Starting phenix.real_space_refine on Wed Mar 4 19:33:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6td6_10464/03_2026/6td6_10464_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6td6_10464/03_2026/6td6_10464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6td6_10464/03_2026/6td6_10464_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6td6_10464/03_2026/6td6_10464_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6td6_10464/03_2026/6td6_10464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6td6_10464/03_2026/6td6_10464.map" } resolution = 4.76 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= -0.014 sd= 0.473 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 5186 2.51 5 N 1259 2.21 5 O 1414 1.98 5 H 7766 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15680 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 13378 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 34, 'TRANS': 807} Chain breaks: 10 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2260 Classifications: {'peptide': 140} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 133} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.89, per 1000 atoms: 0.18 Number of scatterers: 15680 At special positions: 0 Unit cell: (117.04, 83.6, 95.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 O 1414 8.00 N 1259 7.00 C 5186 6.00 H 7766 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 323 " distance=2.02 Simple disulfide: pdb=" SG CYS A 295 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 781 " - pdb=" SG CYS A 801 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 828 " - pdb=" SG CYS A 843 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A1301 " - " ASN A 319 " " NAG C 1 " - " ASN A 767 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 604.5 milliseconds 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1878 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 62.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 19 through 41 removed outlier: 4.509A pdb=" N VAL A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 73 Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.636A pdb=" N TRP A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 286 Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 309 through 318 Processing helix chain 'A' and resid 326 through 341 removed outlier: 4.790A pdb=" N THR A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.590A pdb=" N THR A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 419 removed outlier: 3.957A pdb=" N VAL A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 467 removed outlier: 3.564A pdb=" N LEU A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 453 " --> pdb=" O TRP A 449 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 492 removed outlier: 3.877A pdb=" N THR A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 Processing helix chain 'A' and resid 505 through 511 Processing helix chain 'A' and resid 515 through 531 removed outlier: 4.229A pdb=" N PHE A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 588 removed outlier: 5.216A pdb=" N ALA A 572 " --> pdb=" O ARG A 568 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER A 573 " --> pdb=" O HIS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 593 through 628 removed outlier: 3.708A pdb=" N LYS A 597 " --> pdb=" O ILE A 593 " (cutoff:3.500A) Proline residue: A 619 - end of helix Processing helix chain 'A' and resid 649 through 669 removed outlier: 3.831A pdb=" N TYR A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 690 removed outlier: 3.568A pdb=" N TRP A 690 " --> pdb=" O VAL A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 718 removed outlier: 3.537A pdb=" N SER A 715 " --> pdb=" O PHE A 711 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS A 718 " --> pdb=" O TYR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 721 No H-bonds generated for 'chain 'A' and resid 719 through 721' Processing helix chain 'A' and resid 770 through 785 Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 837 through 854 Proline residue: A 845 - end of helix Processing helix chain 'A' and resid 916 through 935 Processing helix chain 'A' and resid 936 through 937 No H-bonds generated for 'chain 'A' and resid 936 through 937' Processing helix chain 'A' and resid 938 through 942 Processing helix chain 'A' and resid 950 through 982 removed outlier: 5.190A pdb=" N SER A 960 " --> pdb=" O GLN A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1010 removed outlier: 4.291A pdb=" N SER A 988 " --> pdb=" O