT: A 116 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8045 (mtmp) REVERT: A 122 ILE cc_start: 0.8558 (pt) cc_final: 0.8300 (mt) REVERT: A 142 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.6038 (mmp) REVERT: A 180 ARG cc_start: 0.6854 (mtm110) cc_final: 0.6241 (ppt-90) REVERT: A 237 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8941 (ptm) REVERT: A 285 ARG cc_start: 0.7734 (mtp85) cc_final: 0.7236 (mtm110) REVERT: A 296 ASP cc_start: 0.7954 (p0) cc_final: 0.7719 (p0) REVERT: A 316 GLU cc_start: 0.7305 (tt0) cc_final: 0.6985 (mp0) REVERT: A 383 LYS cc_start: 0.8371 (ttpp) cc_final: 0.7882 (tttp) REVERT: A 722 HIS cc_start: 0.6559 (t-90) cc_final: 0.6096 (m-70) REVERT: A 801 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7927 (tttp) REVERT: A 896 GLU cc_start: 0.6866 (pt0) cc_final: 0.6474 (mm-30) REVERT: A 949 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8040 (mp) REVERT: A 977 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7610 (mtp180) REVERT: A 985 LYS cc_start: 0.8012 (mttp) cc_final: 0.7756 (mtmt) outliers start: 16 outliers final: 5 residues processed: 155 average time/residue: 0.6400 time to fit residues: 104.5551 Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 237 MET Chi-restraints excluded: chain A residue 416 ASP 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 989 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN A 722 HIS ** A 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 852 GLN ** A 959 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 = 0.4122 r_free = 0.4122 target = 0.184562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.153787 restraints weight = 8429.422| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.16 r_work: 0.3523 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8912 Z= 0.245 Angle : 0.640 7.295 12175 Z= 0.340 Chirality : 0.046 0.204 1315 Planarity : 0.004 0.033 1453 Dihedral : 16.249 119.445 1424 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.61 % Allowed : 12.53 % Favored : 83.86 % 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: 1.04 (0.26), residues: 982 helix: 1.36 (0.23), residues: 464 sheet: -0.28 (0.37), residues: 166 loop : 0.50 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 13 TYR 0.021 0.002 TYR A 692 PHE 0.015 0.002 PHE A 283 TRP 0.027 0.002 TRP A 856 HIS 0.008 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 8912) covalent geometry : angle 0.64010 (12175) hydrogen bonds : bond 0.05324 ( 466) hydrogen bonds : angle 4.88436 ( 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 167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.311 Fit side-chains REVERT: A 20 GLN cc_start: 0.7488 (tp40) cc_final: 0.7205 (tm-30) REVERT: A 109 MET cc_start: 0.8609 (mmt) cc_final: 0.8152 (mmt) REVERT: A 122 ILE cc_start: 0.8623 (pt) cc_final: 0.8266 (mt) REVERT: A 142 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6686 (mmp) REVERT: A 145 ASN cc_start: 0.5902 (m-40) cc_final: 0.5579 (t0) REVERT: A 180 ARG cc_start: 0.7026 (mtm110) cc_final: 0.6565 (ppt-90) REVERT: A 215 TYR cc_start: 0.7540 (t80) cc_final: 0.7228 (t80) REVERT: A 216 SER cc_start: 0.7538 (t) cc_final: 0.7182 (p) REVERT: A 237 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8990 (ptm) REVERT: A 285 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7425 (mtm180) REVERT: A 316 GLU cc_start: 0.7559 (tt0) cc_final: 0.7314 (mp0) REVERT: A 342 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6782 (ttm170) REVERT: A 383 LYS cc_start: 0.8422 (ttpp) cc_final: 0.8068 (tttp) REVERT: A 598 GLN cc_start: 0.7167 (pp30) cc_final: 0.6695 (mt0) REVERT: A 619 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6588 (tp30) REVERT: A 801 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8034 (tttp) REVERT: A 949 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 977 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7790 (mtp180) REVERT: A 985 LYS cc_start: 0.8280 (mttp) cc_final: 0.8002 (mttt) outliers start: 32 outliers final: 8 residues processed: 153 average time/residue: 0.6393 time to fit residues: 103.2283 Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 619 GLU 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 865 VAL Chi-restraints excluded: chain A residue 949 LEU 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: 