Starting phenix.real_space_refine on Thu Jul 2 10:12:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k9t_36997/07_2026/8k9t_36997_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k9t_36997/07_2026/8k9t_36997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k9t_36997/07_2026/8k9t_36997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k9t_36997/07_2026/8k9t_36997.map" model { file = "/net/cci-nas-00/data/ceres_data/8k9t_36997/07_2026/8k9t_36997_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k9t_36997/07_2026/8k9t_36997_neut.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.107 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 33 5.16 5 C 5046 2.51 5 N 1276 2.21 5 O 1389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7747 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 961, 7520 Classifications: {'peptide': 961} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 61, 'TRANS': 899} Chain breaks: 3 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "A" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'05E': 1, 'CLR': 2, 'LYI': 1, 'MAN': 2, 'PA1': 1, 'PLM': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'80Y': 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: 1.80, per 1000 atoms: 0.23 Number of scatterers: 7747 At special positions: 0 Unit cell: (79.22, 91.336, 134.208, 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 33 16.00 P 3 15.00 O 1389 8.00 N 1276 7.00 C 5046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 449 " distance=2.04 Simple disulfide: pdb=" SG CYS A 574 " - pdb=" SG CYS A 606 " distance=2.03 Simple disulfide: pdb=" SG CYS A 729 " - pdb=" SG CYS A 793 " 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 215.7 milliseconds 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 46.0% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 146 through 170 removed outlier: 3.552A pdb=" N VAL A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.718A pdb=" N SER A 201 " --> pdb=" O ARG A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 237 through 251 Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 281 through 303 removed outlier: 3.640A pdb=" N LEU A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 365 through 384 removed outlier: 3.520A pdb=" N VAL A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.653A pdb=" N SER A 416 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 4.015A pdb=" N TRP A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 462 Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 610 through 613 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 645 through 649 Processing helix chain 'A' and resid 675 through 678 No H-bonds generated for 'chain 'A' and resid 675 through 678' Processing helix chain 'A' and resid 685 through 693 Processing helix chain 'A' and resid 777 through 781 removed outlier: 3.874A pdb=" N GLU A 781 " --> pdb=" O PRO A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 811 Processing helix chain 'A' and resid 811 through 817 removed outlier: 4.155A pdb=" N ARG A 815 " --> pdb=" O LYS A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 822 removed outlier: 3.532A pdb=" N ALA A 821 " --> pdb=" O THR A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 843 removed outlier: 3.667A pdb=" N ILE A 827 " --> pdb=" O PHE A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 858 removed outlier: 3.614A pdb=" N ARG A 857 " --> pdb=" O ASP A 853 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 872 Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 913 through 954 Processing helix chain 'A' and resid 985 through 993 removed outlier: 3.734A pdb=" N LEU A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 990 " --> pdb=" O LEU A 986 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 992 " --> pdb=" O PHE A 988 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 993 " --> pdb=" O LEU A 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 985 through 993' Processing helix chain 'A' and resid 995 through 1022 Processing helix chain 'A' and resid 1023 through 1042 Processing helix chain 'A' and resid 1043 through 1061 removed outlier: 3.500A pdb=" N ASN A1047 " --> pdb=" O ILE A1043 " (cutoff:3.500A) Proline residue: A1049 - end of helix Processing helix chain 'A' and resid 1067 through 1087 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1103 through 1125 removed outlier: 3.672A pdb=" N THR A1110 " --> pdb=" O LEU A1106 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A1111 " --> pdb=" O ARG A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1148 removed outlier: 4.399A pdb=" N GLN A1134 " --> pdb=" O TYR A1130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 removed outlier: 4.968A pdb=" N PHE A 268 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 222 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N PHE A 269 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A 224 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 271 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 226 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL A 321 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE A 351 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 323 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N MET A 353 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY A 325 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN A 348 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A 399 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 350 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE A 401 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR A 352 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 398 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL A 429 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N SER A 400 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 540 Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 528 removed outlier: 4.021A pdb=" N VAL A 524 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 668 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG A 526 " --> pdb=" O GLY A 666 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY A 666 " --> pdb=" O ARG A 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 679 through 681 removed outlier: 3.751A pdb=" N GLU A 749 " --> pdb=" O LEU A 744 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 694 through 698 removed outlier: 4.580A pdb=" N ALA A 719 " --> pdb=" O ASP A 804 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 1041 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1180 1.30 - 1.43: 2111 1.43 - 1.56: 4600 1.56 - 1.68: 7 1.68 - 1.81: 55 Bond restraints: 7953 Sorted by residual: bond pdb=" OA5 LYI A1506 " pdb=" PA6 LYI A1506 " ideal model delta sigma weight residual 1.659 1.554 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CA ILE A 508 " pdb=" C ILE A 508 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.43e+01 bond pdb=" C PRO A 909 " pdb=" O PRO A 909 " ideal model delta sigma weight residual 1.238 1.179 0.059 1.24e-02 6.50e+03 2.24e+01 bond pdb=" O75 80Y B 101 " pdb=" P76 80Y B 101 " ideal model delta sigma weight residual 1.646 1.557 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C GLY A 905 " pdb=" O GLY A 905 " ideal model delta sigma weight residual 1.238 1.174 0.064 1.45e-02 4.76e+03 1.96e+01 ... (remaining 7948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 10576 2.73 - 5.46: 252 5.46 - 8.19: 23 8.19 - 10.92: 6 10.92 - 13.65: 1 Bond angle restraints: 10858 Sorted by residual: angle pdb=" N ALA A1150 " pdb=" CA ALA A1150 " pdb=" C ALA A1150 " ideal model delta sigma weight residual 113.16 99.51 13.65 1.24e+00 6.50e-01 1.21e+02 angle pdb=" C ASN A 230 " pdb=" N ALA A 231 " pdb=" CA ALA A 231 " ideal model delta sigma weight residual 122.40 131.96 -9.56 1.45e+00 4.76e-01 4.35e+01 angle pdb=" N HIS A 443 " pdb=" CA HIS A 443 " pdb=" C HIS A 443 " ideal model delta sigma weight residual 112.23 104.03 8.20 1.26e+00 6.30e-01 4.23e+01 angle pdb=" CA ASN A 230 " pdb=" CB ASN A 230 " pdb=" CG ASN A 230 " ideal model delta sigma weight residual 112.60 118.09 -5.49 1.00e+00 1.00e+00 3.01e+01 angle pdb=" N GLN A 907 " pdb=" CA GLN A 907 " pdb=" C GLN A 907 " ideal model delta sigma weight residual 112.88 106.48 6.40 1.29e+00 6.01e-01 2.46e+01 ... (remaining 10853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 4814 35.79 - 71.57: 105 71.57 - 107.36: 10 107.36 - 143.14: 1 143.14 - 178.92: 4 Dihedral angle restraints: 4934 sinusoidal: 2103 harmonic: 2831 Sorted by residual: dihedral pdb=" C THR A1149 " pdb=" N THR A1149 " pdb=" CA THR A1149 " pdb=" CB THR A1149 " ideal model delta harmonic sigma weight residual -122.00 -138.25 16.25 0 2.50e+00 1.60e-01 4.23e+01 dihedral pdb=" CA GLU A 746 " pdb=" C GLU A 746 " pdb=" N PRO A 747 " pdb=" CA PRO A 747 " ideal