ASN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1042 removed outlier: 3.680A pdb=" N SER A1018 " --> pdb=" O ASN A1014 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A1025 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY A1026 " --> pdb=" O SER A1022 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N PHE A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1076 removed outlier: 6.447A pdb=" N GLY A1060 " --> pdb=" O SER A1056 " (cutoff:3.500A) Proline residue: A1061 - end of helix Processing helix chain 'A' and resid 1081 through 1113 removed outlier: 4.399A pdb=" N LEU A1106 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N MET A1107 " --> pdb=" O THR A1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 159 through 177 removed outlier: 4.524A pdb=" N TYR B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER B 172 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 214 through 216 No H-bonds generated for 'chain 'B' and resid 214 through 216' Processing helix chain 'B' and resid 217 through 228 Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AA2, first strand: chain 'A' and resid 790 through 791 removed outlier: 3.625A pdb=" N GLU A 907 " --> pdb=" O LYS A 791 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS A 865 " --> pdb=" O LYS A 900 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 902 " --> pdb=" O GLY A 863 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLY A 863 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 790 through 791 removed outlier: 3.625A pdb=" N GLU A 907 " --> pdb=" O LYS A 791 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N PHE A 906 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N PHE A 739 " --> pdb=" O PHE A 906 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER A 908 " --> pdb=" O MET A 737 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N MET A 737 " --> pdb=" O SER A 908 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N VAL A 910 " --> pdb=" O MET A 735 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 138 Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 145 removed outlier: 6.100A pdb=" N LEU B 145 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLU B 186 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL B 184 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA B 209 " --> pdb=" O VAL B 184 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7752 1.03 - 1.23: 20 1.23 - 1.42: 3523 1.42 - 1.62: 4509 1.62 - 1.82: 86 Bond restraints: 15890 Sorted by residual: bond pdb=" CB TRP A1011 " pdb=" CG TRP A1011 " ideal model delta sigma weight residual 1.498 1.415 0.083 3.10e-02 1.04e+03 7.09e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.37e+00 bond pdb=" CG1 ILE A1058 " pdb=" CD1 ILE A1058 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.91e+00 bond pdb=" C PHE A 894 " pdb=" N THR A 895 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.37e-02 5.33e+03 5.62e+00 bond pdb=" C SER A 247 " pdb=" N SER A 248 " ideal model delta sigma weight residual 1.331 1.378 -0.047 2.07e-02 2.33e+03 5.13e+00 ... (remaining 15885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.39: 28614 9.39 - 18.79: 3 18.79 - 28.18: 1 28.18 - 37.58: 0 37.58 - 46.97: 2 Bond angle restraints: 28620 Sorted by residual: angle pdb="HD21 ASN A 319 " pdb=" ND2 ASN A 319 " pdb="HD22 ASN A 319 " ideal model delta sigma weight residual 120.00 73.03 46.97 3.00e+00 1.11e-01 2.45e+02 angle pdb=" CG ASN A 319 " pdb=" ND2 ASN A 319 " pdb="HD22 ASN A 319 " ideal model delta sigma weight residual 120.00 74.36 45.64 3.00e+00 1.11e-01 2.31e+02 angle pdb=" CG ASN A 319 " pdb=" ND2 ASN A 319 " pdb="HD21 ASN A 319 " ideal model delta sigma weight residual 120.00 147.36 -27.36 3.00e+00 1.11e-01 8.32e+01 angle pdb=" CA LEU A 409 " pdb=" C LEU A 409 " pdb=" N LEU A 410 " ideal model delta sigma weight residual 118.27 113.05 5.22 1.30e+00 5.92e-01 1.61e+01 angle pdb=" C VAL A 688 " pdb=" CA VAL A 688 " pdb=" CB VAL A 688 " ideal model delta sigma weight residual 112.24 107.17 5.07 1.34e+00 5.57e-01 1.43e+01 ... (remaining 28615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.21: 6929 25.21 - 50.43: 552 50.43 - 75.64: 95 75.64 - 100.86: 15 100.86 - 126.07: 10 Dihedral angle restraints: 7601 sinusoidal: 3970 harmonic: 3631 Sorted by residual: dihedral pdb=" CA LEU A 369 " pdb=" C LEU A 369 " pdb=" N ASN A 370 " pdb=" CA ASN A 370 " ideal model delta harmonic sigma weight residual -180.00 -135.06 -44.94 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA LYS A 699 " pdb=" C LYS A 699 " pdb=" N SER A 