1.9990 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 81 optimal weight: 0.0970 chunk 90 optimal weight: 0.0030 chunk 15 optimal weight: 0.9980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 573 ASN A 946 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 = 0.189264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159670 restraints weight = 8603.895| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.12 r_work: 0.3591 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8912 Z= 0.132 Angle : 0.537 9.146 12175 Z= 0.286 Chirality : 0.041 0.175 1315 Planarity : 0.003 0.027 1453 Dihedral : 15.986 118.376 1424 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.72 % Allowed : 14.45 % Favored : 81.83 % 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: 1.58 (0.23), residues: 466 sheet: -0.35 (0.38), residues: 170 loop : 0.45 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 871 TYR 0.014 0.001 TYR A 692 PHE 0.011 0.001 PHE A 294 TRP 0.017 0.001 TRP A 856 HIS 0.006 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8912) covalent geometry : angle 0.53668 (12175) hydrogen bonds : bond 0.04132 ( 466) hydrogen bonds : angle 4.61937 ( 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: 33 poor density : 127 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 64 ARG cc_start: 0.7808 (mtp180) cc_final: 0.7568 (mtp85) REVERT: A 109 MET cc_start: 0.8646 (mmt) cc_final: 0.8142 (mmt) REVERT: A 122 ILE cc_start: 0.8541 (pt) cc_final: 0.8176 (mt) REVERT: A 142 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6464 (mmp) REVERT: A 145 ASN cc_start: 0.5936 (m-40) cc_final: 0.5556 (t0) REVERT: A 215 TYR cc_start: 0.7453 (t80) cc_final: 0.7164 (t80) REVERT: A 285 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7375 (mtm110) REVERT: A 316 GLU cc_start: 0.7504 (tt0) cc_final: 0.7280 (mp0) REVERT: A 383 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8014 (tttp) REVERT: A 547 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.5665 (mpp) REVERT: A 598 GLN cc_start: 0.7202 (pp30) cc_final: 0.6707 (mt0) REVERT: A 619 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6545 (tp30) REVERT: A 801 LYS cc_start: 0.8372 (ttmm) cc_final: 0.7945 (tttp) REVERT: A 896 GLU cc_start: 0.6921 (pt0) cc_final: 0.6703 (mm-30) REVERT: A 949 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 985 LYS cc_start: 0.8200 (mttp) cc_final: 0.7919 (mttt) outliers start: 33 outliers final: 11 residues processed: 145 average time/residue: 0.6235 time to fit residues: 95.2269 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 : 0.192 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 602 LYS Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 948 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.188459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.158785 restraints weight = 8501.424| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.10 r_work: 0.3577 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3373 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= 0.139 Angle : 0.530 7.514 12175 Z= 0.282 Chirality : 0.041 0.180 1315 Planarity : 0.003 0.030 1453 Dihedral : 15.854 117.184 1424 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.05 % Allowed : 15.69 % Favored : 81.26 % 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: 1.65 (0.23), residues: 465 sheet: -0.33 (0.38), residues: 170 loop : 0.41 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 180 TYR 0.015 0.001 TYR A 692 PHE 0.010 0.001 PHE A 240 TRP 0.016 0.001 TRP A 856 HIS 0.006 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8912) covalent geometry : angle 0.53022 (12175) hydrogen bonds : bond 0.04133 ( 466) hydrogen bonds : angle 4.54366 ( 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 144 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.358 Fit side-chains REVERT: A 20 GLN cc_start: 0.7540 (tp-100) cc_final: 0.7132 (tm-30) REVERT: A 64 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7556 (mtp85) REVERT: A 109 MET cc_start: 0.8589 (mmt) cc_final: 0.8112 (mmt) REVERT: A 142 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6480 (mmp) REVERT: A 145 ASN cc_start: 0.5854 (m-40) cc_final: 0.5559 (t0) REVERT: A 191 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: A 285 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7383 (mtm110) REVERT: A 316 GLU cc_start: 0.7513 (tt0) cc_final: 0.7278 (mp0) REVERT: A 342 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6580 (ttm170) REVERT: A 383 LYS cc_start: 0.8311 (ttpp) cc_final: 0.8088 (tttp) REVERT: A 547 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.5750 (mpp) REVERT: A 598 GLN cc_start: 0.7191 (pp30) cc_final: 0.6711 (mt0) REVERT: A 619 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6628 (tp30) REVERT: A 730 LYS cc_start: 0.7130 (ttpp) cc_final: 0.6483 (tmmt) REVERT: A 896 GLU cc_start: 0.6895 (pt0) cc_final: 0.6608 (mm-30) REVERT: A 949 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8031 (mp) REVERT: A 985 LYS cc_start: 0.8196 (mttp) cc_final: 0.7920 (mttt) outliers start: 27 outliers final: 10 residues processed: 129 average time/residue: 0.6338 time to fit residues: 86.3222 Evaluate side-chains 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 484 THR 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 619 GLU Chi-restraints excluded: chain A residue 642 TYR 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 948 VAL Chi-restraints excluded: chain A residue 949 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4077 r_free = 0.4077 target = 0.183322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152326 restraints weight = 8045.653| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.02 r_work: 0.3417 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8912 Z= 0.167 Angle : 0.550 7.974 12175 Z= 0.293 Chirality : 0.042 0.188 1315 Planarity : 0.004 0.055 1453 Dihedral : 15.938 116.706 1424 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.18 % Allowed : 15.58 % 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: 1.23 (0.26), residues: 982 helix: 1.63 (0.23), residues: 464 sheet: -0.21 (0.38), residues: 171 loop : 0.43 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 185 TYR 0.016 0.001 TYR A 692 PHE 0.011 0.001 PHE A 240 TRP 0.020 0.002 TRP A 856 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8912) covalent geometry : angle 0.54994 (12175) hydrogen bonds : bond 0.04311 ( 466) hydrogen bonds : angle 4.57490 ( 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 158 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.279 Fit side-chains REVERT: A 20 GLN cc_start: 0.7651 (tp-100) cc_final: 0.7266 (tm-30) REVERT: A 64 ARG cc_start: 0.7813 (mtp180) cc_final: 0.7536 (mtp85) REVERT: A 109 MET cc_start: 0.8572 (mmt) cc_final: 0.8105 (mmt) REVERT: A 142 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6611 (mmp) REVERT: A 145 ASN cc_start: 0.5947 (m-40) cc_final: 0.5535 (t0) REVERT: A 185 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7334 (mtm-85) REVERT: A 191 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: A 285 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7425 (mtm110) REVERT: A 316 GLU cc_start: 0.7519 (tt0) cc_final: 0.7246 (mp0) REVERT: A 342 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6653 (ttm170) REVERT: A 383 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7955 (tttp) REVERT: A 547 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.5748 (mpp) REVERT: A 598 GLN cc_start: 0.7183 (pp30) cc_final: 0.6703 (mt0) REVERT: A 619 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6655 (tp30) REVERT: A 722 HIS cc_start: 0.6796 (t70) cc_final: 0.6414 (m-70) REVERT: A 854 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7797 (t0) REVERT: A 896 GLU cc_start: 0.6927 (pt0) cc_final: 0.6627 (mm-30) REVERT: A 949 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8117 (mp) REVERT: A 985 LYS cc_start: 0.8200 (mttp) cc_final: 0.7901 (mttt) outliers start: 37 outliers final: 11 residues processed: 139 average time/residue: 0.6386 time to fit residues: 93.5664 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 484 THR 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 619 GLU Chi-restraints excluded: chain A residue 642 TYR Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 779 THR Chi-restraints excluded: chain A residue 854 ASP Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 949 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 573 ASN A 946 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.183981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.154737 restraints weight = 