model delta harmonic sigma weight residual 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" N THR A1149 " pdb=" C THR A1149 " pdb=" CA THR A1149 " pdb=" CB THR A1149 " ideal model delta harmonic sigma weight residual 123.40 136.48 -13.08 0 2.50e+00 1.60e-01 2.74e+01 ... (remaining 4931 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1218 0.112 - 0.224: 52 0.224 - 0.336: 10 0.336 - 0.448: 1 0.448 - 0.560: 1 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA THR A1149 " pdb=" N THR A1149 " pdb=" C THR A1149 " pdb=" CB THR A1149 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" CA LEU A 903 " pdb=" N LEU A 903 " pdb=" C LEU A 903 " pdb=" CB LEU A 903 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA PRO A 909 " pdb=" N PRO A 909 " pdb=" C PRO A 909 " pdb=" CB PRO A 909 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1279 not shown) Planarity restraints: 1339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 229 " -0.020 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C GLY A 229 " 0.065 2.00e-02 2.50e+03 pdb=" O GLY A 229 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN A 230 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 379 " -0.026 2.00e-02 2.50e+03 2.36e-02 1.40e+01 pdb=" CG TRP A 379 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 379 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 379 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 379 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 379 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 379 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 379 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 379 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 379 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 330 " -0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C GLY A 330 " 0.056 2.00e-02 2.50e+03 pdb=" O GLY A 330 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 331 " -0.019 2.00e-02 2.50e+03 ... (remaining 1336 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1818 2.79 - 3.32: 7150 3.32 - 3.84: 13185 3.84 - 4.37: 16249 4.37 - 4.90: 27312 Nonbonded interactions: 65714 Sorted by model distance: nonbonded pdb=" NH2 ARG A 178 " pdb=" OE2 GLU A 634 " model vdw 2.261 3.120 nonbonded pdb=" OG SER A 716 " pdb=" NH2 ARG A 815 " model vdw 2.299 3.120 nonbonded pdb=" NH1 ARG A 741 " pdb=" OE1 GLN A 786 " model vdw 2.316 3.120 nonbonded pdb=" NE2 GLN A 835 " pdb=" O ILE A 846 " model vdw 2.334 3.120 nonbonded pdb=" OD2 ASP A 442 " pdb=" O4 MAN A1502 " model vdw 2.347 3.040 ... (remaining 65709 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.009 0.105 7962 Z= 0.485 Angle : 0.937 13.648 10864 Z= 0.578 Chirality : 0.059 0.560 1282 Planarity : 0.006 0.063 1339 Dihedral : 15.861 178.925 3087 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % Rotamer: Outliers : 0.97 % Allowed : 1.57 % Favored : 97.46 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 955 helix: 0.70 (0.26), residues: 369 sheet: 1.20 (0.43), residues: 147 loop : -0.26 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 220 TYR 0.013 0.002 TYR A 743 PHE 0.046 0.002 PHE A 845 TRP 0.064 0.003 TRP A 379 HIS 0.009 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00859 / 0.47 ( 7953) covalent geometry : angle 0.93700 / 0.58 (10858) SS BOND : bond 0.00511 / 0.32 ( 3) SS BOND : angle 0.82975 / 0.56 ( 6) hydrogen bonds : bond 0.17128 / 11.33 ( 375) hydrogen bonds : angle 7.12572 / 5.09 ( 1041) Misc. bond : bond 0.04578 / 3.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 175 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8178 (mtpp) REVERT: A 188 LYS cc_start: 0.8378 (ttpp) cc_final: 0.8113 (ttmm) REVERT: A 275 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: A 346 SER cc_start: 0.8838 (t) cc_final: 0.8599 (p) REVERT: A 386 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7814 (ptmt) REVERT: A 484 LYS cc_start: 0.7862 (tppt) cc_final: 0.7390 (tttm) REVERT: A 550 LYS cc_start: 0.7918 (mtpp) cc_final: 0.7607 (mttp) REVERT: A 568 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7871 (mtmm) REVERT: A 570 GLU cc_start: 0.7535 (tt0) cc_final: 0.7307 (tt0) REVERT: A 697 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7630 (ttm-80) REVERT: A 723 ARG cc_start: 0.7636 (mtp-110) cc_final: 0.7352 (ttm170) REVERT: A 774 MET cc_start: 0.7600 (ttm) cc_final: 0.6455 (mpt) REVERT: A 781 GLU cc_start: 0.7692 (pt0) cc_final: 