700 " pdb=" CA SER A 700 " ideal model delta harmonic sigma weight residual -180.00 -139.38 -40.62 0 5.00e+00 4.00e-02 6.60e+01 dihedral pdb=" CB CYS A 295 " pdb=" SG CYS A 295 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 147.48 -54.48 1 1.00e+01 1.00e-02 4.02e+01 ... (remaining 7598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 1260 0.329 - 0.658: 1 0.658 - 0.986: 0 0.986 - 1.315: 0 1.315 - 1.644: 1 Chirality restraints: 1262 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-02 2.50e+03 6.75e+03 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 319 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CB VAL A 518 " pdb=" CA VAL A 518 " pdb=" CG1 VAL A 518 " pdb=" CG2 VAL A 518 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1259 not shown) Planarity restraints: 2297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 771 " -0.044 5.00e-02 4.00e+02 6.74e-02 7.28e+00 pdb=" N PRO A 772 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 772 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 772 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 310 " -0.044 5.00e-02 4.00e+02 6.66e-02 7.10e+00 pdb=" N PRO A 311 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 614 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C MET A 614 " 0.043 2.00e-02 2.50e+03 pdb=" O MET A 614 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A 615 " -0.014 2.00e-02 2.50e+03 ... (remaining 2294 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 524 2.03 - 2.67: 26008 2.67 - 3.31: 49332 3.31 - 3.96: 58801 3.96 - 4.60: 89778 Nonbonded interactions: 224443 Sorted by model distance: nonbonded pdb=" O VAL A 606 " pdb=" HG1 THR A 609 " model vdw 1.385 2.450 nonbonded pdb=" O SER A 783 " pdb="HE21 GLN A 787 " model vdw 1.426 2.450 nonbonded pdb=" O GLN A 782 " pdb="HE21 GLN A 786 " model vdw 1.431 2.450 nonbonded pdb=" O THR A 66 " pdb="HD21 ASN A 70 " model vdw 1.444 2.450 nonbonded pdb=" O GLU A 626 " pdb=" H PHE A 629 " model vdw 1.445 2.450 ... (remaining 224438 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 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: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.600 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 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 : 0.010 0.095 8132 Z= 0.470 Angle : 1.248 40.613 11067 Z= 0.667 Chirality : 0.071 1.644 1262 Planarity : 0.007 0.067 1365 Dihedral : 17.681 126.071 2890 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 55.96 Ramachandran Plot: Outliers : 0.42 % Allowed : 22.80 % Favored : 76.78 % Rotamer: Outliers : 0.35 % Allowed : 11.83 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -6.33 (0.19), residues: 956 helix: -4.18 (0.13), residues: 517 sheet: -4.06 (0.80), residues: 26 loop : -4.15 (0.25), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 812 TYR 0.037 0.003 TYR A 487 PHE 0.035 0.003 PHE A 521 TRP 0.015 0.002 TRP A 617 HIS 0.008 0.002 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00977 ( 8124) covalent geometry : angle 1.11219 (11048) SS BOND : bond 0.00732 ( 5) SS BOND : angle 2.33378 ( 10) hydrogen bonds : bond 0.17199 ( 443) hydrogen bonds : angle 8.25705 ( 1281) link_BETA1-4 : bond 0.05977 ( 1) link_BETA1-4 : angle 33.85434 ( 3) link_NAG-ASN : bond 0.01616 ( 2) link_NAG-ASN : angle 3.86405 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.8138 (t80) cc_final: 0.7924 (t80) REVERT: A 613 LEU cc_start: 0.8547 (mm) cc_final: 0.7895 (tt) REVERT: A 840 PHE cc_start: 0.8983 (t80) cc_final: 0.8715 (t80) REVERT: A 1017 GLU cc_start: 0.9128 (mp0) cc_final: 0.8863 (mp0) REVERT: A 1084 TYR cc_start: 0.8205 (m-10) cc_final: 0.7995 (m-10) REVERT: A 1095 MET cc_start: 0.8025 (tpp) cc_final: 0.7734 (tpp) REVERT: A 1107 MET cc_start: 0.7647 (mmm) cc_final: 0.7439 (tmm) REVERT: B 122 LEU cc_start: 0.5019 (mp) cc_final: 0.4734 (tp) REVERT: B 230 PHE cc_start: 0.7394 (m-80) cc_final: 0.7179 (m-80) outliers start: 3 outliers final: 2 residues processed: 171 average time/residue: 0.1769 time to fit residues: 41.9247 Evaluate side-chains 129 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 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 10 ASN A 774 GLN A 838 HIS ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 GLN A 928 HIS ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 240 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.121454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.097640 restraints weight = 109974.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.100960 restraints weight = 65561.