8029.870| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.94 r_work: 0.3438 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8912 Z= 0.154 Angle : 0.548 8.338 12175 Z= 0.291 Chirality : 0.042 0.186 1315 Planarity : 0.003 0.026 1453 Dihedral : 15.892 115.820 1424 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.29 % Allowed : 16.25 % Favored : 79.46 % 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: 1.25 (0.26), residues: 982 helix: 1.67 (0.23), residues: 464 sheet: -0.25 (0.38), residues: 171 loop : 0.43 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 180 TYR 0.015 0.001 TYR A 692 PHE 0.010 0.001 PHE A 240 TRP 0.022 0.001 TRP A 856 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8912) covalent geometry : angle 0.54849 (12175) hydrogen bonds : bond 0.04196 ( 466) hydrogen bonds : angle 4.54967 ( 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 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.323 Fit side-chains REVERT: A 20 GLN cc_start: 0.7567 (tp-100) cc_final: 0.7236 (tm-30) REVERT: A 64 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7586 (mtp85) REVERT: A 109 MET cc_start: 0.8568 (mmt) cc_final: 0.8128 (mmt) REVERT: A 133 ARG cc_start: 0.7472 (ttt90) cc_final: 0.7190 (ttt180) REVERT: A 142 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6600 (mmp) REVERT: A 145 ASN cc_start: 0.6025 (m-40) cc_final: 0.5622 (t0) REVERT: A 185 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7196 (mtm-85) REVERT: A 191 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: A 229 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7395 (m-40) REVERT: A 237 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.9036 (ptm) REVERT: A 285 ARG cc_start: 0.7854 (mtp85) cc_final: 0.7420 (mtm110) REVERT: A 316 GLU cc_start: 0.7500 (tt0) cc_final: 0.7263 (mp0) REVERT: A 342 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6633 (ttm170) REVERT: A 383 LYS cc_start: 0.8271 (ttpp) cc_final: 0.8033 (tttp) REVERT: A 487 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7009 (ptm160) REVERT: A 547 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.5790 (mpp) REVERT: A 598 GLN cc_start: 0.7134 (pp30) cc_final: 0.6661 (mt0) REVERT: A 722 HIS cc_start: 0.6837 (t70) cc_final: 0.6441 (m-70) REVERT: A 896 GLU cc_start: 0.6880 (pt0) cc_final: 0.6624 (mm-30) REVERT: A 949 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8108 (mp) REVERT: A 985 LYS cc_start: 0.8192 (mttp) cc_final: 0.7865 (mttt) outliers start: 38 outliers final: 12 residues processed: 134 average time/residue: 0.6690 time to fit residues: 94.6918 Evaluate side-chains 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 547 MET 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 642 TYR Chi-restraints excluded: chain A residue 726 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.183173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153720 restraints weight = 7982.353| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.94 r_work: 0.3427 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8912 Z= 0.162 Angle : 0.559 9.046 12175 Z= 0.298 Chirality : 0.042 0.188 1315 Planarity : 0.004 0.027 1453 Dihedral : 15.938 114.689 1424 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.61 % Allowed : 17.27 % Favored : 79.12 % 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: 1.23 (0.26), residues: 982 helix: 1.67 (0.23), residues: 465 sheet: -0.35 (0.38), residues: 170 loop : 0.44 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 185 TYR 0.016 0.001 TYR A 692 PHE 0.009 0.001 PHE A 294 TRP 0.028 0.002 TRP A 856 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8912) covalent geometry : angle 0.55896 (12175) hydrogen bonds : bond 0.04265 ( 466) hydrogen bonds : angle 4.56381 ( 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 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 111 time to evaluate : 0.355 Fit side-chains REVERT: A 20 GLN cc_start: 0.7580 (tp-100) cc_final: 0.7266 (tm-30) REVERT: A 64 ARG cc_start: 0.7818 (mtp180) cc_final: 0.7585 (mtp85) REVERT: A 109 MET cc_start: 0.8570 (mmt) cc_final: 0.8146 (mmt) REVERT: A 133 ARG cc_start: 0.7466 (ttt90) cc_final: 0.7174 (ttt180) REVERT: A 142 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6629 (mmp) REVERT: A 145 ASN cc_start: 0.6094 (m-40) cc_final: 0.5676 (t0) REVERT: A 191 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: A 215 TYR cc_start: 0.7307 (t80) cc_final: 0.7058 (t80) REVERT: A 229 ASN cc_start: 0.7688 (OUTLIER) cc_final: 0.7460 (m-40) REVERT: A 285 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7421 (mtm180) REVERT: A 316 GLU cc_start: 0.7523 (tt0) cc_final: 0.7238 (mp0) REVERT: A 342 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6630 (ttm170) REVERT: A 383 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7924 (tttp) REVERT: A 487 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6989 (ptm160) REVERT: A 547 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.5817 (mpp) REVERT: A 598 GLN cc_start: 0.7144 (pp30) cc_final: 0.6642 (mt0) REVERT: A 619 GLU cc_start: 0.7040 (tp30) cc_final: 0.6826 (tp30) REVERT: A 722 HIS cc_start: 0.6869 (t70) cc_final: 0.6450 (m-70) REVERT: A 730 LYS cc_start: 0.7105 (ttpp) cc_final: 0.6461 (tmmt) REVERT: A 854 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: A 896 GLU cc_start: 0.6889 (pt0) cc_final: 0.6604 (mm-30) REVERT: A 949 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8117 (mp) REVERT: A 985 LYS cc_start: 0.8229 (mttp) cc_final: 0.7918 (mttt) outliers start: 32 outliers final: 12 residues processed: 129 average time/residue: 0.6559 time to fit residues: 89.4062 Evaluate side-chains 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 586 LEU 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 91 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.185186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.156398 restraints weight = 8051.398| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.91 r_work: 0.3458 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8912 Z= 0.136 Angle : 0.538 8.683 12175 Z= 0.287 Chirality : 0.041 0.178 1315 Planarity : 0.003 0.027 1453 Dihedral : 15.815 113.704 1424 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.05 % Allowed : 17.72 % Favored : 79.23 % 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: 1.26 (0.26), residues: 982 helix: 1.70 (0.23), residues: 468 sheet: -0.24 (0.38), residues: 171 loop : 0.38 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.013 0.001 TYR A 692 PHE 0.010 0.001 PHE A 283 TRP 0.029 0.001 TRP A 856 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8912) covalent geometry : angle 0.53766 (12175) hydrogen bonds : bond 0.04033 ( 466) hydrogen bonds : angle 4.50077 ( 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 145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.235 Fit side-chains REVERT: A 20 GLN cc_start: 0.7554 (tp-100) cc_final: 0.7270 (tm-30) REVERT: A 64 ARG cc_start: 0.7805 (mtp180) cc_final: 0.7574 (mtp85) REVERT: A 109 MET cc_start: 0.8551 (mmt) cc_final: 0.8019 (mmt) REVERT: A 133 ARG cc_start: 0.7424 (ttt90) cc_final: 0.7126 (ttt180) REVERT: A 142 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6533 (mmp) REVERT: A 145 ASN cc_start: 0.6047 (m-40) cc_final: 0.5642 (t0) REVERT: A 191 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7206 (pm20) REVERT: A 215 TYR cc_start: 0.7255 (t80) cc_final: 0.7016 (t80) REVERT: A 229 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7442 (m-40) REVERT: A 237 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.8894 (ptm) REVERT: A 285 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7436 (mtm180) REVERT: A 316 GLU cc_start: 0.7471 (tt0) cc_final: 0.7204 (mp0) REVERT: A 342 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6683 (ttm170) REVERT: A 383 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7992 (tttp) REVERT: A 487 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6788 (ptm160) REVERT: A 598 GLN cc_start: 0.7135 (pp30) cc_final: 0.6642 (mt0) REVERT: A 619 GLU cc_start: 0.7046 (tp30) cc_final: 0.6762 (tp30) REVERT: A 722 HIS cc_start: 0.6796 (t70) cc_final: 0.6471 (m90) REVERT: A 896 GLU cc_start: 0.6850 (pt0) cc_final: 0.6516 (mm-30) REVERT: A 949 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8052 (mp) REVERT: A 985 LYS cc_start: 0.8193 (mttp) cc_final: 0.7887 (mttt) outliers start: 27 outliers final: 13 residues processed: 131 average time/residue: 0.5904 time to fit residues: 81.8945 Evaluate side-chains 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 586 LEU 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 