0.7322 (mm-30) REVERT: A 871 THR cc_start: 0.8439 (m) cc_final: 0.8191 (m) REVERT: A 1013 ARG cc_start: 0.6745 (ttm170) cc_final: 0.5894 (ttt-90) REVERT: A 1015 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7930 (tm-30) outliers start: 8 outliers final: 4 residues processed: 142 average time/residue: 0.5660 time to fit residues: 84.7653 Evaluate side-chains 94 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 537 HIS A 608 ASN A 794 ASN A 798 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102833 restraints weight = 9248.361| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.03 r_work: 0.3198 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7962 Z= 0.162 Angle : 0.597 9.427 10864 Z= 0.304 Chirality : 0.043 0.134 1282 Planarity : 0.005 0.058 1339 Dihedral : 13.701 179.776 1382 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.99 % Favored : 97.91 % Rotamer: Outliers : 1.57 % Allowed : 7.62 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.27), residues: 955 helix: 1.57 (0.27), residues: 367 sheet: 0.92 (0.41), residues: 157 loop : 0.08 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 621 TYR 0.011 0.001 TYR A 996 PHE 0.021 0.001 PHE A 826 TRP 0.015 0.002 TRP A 379 HIS 0.004 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 7953) covalent geometry : angle 0.59734 / 0.30 (10858) SS BOND : bond 0.00282 / 0.19 ( 3) SS BOND : angle 0.25640 / 0.17 ( 6) hydrogen bonds : bond 0.04327 / 2.90 ( 375) hydrogen bonds : angle 5.19685 / 3.80 ( 1041) Misc. bond : bond 0.00165 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.178 Fit side-chains REVERT: A 246 ASN cc_start: 0.8439 (m110) cc_final: 0.7951 (m-40) REVERT: A 256 GLU cc_start: 0.7482 (tt0) cc_final: 0.6830 (pp20) REVERT: A 276 ASP cc_start: 0.7929 (m-30) cc_final: 0.7594 (m-30) REVERT: A 346 SER cc_start: 0.9006 (t) cc_final: 0.8741 (p) REVERT: A 386 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7811 (ptmt) REVERT: A 442 ASP cc_start: 0.8361 (m-30) cc_final: 0.8154 (m-30) REVERT: A 484 LYS cc_start: 0.8220 (tppt) cc_final: 0.7727 (tttm) REVERT: A 508 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6918 (mm) REVERT: A 521 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6877 (mm-30) REVERT: A 550 LYS cc_start: 0.8272 (mtpp) cc_final: 0.8034 (mtpt) REVERT: A 568 LYS cc_start: 0.8127 (mtmt) cc_final: 0.7790 (mtpm) REVERT: A 570 GLU cc_start: 0.7855 (tt0) cc_final: 0.7507 (tt0) REVERT: A 621 ARG cc_start: 0.7873 (mtm110) cc_final: 0.7552 (mtm-85) REVERT: A 697 ARG cc_start: 0.8134 (ttm-80) cc_final: 0.7460 (tpt170) REVERT: A 723 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7913 (ttp80) REVERT: A 774 MET cc_start: 0.7818 (ttm) cc_final: 0.6460 (mpt) REVERT: A 781 GLU cc_start: 0.7968 (pt0) cc_final: 0.7299 (mm-30) REVERT: A 938 ARG cc_start: 0.7513 (mmm-85) cc_final: 0.7273 (mmt-90) REVERT: A 994 ILE cc_start: 0.8405 (mm) cc_final: 0.7789 (tt) REVERT: A 1013 ARG cc_start: 0.7391 (ttm170) cc_final: 0.6230 (ttp-170) outliers start: 13 outliers final: 6 residues processed: 123 average time/residue: 0.4919 time to fit residues: 63.9051 Evaluate side-chains 108 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 837 GLN A 907 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098365 restraints weight = 9197.163| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.09 r_work: 0.3098 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7962 Z= 0.171 Angle : 0.555 5.892 10864 Z= 0.283 Chirality : 0.043 0.142 1282 Planarity : 0.005 0.059 1339 Dihedral : 12.569 172.635 1377 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.88 % Favored : 98.01 % Rotamer: Outliers : 1.45 % Allowed : 9.43 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.28), residues: 955 helix: 1.79 (0.27), residues: 370 sheet: 0.62 (0.39), residues: 171 loop : 0.25 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1022 TYR 0.013 0.001 TYR A 996 PHE 0.019 0.001 PHE A 826 TRP 0.017 0.002 TRP A1153 HIS 0.003 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 7953) covalent geometry : angle 0.55543 / 0.28 (10858) SS BOND : bond 0.00226 / 0.14 ( 3) SS BOND : angle 0.22511 / 0.16 ( 6) hydrogen bonds : bond 0.04299 / 2.90 ( 375) hydrogen bonds : angle 5.02481 / 3.67 ( 1041) Misc. bond : bond 0.00131 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.182 Fit side-chains REVERT: A 140 ARG cc_start: 0.7593 (ttt180) cc_final: 0.7373 (ttt180) REVERT: A 256 GLU cc_start: 