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.102865 restraints weight = 43885.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.104375 restraints weight = 33480.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.105356 restraints weight = 27303.690| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8132 Z= 0.200 Angle : 0.807 10.177 11067 Z= 0.426 Chirality : 0.045 0.325 1262 Planarity : 0.006 0.055 1365 Dihedral : 11.981 109.068 1114 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.13 % Favored : 87.76 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -4.66 (0.23), residues: 956 helix: -2.85 (0.17), residues: 542 sheet: -2.95 (0.79), residues: 36 loop : -3.29 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 238 TYR 0.026 0.002 TYR A 586 PHE 0.017 0.002 PHE A 470 TRP 0.018 0.002 TRP A 617 HIS 0.009 0.002 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 8124) covalent geometry : angle 0.79998 (11048) SS BOND : bond 0.00468 ( 5) SS BOND : angle 2.14288 ( 10) hydrogen bonds : bond 0.07418 ( 443) hydrogen bonds : angle 6.48105 ( 1281) link_BETA1-4 : bond 0.01618 ( 1) link_BETA1-4 : angle 1.50475 ( 3) link_NAG-ASN : bond 0.01796 ( 2) link_NAG-ASN : angle 3.89925 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.9688 (ttm-80) cc_final: 0.9420 (tpt90) REVERT: A 416 TRP cc_start: 0.8798 (m-10) cc_final: 0.8585 (m-10) REVERT: A 596 ILE cc_start: 0.8702 (mm) cc_final: 0.8319 (mm) REVERT: A 840 PHE cc_start: 0.9052 (t80) cc_final: 0.8773 (t80) REVERT: A 848 ILE cc_start: 0.8419 (mm) cc_final: 0.7988 (mt) REVERT: A 932 MET cc_start: 0.9136 (tpt) cc_final: 0.8725 (tpp) REVERT: A 1077 MET cc_start: 0.8351 (mmm) cc_final: 0.7233 (ppp) REVERT: A 1084 TYR cc_start: 0.8353 (m-10) cc_final: 0.8002 (m-10) REVERT: B 105 LYS cc_start: 0.7204 (mmtt) cc_final: 0.6662 (mttt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1659 time to fit residues: 40.3682 Evaluate side-chains 132 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN B 106 GLN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 HIS ** 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 = 0.4084 r_free = 0.4084 target = 0.122094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.097474 restraints weight = 107066.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.101071 restraints weight = 63675.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.103359 restraints weight = 42639.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.104866 restraints weight = 31855.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.105794 restraints weight = 25816.446| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8132 Z= 0.158 Angle : 0.689 7.986 11067 Z= 0.364 Chirality : 0.042 0.259 1262 Planarity : 0.005 0.051 1365 Dihedral : 8.858 85.186 1114 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.17 (0.25), residues: 956 helix: -1.53 (0.19), residues: 552 sheet: -2.54 (0.78), residues: 33 loop : -2.82 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1111 TYR 0.028 0.002 TYR B 100 PHE 0.021 0.002 PHE A 922 TRP 0.019 0.001 TRP A 463 HIS 0.004 0.001 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8124) covalent geometry : angle 0.67984 (11048) SS BOND : bond 0.00268 ( 5) SS BOND : angle 1.34089 ( 10) hydrogen bonds : bond 0.06048 ( 443) hydrogen bonds : angle 5.72716 ( 1281) link_BETA1-4 : bond 0.00716 ( 1) link_BETA1-4 : angle 3.76254 ( 3) link_NAG-ASN : bond 0.01370 ( 2) link_NAG-ASN : angle 3.92088 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.9721 (ttm-80) cc_final: 0.9435 (tpt90) REVERT: A 416 TRP cc_start: 0.8760 (m-10) cc_final: 0.8352 (m-10) REVERT: A 489 PHE cc_start: 0.9066 (t80) cc_final: 0.8752 (t80) REVERT: A 511 ILE cc_start: 0.9324 (mt) cc_final: 0.9005 (tt) REVERT: A 618 LEU cc_start: 0.9281 (tp) cc_final: 0.8660 (tp) REVERT: A 840 PHE cc_start: 0.9078 (t80) cc_final: 0.8796 (t80) REVERT: A 848 ILE cc_start: 0.8394 (mm) cc_final: 0.8014 (mt) REVERT: A 923 TYR cc_start: 0.8647 (t80) cc_final: 0.8336 (t80) REVERT: A 932 MET cc_start: 0.9293 (tpt) cc_final: 0.8897 (tpp) REVERT: A 1077 MET cc_start: 0.8454 (mmm) cc_final: 0.7143 (ppp) REVERT: A 1084 TYR cc_start: 0.8382 (m-10) cc_final: 0.7989 (m-10) REVERT: B 167 ASN cc_start: 0.8162 (m-40) cc_final: 0.7746 (t0) REVERT: B 230 PHE cc_start: 0.7384 (m-80) cc_final: 0.6968 (m-80) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1446 time to fit residues: 36.2774 Evaluate side-chains 127 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 96 optimal weight: 30.0000 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN ** A 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.117581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.093292 restraints weight = 108516.