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 Chi-restraints excluded: chain A residue 960 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 474 HIS A 573 ASN ** A 959 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 = 0.4112 r_free = 0.4112 target = 0.186738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.157544 restraints weight = 7968.124| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.91 r_work: 0.3480 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8912 Z= 0.127 Angle : 0.540 9.654 12175 Z= 0.288 Chirality : 0.041 0.220 1315 Planarity : 0.003 0.027 1453 Dihedral : 15.717 112.196 1424 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.14 % Allowed : 18.74 % Favored : 79.12 % 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: 1.25 (0.26), residues: 982 helix: 1.73 (0.23), residues: 468 sheet: -0.37 (0.38), residues: 166 loop : 0.38 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.015 0.001 TYR A 717 PHE 0.010 0.001 PHE A 240 TRP 0.034 0.002 TRP A 856 HIS 0.008 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8912) covalent geometry : angle 0.54028 (12175) hydrogen bonds : bond 0.03953 ( 466) hydrogen bonds : angle 4.46910 ( 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 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.248 Fit side-chains REVERT: A 64 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7807 (mtp85) REVERT: A 109 MET cc_start: 0.8616 (mmt) cc_final: 0.8123 (mmt) REVERT: A 133 ARG cc_start: 0.7589 (ttt90) cc_final: 0.7290 (ttt180) REVERT: A 142 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6472 (mmp) REVERT: A 145 ASN cc_start: 0.6083 (m-40) cc_final: 0.5664 (t0) REVERT: A 191 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7287 (pm20) REVERT: A 215 TYR cc_start: 0.7255 (t80) cc_final: 0.6988 (t80) REVERT: A 229 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7397 (m-40) REVERT: A 237 MET cc_start: 0.9331 (OUTLIER) cc_final: 0.9053 (ptm) REVERT: A 285 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7510 (mtm180) REVERT: A 316 GLU cc_start: 0.7789 (tt0) cc_final: 0.7339 (mp0) REVERT: A 342 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.6786 (ttm170) REVERT: A 383 LYS cc_start: 0.8323 (ttpp) cc_final: 0.8015 (tttp) REVERT: A 598 GLN cc_start: 0.7268 (pp30) cc_final: 0.6644 (mt0) REVERT: A 619 GLU cc_start: 0.7180 (tp30) cc_final: 0.6930 (tp30) REVERT: A 623 ARG cc_start: 0.8001 (ttp80) cc_final: 0.7695 (ptp90) REVERT: A 722 HIS cc_start: 0.6887 (t70) cc_final: 0.6532 (m90) REVERT: A 896 GLU cc_start: 0.7021 (pt0) cc_final: 0.6489 (mm-30) REVERT: A 949 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8045 (mp) REVERT: A 985 LYS cc_start: 0.8275 (mttp) cc_final: 0.7925 (mttt) outliers start: 19 outliers final: 11 residues processed: 126 average time/residue: 0.6043 time to fit residues: 80.7457 Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 142 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 586 LEU 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 828 ILE Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 949 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 85 optimal weight: 0.0670 chunk 86 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4096 r_free = 0.4096 target = 0.185707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152243 restraints weight = 7989.111| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.28 r_work: 0.3441 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8912 Z= 0.123 Angle : 0.536 9.603 12175 Z= 0.287 Chirality : 0.041 0.238 1315 Planarity : 0.003 0.027 1453 Dihedral : 15.588 110.680 1424 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.14 % Allowed : 18.51 % Favored : 79.35 % 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: 1.31 (0.26), residues: 982 helix: 1.79 (0.23), residues: 468 sheet: -0.34 (0.38), residues: 166 loop : 0.38 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.017 0.001 TYR A 717 PHE 0.010 0.001 PHE A 240 TRP 0.038 0.002 TRP A 856 HIS 0.005 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8912) covalent geometry : angle 0.53625 (12175) hydrogen bonds : bond 0.03873 ( 466) hydrogen bonds : angle 4.45010 ( 1325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3031.40 seconds wall clock time: 52 minutes 25.54 seconds (3145.54 seconds total)