0.7432 (tt0) cc_final: 0.6901 (pp20) REVERT: A 339 MET cc_start: 0.9079 (mmm) cc_final: 0.8864 (mmp) REVERT: A 386 LYS cc_start: 0.8432 (ttmt) cc_final: 0.7804 (ptmt) REVERT: A 484 LYS cc_start: 0.8229 (tppt) cc_final: 0.7685 (tttm) REVERT: A 521 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6824 (mp0) REVERT: A 550 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7853 (mttp) REVERT: A 568 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7786 (mttm) REVERT: A 570 GLU cc_start: 0.7804 (tt0) cc_final: 0.7319 (tt0) REVERT: A 723 ARG cc_start: 0.8023 (mtp-110) cc_final: 0.7662 (ttp80) REVERT: A 774 MET cc_start: 0.7875 (ttm) cc_final: 0.6439 (mpt) REVERT: A 781 GLU cc_start: 0.7936 (pt0) cc_final: 0.7196 (mm-30) REVERT: A 903 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8240 (tt) REVERT: A 994 ILE cc_start: 0.8326 (mm) cc_final: 0.7709 (tt) REVERT: A 1013 ARG cc_start: 0.7321 (ttm170) cc_final: 0.6121 (ttp-170) REVERT: A 1079 ILE cc_start: 0.8268 (mm) cc_final: 0.8051 (mt) outliers start: 12 outliers final: 7 residues processed: 119 average time/residue: 0.5686 time to fit residues: 71.1271 Evaluate side-chains 108 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 758 GLN A 837 GLN A 907 GLN A1089 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.131735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.097607 restraints weight = 9292.147| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.12 r_work: 0.3121 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7962 Z= 0.170 Angle : 0.543 6.709 10864 Z= 0.275 Chirality : 0.043 0.136 1282 Planarity : 0.005 0.057 1339 Dihedral : 12.377 171.893 1375 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 1.69 % Allowed : 9.79 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.28), residues: 955 helix: 1.96 (0.27), residues: 369 sheet: 0.29 (0.38), residues: 188 loop : 0.40 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 621 TYR 0.013 0.001 TYR A 996 PHE 0.020 0.001 PHE A 826 TRP 0.012 0.001 TRP A 448 HIS 0.004 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 7953) covalent geometry : angle 0.54293 / 0.28 (10858) SS BOND : bond 0.00396 / 0.28 ( 3) SS BOND : angle 0.30105 / 0.24 ( 6) hydrogen bonds : bond 0.03990 / 2.69 ( 375) hydrogen bonds : angle 4.91491 / 3.59 ( 1041) Misc. bond : bond 0.00080 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.245 Fit side-chains REVERT: A 140 ARG cc_start: 0.7570 (ttt180) cc_final: 0.7269 (ttt180) REVERT: A 256 GLU cc_start: 0.7176 (tt0) cc_final: 0.6802 (pp20) REVERT: A 386 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7792 (ptmt) REVERT: A 484 LYS cc_start: 0.8244 (tppt) cc_final: 0.7761 (tttp) REVERT: A 495 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7120 (mt-10) REVERT: A 550 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7933 (mtpp) REVERT: A 568 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7886 (mtpp) REVERT: A 570 GLU cc_start: 0.7888 (tt0) cc_final: 0.7409 (tt0) REVERT: A 621 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7824 (mtm-85) REVERT: A 723 ARG cc_start: 0.8050 (mtp-110) cc_final: 0.7779 (ttp80) REVERT: A 774 MET cc_start: 0.7939 (ttm) cc_final: 0.6424 (mpt) REVERT: A 781 GLU cc_start: 0.7980 (pt0) cc_final: 0.7236 (mm-30) REVERT: A 903 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8226 (tt) REVERT: A 994 ILE cc_start: 0.8300 (mm) cc_final: 0.7672 (tt) REVERT: A 1013 ARG cc_start: 0.7313 (ttm170) cc_final: 0.6122 (ttp-170) REVERT: A 1079 ILE cc_start: 0.8370 (mm) cc_final: 0.8152 (mt) outliers start: 14 outliers final: 10 residues processed: 111 average time/residue: 0.5642 time to fit residues: 66.0482 Evaluate side-chains 111 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1076 MET Chi-restraints excluded: chain B residue 2 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 0.2980 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 758 GLN A 837 GLN A 907 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.101697 restraints weight = 9130.009| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.00 r_work: 0.3127 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7962 Z= 0.112 Angle : 0.491 6.764 10864 Z= 0.249 Chirality : 0.041 0.130 1282 Planarity : 0.004 0.056 1339 Dihedral : 12.028 172.588 1375 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 1.45 % Allowed : 11.25 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.28), residues: 955 helix: 