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.096691 restraints weight = 64181.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.098794 restraints weight = 43239.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.100093 restraints weight = 32635.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.100957 restraints weight = 27059.846| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8132 Z= 0.258 Angle : 0.768 8.803 11067 Z= 0.412 Chirality : 0.042 0.270 1262 Planarity : 0.005 0.051 1365 Dihedral : 8.496 69.322 1114 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.12 (0.25), residues: 956 helix: -1.46 (0.19), residues: 550 sheet: -3.15 (0.63), residues: 39 loop : -2.77 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 57 TYR 0.027 0.002 TYR A 291 PHE 0.021 0.002 PHE B 230 TRP 0.022 0.002 TRP A 463 HIS 0.005 0.001 HIS A1117 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 8124) covalent geometry : angle 0.75757 (11048) SS BOND : bond 0.00444 ( 5) SS BOND : angle 1.44699 ( 10) hydrogen bonds : bond 0.06312 ( 443) hydrogen bonds : angle 6.02597 ( 1281) link_BETA1-4 : bond 0.00389 ( 1) link_BETA1-4 : angle 4.16821 ( 3) link_NAG-ASN : bond 0.01297 ( 2) link_NAG-ASN : angle 4.25852 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.9189 (mmt) cc_final: 0.8859 (mmm) REVERT: A 292 ARG cc_start: 0.9720 (ttm-80) cc_final: 0.9427 (tpt90) REVERT: A 489 PHE cc_start: 0.9103 (t80) cc_final: 0.8875 (t80) REVERT: A 511 ILE cc_start: 0.9388 (mt) cc_final: 0.9119 (tt) REVERT: A 596 ILE cc_start: 0.8895 (mm) cc_final: 0.8547 (mm) REVERT: A 735 MET cc_start: 0.6856 (ttm) cc_final: 0.6413 (ttm) REVERT: A 840 PHE cc_start: 0.9141 (t80) cc_final: 0.8918 (t80) REVERT: A 932 MET cc_start: 0.9353 (tpt) cc_final: 0.8951 (tpp) REVERT: A 1077 MET cc_start: 0.8351 (mmm) cc_final: 0.7517 (ppp) REVERT: A 1084 TYR cc_start: 0.8606 (m-10) cc_final: 0.8306 (m-10) REVERT: A 1101 TYR cc_start: 0.8375 (m-80) cc_final: 0.8157 (m-80) REVERT: B 167 ASN cc_start: 0.8029 (m-40) cc_final: 0.7708 (t0) REVERT: B 189 ASP cc_start: 0.3771 (t0) cc_final: 0.2087 (t0) REVERT: B 206 VAL cc_start: 0.2828 (p) cc_final: 0.2611 (p) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1529 time to fit residues: 34.5967 Evaluate side-chains 122 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.117860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.093827 restraints weight = 109208.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.097239 restraints weight = 65070.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.099079 restraints weight = 43757.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.100534 restraints weight = 34011.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.101468 restraints weight = 27813.297| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8132 Z= 0.224 Angle : 0.722 9.340 11067 Z= 0.385 Chirality : 0.041 0.251 1262 Planarity : 0.005 0.050 1365 Dihedral : 8.016 59.906 1114 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.92 (0.25), residues: 956 helix: -1.25 (0.20), residues: 554 sheet: -3.11 (0.65), residues: 37 loop : -2.79 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1040 TYR 0.024 0.002 TYR A 291 PHE 0.024 0.002 PHE A 521 TRP 0.019 0.002 TRP A 463 HIS 0.008 0.001 HIS A 569 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 8124) covalent geometry : angle 0.71086 (11048) SS BOND : bond 0.00362 ( 5) SS BOND : angle 1.43466 ( 10) hydrogen bonds : bond 0.06113 ( 443) hydrogen bonds : angle 5.84502 ( 1281) link_BETA1-4 : bond 0.01013 ( 1) link_BETA1-4 : angle 4.24871 ( 3) link_NAG-ASN : bond 0.01226 ( 2) link_NAG-ASN : angle 4.40629 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.9150 (mmt) cc_final: 0.8810 (mmm) REVERT: A 292 ARG cc_start: 0.9721 (ttm-80) cc_final: 0.9448 (tpt90) REVERT: A 511 ILE cc_start: 0.9341 (mt) cc_final: 0.9003 (tt) REVERT: A 596 ILE cc_start: 0.8868 (mm) cc_final: 0.8483 (mt) REVERT: A 737 MET cc_start: 0.7371 (mpp) cc_final: 0.7133 (mpp) REVERT: A 932 MET cc_start: 0.9312 (tpt) cc_final: 0.8890 (tpp) REVERT: A 1076 MET cc_start: 0.8335 (tpp) cc_final: 0.7635 (tpp) REVERT: A 1077 MET cc_start: 0.8301 (mmm) cc_final: 0.7794 (ttp) REVERT: A 1095 MET cc_start: 0.8201 (tpp) cc_final: 0.7735 (tpt) REVERT: B 167 ASN cc_start: 0.7948 (m-40) cc_final: 0.7591 (t0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1613 time to fit residues: 35.4286 Evaluate side-chains 125 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 30.0000 chunk 81 optimal weight: 0.9990 chunk 92 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 437 ASN ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.121528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.095574 restraints weight = 105116.