2.18 (0.27), residues: 369 sheet: 0.32 (0.38), residues: 188 loop : 0.45 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 621 TYR 0.009 0.001 TYR A 743 PHE 0.015 0.001 PHE A 826 TRP 0.012 0.001 TRP A 448 HIS 0.003 0.000 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 7953) covalent geometry : angle 0.49130 / 0.25 (10858) SS BOND : bond 0.00112 / 0.07 ( 3) SS BOND : angle 0.32856 / 0.25 ( 6) hydrogen bonds : bond 0.03511 / 2.36 ( 375) hydrogen bonds : angle 4.74498 / 3.46 ( 1041) Misc. bond : bond 0.00058 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.222 Fit side-chains REVERT: A 256 GLU cc_start: 0.7097 (tt0) cc_final: 0.6608 (pp20) REVERT: A 386 LYS cc_start: 0.8414 (ttmt) cc_final: 0.7772 (ptmt) REVERT: A 484 LYS cc_start: 0.8191 (tppt) cc_final: 0.7760 (tttp) REVERT: A 495 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7178 (mt-10) REVERT: A 521 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6728 (tt0) REVERT: A 550 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7885 (mtpt) REVERT: A 568 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7733 (mtpp) REVERT: A 570 GLU cc_start: 0.7868 (tt0) cc_final: 0.7362 (tt0) REVERT: A 723 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7766 (ttp80) REVERT: A 774 MET cc_start: 0.7926 (ttm) cc_final: 0.6463 (mpt) REVERT: A 781 GLU cc_start: 0.7979 (pt0) cc_final: 0.7222 (mm-30) REVERT: A 903 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8249 (tt) REVERT: A 994 ILE cc_start: 0.8261 (mm) cc_final: 0.7595 (tt) REVERT: A 1013 ARG cc_start: 0.7253 (ttm170) cc_final: 0.6065 (ttp-170) REVERT: A 1076 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7619 (mmm) REVERT: A 1079 ILE cc_start: 0.8277 (mm) cc_final: 0.8056 (mt) outliers start: 12 outliers final: 4 residues processed: 111 average time/residue: 0.4923 time to fit residues: 57.6749 Evaluate side-chains 109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.0010 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 ASN A 837 GLN A 907 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100517 restraints weight = 9251.589| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.09 r_work: 0.3129 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7962 Z= 0.111 Angle : 0.498 6.819 10864 Z= 0.252 Chirality : 0.041 0.132 1282 Planarity : 0.004 0.055 1339 Dihedral : 11.852 173.503 1374 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 1.45 % Allowed : 11.49 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.28), residues: 955 helix: 2.34 (0.27), residues: 364 sheet: 0.28 (0.38), residues: 190 loop : 0.43 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 621 TYR 0.011 0.001 TYR A 743 PHE 0.016 0.001 PHE A 826 TRP 0.011 0.001 TRP A 448 HIS 0.003 0.000 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 7953) covalent geometry : angle 0.49600 / 0.25 (10858) SS BOND : bond 0.00477 / 0.32 ( 3) SS BOND : angle 1.89007 / 1.29 ( 6) hydrogen bonds : bond 0.03445 / 2.32 ( 375) hydrogen bonds : angle 4.70233 / 3.42 ( 1041) Misc. bond : bond 0.00051 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.180 Fit side-chains REVERT: A 256 GLU cc_start: 0.7153 (tt0) cc_final: 0.6639 (pp20) REVERT: A 484 LYS cc_start: 0.8225 (tppt) cc_final: 0.7822 (tttp) REVERT: A 495 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7179 (mt-10) REVERT: A 521 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6717 (tt0) REVERT: A 550 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7882 (mtpt) REVERT: A 568 LYS cc_start: 0.8194 (mtmt) cc_final: 0.7783 (mtpp) REVERT: A 570 GLU cc_start: 0.7895 (tt0) cc_final: 0.7406 (tt0) REVERT: A 621 ARG cc_start: 0.8042 (mtm110) cc_final: 0.7762 (mtm-85) REVERT: A 723 ARG cc_start: 0.8061 (mtp-110) cc_final: 0.7812 (ttp80) REVERT: A 734 ASP cc_start: 0.8358 (p0) cc_final: 0.8148 (p0) REVERT: A 774 MET cc_start: 0.7922 (ttm) cc_final: 0.6460 (mpt) REVERT: A 781 GLU cc_start: 0.8014 (pt0) cc_final: 0.7255 (mm-30) REVERT: A 903 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8277 (tt) REVERT: A 994 ILE cc_start: 0.8134 (mm) cc_final: 0.7503 (tt) REVERT: A 1013 ARG cc_start: 0.7329 (ttm170) cc_final: 0.6128 (ttp-170) REVERT: A 1076 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7665 (mmm) REVERT: A 1079 ILE cc_start: 0.8332 (mm) cc_final: 0.8109 (mt) outliers start: 12 outliers final: 5 residues processed: 111 average time/residue: 0.5135 time to fit residues: 60.3683 Evaluate side-chains 108 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 0.0670 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 ASN A 837 GLN A 907 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.133328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100860 restraints weight = 9170.449| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.01 r_work: 0.3118 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7962 Z= 0.134 Angle : 0.505 6.838 10864 Z= 0.256 Chirality : 0.041 0.132 1282 Planarity : 0.004 0.054 1339 Dihedral : 11.814 175.021 1374 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.78 % Favored : 98.12 % Rotamer: Outliers : 1.45 % Allowed : 11.73 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.28), residues: 955 helix: 2.31 (0.27), residues: 365 sheet: 0.37 (0.38), residues: 188 loop : 0.49 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 621 TYR 0.012 0.001 TYR A 996 PHE 0.018 0.001 PHE A 826 TRP 0.008 0.001 TRP A1042 HIS 0.002 0.000 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 7953) covalent geometry : angle 0.50374 / 0.26 (10858) SS BOND : bond 0.00431 / 0.29 ( 3) SS BOND : angle 1.78029 / 1.19 ( 6) hydrogen bonds : bond 0.03605 / 2.43 ( 375) hydrogen bonds : angle 4.72769 / 3.44 ( 1041) Misc. bond : bond 0.00059 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.284 Fit side-chains REVERT: A 256 GLU cc_start: 0.7137 (tt0) cc_final: 0.6628 (pp20) REVERT: A 339 MET cc_start: 0.9070 (mmm) cc_final: 0.8854 (mmp) REVERT: A 484 LYS cc_start: 0.8195 (tppt) cc_final: 0.7801 (tttp) REVERT: A 495 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7168 (mt-10) REVERT: A 521 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6775 (tt0) REVERT: A 550 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7794 (mtpt) REVERT: A 568 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7927 (mtpp) REVERT: A 570 GLU cc_start: 0.7908 (tt0) cc_final: 0.7441 (tt0) REVERT: A 624 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7787 (ttp80) REVERT: A 723 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7778 (ttp80) REVERT: A 734 ASP cc_start: 0.8340 (p0) cc_final: 0.8117 (p0) REVERT: A 774 MET cc_start: 0.7899 (ttm) cc_final: 0.6399 (mpt) REVERT: A 781 GLU cc_start: 0.7998 (pt0) cc_final: 0.7237 (mm-30) REVERT: A 903 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8217 (tt) REVERT: A 1013 ARG cc_start: 0.7280 (ttm170) cc_final: 0.6080 (ttp-170) REVERT: A 1076 MET cc_start: 0.7939 (OUTLIER) cc_final: 0.7677 (mmm) REVERT: A 1079 ILE cc_start: 0.8297 (mm) cc_final: 0.8074 (mt) outliers start: 12 outliers final: 5 residues processed: 108 average time/residue: 0.5189 time to fit residues: 59.3383 Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 44 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 ASN A 837 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100485 restraints weight = 9192.913| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.03 r_work: 0.3120 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7962 Z= 0.131 Angle : 0.503 7.123 10864 Z= 0.254 Chirality : 0.041 0.132 1282 Planarity : 0.004 0.054 1339 Dihedral : 11.760 175.445 1374 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 1.33 % Allowed : 12.09 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.28), residues: 955 helix: 2.32 (0.27), residues: 365 sheet: 0.37 (0.38), residues: 188 loop : 0.48 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 621 TYR 0.012 0.001 TYR A 996 PHE 0.018 0.001 PHE A 826 TRP 0.010 0.001 TRP A 448 HIS 0.003 0.000 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 7953) covalent geometry : angle 0.50158 / 0.25 (10858) SS BOND : bond 0.00380 / 0.24 ( 3) SS BOND : angle 1.42561 / 0.83 ( 6) hydrogen bonds : bond 0.03570 / 2.40 ( 375) hydrogen bonds : angle 4.70592 / 3.42 ( 1041) Misc. bond : bond 0.00061 / 0.