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099115 restraints weight = 61679.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.101462 restraints weight = 41386.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.103026 restraints weight = 31033.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.103928 restraints weight = 25153.674| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8132 Z= 0.132 Angle : 0.630 9.784 11067 Z= 0.328 Chirality : 0.040 0.198 1262 Planarity : 0.004 0.052 1365 Dihedral : 6.990 47.963 1114 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.84 (0.27), residues: 956 helix: -0.34 (0.21), residues: 556 sheet: -2.66 (0.70), residues: 37 loop : -2.41 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1057 TYR 0.033 0.001 TYR A 586 PHE 0.027 0.002 PHE A 521 TRP 0.016 0.001 TRP A 617 HIS 0.009 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8124) covalent geometry : angle 0.61827 (11048) SS BOND : bond 0.00287 ( 5) SS BOND : angle 0.98864 ( 10) hydrogen bonds : bond 0.05351 ( 443) hydrogen bonds : angle 5.21247 ( 1281) link_BETA1-4 : bond 0.00604 ( 1) link_BETA1-4 : angle 3.83590 ( 3) link_NAG-ASN : bond 0.01110 ( 2) link_NAG-ASN : angle 4.39209 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.9147 (mmt) cc_final: 0.8786 (mmm) REVERT: A 292 ARG cc_start: 0.9738 (ttm-80) cc_final: 0.9437 (tpt90) REVERT: A 416 TRP cc_start: 0.8765 (m-10) cc_final: 0.8308 (m-10) REVERT: A 431 MET cc_start: 0.8399 (ptp) cc_final: 0.7878 (pmm) REVERT: A 511 ILE cc_start: 0.9367 (mt) cc_final: 0.9100 (tt) REVERT: A 563 MET cc_start: 0.7582 (mtm) cc_final: 0.7100 (mmt) REVERT: A 596 ILE cc_start: 0.8823 (mm) cc_final: 0.8402 (mt) REVERT: A 613 LEU cc_start: 0.8833 (mm) cc_final: 0.8470 (tt) REVERT: A 840 PHE cc_start: 0.9325 (t80) cc_final: 0.8711 (t80) REVERT: A 932 MET cc_start: 0.9320 (tpt) cc_final: 0.8897 (tpp) REVERT: A 1051 THR cc_start: 0.8377 (m) cc_final: 0.7993 (m) REVERT: A 1076 MET cc_start: 0.8405 (tpp) cc_final: 0.7652 (tpt) REVERT: B 167 ASN cc_start: 0.7820 (m-40) cc_final: 0.7534 (t0) REVERT: B 230 PHE cc_start: 0.7231 (m-80) cc_final: 0.6911 (m-80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1669 time to fit residues: 41.0526 Evaluate side-chains 128 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 0.5980 chunk 51 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 54 optimal weight: 0.2980 chunk 97 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A1080 ASN B 200 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.120468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.096119 restraints weight = 102193.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.099689 restraints weight = 60089.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.101779 restraints weight = 40713.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.103293 restraints weight = 31273.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.104141 restraints weight = 25616.270| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8132 Z= 0.155 Angle : 0.636 10.633 11067 Z= 0.334 Chirality : 0.040 0.211 1262 Planarity : 0.004 0.050 1365 Dihedral : 6.601 42.426 1114 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.71 (0.27), residues: 956 helix: -0.20 (0.21), residues: 559 sheet: -2.41 (0.73), residues: 37 loop : -2.46 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.014 0.001 TYR A 291 PHE 0.020 0.002 PHE A1100 TRP 0.019 0.001 TRP A 463 HIS 0.004 0.001 HIS A1038 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8124) covalent geometry : angle 0.62278 (11048) SS BOND : bond 0.00398 ( 5) SS BOND : angle 1.15352 ( 10) hydrogen bonds : bond 0.05199 ( 443) hydrogen bonds : angle 5.22263 ( 1281) link_BETA1-4 : bond 0.00106 ( 1) link_BETA1-4 : angle 3.61755 ( 3) link_NAG-ASN : bond 0.00850 ( 2) link_NAG-ASN : angle 4.69878 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.9095 (mmt) cc_final: 0.8755 (mmm) REVERT: A 292 ARG cc_start: 0.9727 (ttm-80) cc_final: 0.9414 (tpt90) REVERT: A 431 MET cc_start: 0.8403 (ptp) cc_final: 0.7884 (pmm) REVERT: A 459 MET cc_start: 0.9124 (ttm) cc_final: 0.8745 (tpp) REVERT: A 511 ILE cc_start: 0.9347 (mt) cc_final: 0.9037 (tt) REVERT: A 563 MET cc_start: 0.7554 (mtm) cc_final: 0.7054 (mmt) REVERT: A 596 ILE cc_start: 0.8903 (mm) cc_final: 0.8522 (mt) REVERT: A 618 LEU cc_start: 0.9158 (tp) cc_final: 0.8876 (tp) REVERT: A 840 PHE cc_start: 0.9186 (t80) cc_final: 0.8629 (t80) REVERT: A 932 MET cc_start: 0.9294 (tpt) cc_final: 0.8881 (tpp) REVERT: B 167 ASN cc_start: 0.7896 (m-40) cc_final: 0.7521 (t0) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1599 time to fit residues: 38.0385 Evaluate side-chains 132 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 96 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 ASN B 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.121681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.097139 restraints weight = 102342.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.100895 restraints weight = 60239.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.103009 restraints weight = 40359.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104590 restraints weight = 30948.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.105443 restraints weight = 25278.262| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8132 Z= 0.133 Angle : 0.605 10.842 11067 Z= 0.316 Chirality : 0.039 0.203 1262 Planarity : 0.004 0.055 1365 Dihedral : 6.181 38.414 1114 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -1.28 (0.28), residues: 956 helix: 0.13 (0.21), residues: 560 sheet: -2.04 (0.72), residues: 39 loop : -2.27 (0.36), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 785 TYR 0.011 0.001 TYR A 291 PHE 0.020 0.001 PHE A 521 TRP 0.016 0.001 TRP A 463 HIS 0.008 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8124) covalent geometry : angle 0.59221 (11048) SS BOND : bond 0.00372 ( 5) SS BOND : angle 1.08116 ( 10) hydrogen bonds : bond 0.04911 ( 443) hydrogen bonds : angle 5.00853 ( 1281) link_BETA1-4 : bond 0.00323 ( 1) link_BETA1-4 : angle 3.40642 ( 3) link_NAG-ASN : bond 0.00959 ( 2) link_NAG-ASN : angle 4.70780 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8973 (mmt) cc_final: 0.8675 (mmm) REVERT: A 292 ARG cc_start: 0.9724 (ttm-80) cc_final: 0.9421 (tpt90) REVERT: A 416 TRP cc_start: 0.8717 (m-10) cc_final: 0.8125 (m-10) REVERT: A 431 MET cc_start: 0.8371 (ptp) cc_final: 0.7837 (pmm) REVERT: A 613 LEU cc_start: 0.8904 (mm) cc_final: 0.8593 (tt) REVERT: A 840 PHE cc_start: 0.9196 (t80) cc_final: 0.8658 (t80) REVERT: A 932 MET cc_start: 0.9249 (tpt) cc_final: 0.8848 (tpp) REVERT: A 1076 MET cc_start: 0.8340 (tpp) cc_final: 0.8052 (tpt) REVERT: B 167 ASN cc_start: 0.7975 (m-40) cc_final: 0.7593 (t0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1683 time to fit residues: 39.9216 Evaluate side-chains 133 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.122374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.097803 restraints weight = 102226.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.101572 restraints weight = 60487.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.103743 restraints weight = 40463.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.105257 restraints weight = 31135.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.106176 restraints weight = 25313.293| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8132 Z= 0.126 Angle : 0.593 11.146 11067 Z= 0.309 Chirality : 0.039 0.205 1262 Planarity : 0.004 0.054 1365 Dihedral : 5.795 37.685 1114 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.96 (0.28), residues: 956 helix: 0.42 (0.22), residues: 561 sheet: -1.93 (0.74), residues: 39 loop : -2.20 (0.37), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 785 TYR 0.011 0.001 TYR A 916 PHE 0.021 0.001 PHE A 470 TRP 0.019 0.001 TRP A 617 HIS 0.007 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8124) covalent geometry : angle 0.57948 (11048) SS BOND : bond 0.00271 ( 5) SS BOND : angle 0.77443 ( 10) hydrogen bonds : bond 0.04743 ( 443) hydrogen bonds : angle 4.85152 ( 1281) link_BETA1-4 : bond 0.00309 ( 1) link_BETA1-4 : angle 3.30727 ( 3) link_NAG-ASN : bond 0.00878 ( 2) link_NAG-ASN : angle 4.79253 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8971 (mmt) cc_final: 0.8672 (mmm) REVERT: A 292 ARG cc_start: 0.9710 (ttm-80) cc_final: 0.9411 (tpt90) REVERT: A 431 MET cc_start: 0.8357 (ptp) cc_final: 0.7829 (pmm) REVERT: A 459 MET cc_start: 0.9215 (ttm) cc_final: 0.8661 (tpp) REVERT: A 618 LEU cc_start: 0.9134 (tp) cc_final: 0.8898 (tp) REVERT: A 840 PHE cc_start: 0.9239 (t80) cc_final: 0.8684 (t80) REVERT: A 932 MET cc_start: 0.9275 (tpt) cc_final: 0.8886 (tpp) REVERT: A 1076 MET cc_start: 0.8423 (tpp) cc_final: 0.8166 (tpt) REVERT: A 1101 TYR cc_start: 0.8522 (m-80) cc_final: 0.8315 (m-10) REVERT: B 167 ASN cc_start: 0.7936 (m-40) cc_final: 0.7588 (t0) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1600 time to fit residues: 37.6280 Evaluate side-chains 136 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 51 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.0770 chunk 30 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A 503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.121206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.096855 restraints weight = 102960.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.100471 restraints weight = 61537.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.102477 restraints weight = 41708.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.103897 restraints weight = 31932.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.104841 restraints weight = 26216.409| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8132 Z= 0.151 Angle : 0.608 11.467 11067 Z= 0.320 Chirality : 0.039 0.221 1262 Planarity : 0.004 0.053 1365 Dihedral : 5.678 37.175 1114 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.93 (0.28), residues: 956 helix: 0.47 (0.22), residues: 561 sheet: -2.01 (0.72), residues: 39 loop : -2.24 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 785 TYR 0.037 0.001 TYR A 852 PHE 0.023 0.002 PHE A 470 TRP 0.019 0.001 TRP A 617 HIS 0.006 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8124) covalent geometry : angle 0.59377 (11048) SS BOND : bond 0.00279 ( 5) SS BOND : angle 0.81514 ( 10) hydrogen bonds : bond 0.04820 ( 443) hydrogen bonds : angle 4.92367 ( 1281) link_BETA1-4 : bond 0.00012 ( 1) link_BETA1-4 : angle 3.54999 ( 3) link_NAG-ASN : bond 0.00880 ( 2) link_NAG-ASN : angle 4.96186 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1912 Ramachandran restraints generated. 956 Oldfield, 0 Emsley, 956 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 327 is missing expected H atoms. Skipping. Residue ILE 492 is missing expected H atoms. Skipping. Residue SER 770 is missing expected H atoms. Skipping. Residue LYS 165 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8866 (mmt) cc_final: 0.8580 (mmm) REVERT: A 292 ARG cc_start: 0.9695 (ttm-80) cc_final: 0.9404 (tpt90) REVERT: A 431 MET cc_start: 0.8356 (ptp) cc_final: 0.7854 (pmm) REVERT: A 459 MET cc_start: 0.9200 (ttm) cc_final: 0.8640 (tpp) REVERT: A 618 LEU cc_start: 0.9105 (tp) cc_final: 0.8863 (tp) REVERT: A 735 MET cc_start: 0.6802 (ttm) cc_final: 0.6498 (ttm) REVERT: A 840 PHE cc_start: 0.9145 (t80) cc_final: 0.8623 (t80) REVERT: A 932 MET cc_start: 0.9228 (tpt) cc_final: 0.8816 (tpp) REVERT: A 1014 ASN cc_start: 0.7275 (m-40) cc_final: 0.6963 (t0) REVERT: A 1076 MET cc_start: 0.8395 (tpp) cc_final: 0.8082 (tpt) REVERT: B 167 ASN cc_start: 0.7970 (m-40) cc_final: 0.7653 (t0) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1660 time to fit residues: 38.6696 Evaluate side-chains 132 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 93 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN ** A1038 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.124892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.099850 restraints weight = 102734.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.103632 restraints weight = 61667.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.105830 restraints weight = 41929.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.107190 restraints weight = 32070.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.108235 restraints weight = 26765.806| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8132 Z= 0.114 Angle : 0.573 11.581 11067 Z= 0.296 Chirality : 0.039 0.200 1262 Planarity : 0.004 0.055 1365 Dihedral : 5.320 36.540 1114 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.41 (0.29), residues: 956 helix: 0.90 (0.22), residues: 561 sheet: -1.84 (0.74), residues: 39 loop : -2.04 (0.37), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 785 TYR 0.023 0.001 TYR A 852 PHE 0.026 0.001 PHE A 470 TRP 0.015 0.001 TRP A 617 HIS 0.008 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8124) covalent geometry : angle 0.55976 (11048) SS BOND : bond 0.00265 ( 5) SS BOND : angle 0.74144 ( 10) hydrogen bonds : bond 0.04478 ( 443) hydrogen bonds : angle 4.60486 ( 1281) link_BETA1-4 : bond 0.00017 ( 1) link_BETA1-4 : angle 2.84355 ( 3) link_NAG-ASN : bond 0.00842 ( 2) link_NAG-ASN : angle 4.90792 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2638.10 seconds wall clock time: 45 minutes 44.45 seconds (2744.45 seconds total)