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.244 Fit side-chains REVERT: A 256 GLU cc_start: 0.7159 (tt0) cc_final: 0.6683 (pp20) REVERT: A 339 MET cc_start: 0.9089 (mmm) cc_final: 0.8864 (mmp) REVERT: A 484 LYS cc_start: 0.8220 (tppt) cc_final: 0.7840 (tttp) REVERT: A 495 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7192 (mt-10) REVERT: A 521 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6804 (tt0) REVERT: A 550 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7851 (mtpt) REVERT: A 568 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7918 (mtpp) REVERT: A 570 GLU cc_start: 0.8005 (tt0) cc_final: 0.7499 (tt0) REVERT: A 621 ARG cc_start: 0.8061 (mtm110) cc_final: 0.7785 (mtm-85) REVERT: A 624 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7843 (ttp80) REVERT: A 723 ARG cc_start: 0.8026 (mtp-110) cc_final: 0.7794 (ttp80) REVERT: A 734 ASP cc_start: 0.8312 (p0) cc_final: 0.8095 (p0) REVERT: A 774 MET cc_start: 0.7918 (ttm) cc_final: 0.6428 (mpt) REVERT: A 781 GLU cc_start: 0.8007 (pt0) cc_final: 0.7268 (mm-30) REVERT: A 903 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8250 (tt) REVERT: A 994 ILE cc_start: 0.8100 (mm) cc_final: 0.7469 (tt) REVERT: A 1013 ARG cc_start: 0.7327 (ttm170) cc_final: 0.6131 (ttp-170) REVERT: A 1076 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7690 (mmm) REVERT: A 1079 ILE cc_start: 0.8328 (mm) cc_final: 0.8105 (mt) outliers start: 11 outliers final: 6 residues processed: 106 average time/residue: 0.5350 time to fit residues: 59.8929 Evaluate side-chains 105 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 ASN A 837 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.133735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101004 restraints weight = 9138.566| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.03 r_work: 0.3128 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7962 Z= 0.122 Angle : 0.495 7.092 10864 Z= 0.250 Chirality : 0.041 0.131 1282 Planarity : 0.004 0.054 1339 Dihedral : 11.589 175.470 1374 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.88 % Favored : 98.01 % Rotamer: Outliers : 1.21 % Allowed : 12.33 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.28), residues: 955 helix: 2.37 (0.27), residues: 365 sheet: 0.37 (0.38), residues: 188 loop : 0.48 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 621 TYR 0.011 0.001 TYR A 996 PHE 0.017 0.001 PHE A 826 TRP 0.010 0.001 TRP A 448 HIS 0.002 0.000 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 7953) covalent geometry : angle 0.49409 / 0.25 (10858) SS BOND : bond 0.00330 / 0.22 ( 3) SS BOND : angle 1.31795 / 0.78 ( 6) hydrogen bonds : bond 0.03472 / 2.34 ( 375) hydrogen bonds : angle 4.68471 / 3.41 ( 1041) Misc. bond : bond 0.00054 / 0.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.242 Fit side-chains REVERT: A 256 GLU cc_start: 0.7152 (tt0) cc_final: 0.6664 (pp20) REVERT: A 275 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: A 339 MET cc_start: 0.9048 (mmm) cc_final: 0.8817 (mmp) REVERT: A 484 LYS cc_start: 0.8229 (tppt) cc_final: 0.7846 (tttp) REVERT: A 495 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7171 (mt-10) REVERT: A 521 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6847 (tt0) REVERT: A 550 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7757 (mtpp) REVERT: A 568 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7903 (mtpp) REVERT: A 570 GLU cc_start: 0.8003 (tt0) cc_final: 0.7510 (tt0) REVERT: A 621 ARG cc_start: 0.8063 (mtm110) cc_final: 0.7779 (mtm-85) REVERT: A 624 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7848 (ttp80) REVERT: A 723 ARG cc_start: 0.8002 (mtp-110) cc_final: 0.7787 (ttp80) REVERT: A 734 ASP cc_start: 0.8339 (p0) cc_final: 0.8119 (p0) REVERT: A 774 MET cc_start: 0.7917 (ttm) cc_final: 0.6425 (mpt) REVERT: A 781 GLU cc_start: 0.8001 (pt0) cc_final: 0.7261 (mm-30) REVERT: A 903 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8256 (tt) REVERT: A 1013 ARG cc_start: 0.7310 (ttm170) cc_final: 0.6118 (ttp-170) REVERT: A 1073 PHE cc_start: 0.7746 (m-10) cc_final: 0.7395 (m-10) REVERT: A 1076 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7699 (mmm) REVERT: A 1079 ILE cc_start: 0.8323 (mm) cc_final: 0.8100 (mt) REVERT: A 1093 ARG cc_start: 0.8285 (ttt180) cc_final: 0.8054 (ttp80) outliers start: 10 outliers final: 6 residues processed: 104 average time/residue: 0.5698 time to fit residues: 62.4910 Evaluate side-chains 106 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1052 VAL Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 78 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 52 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 ASN A 837 GLN A1056 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102017 restraints weight = 9123.414| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.03 r_work: 0.3170 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7962 Z= 0.104 Angle : 0.478 5.369 10864 Z= 0.243 Chirality : 0.040 0.130 1282 Planarity : 0.004 0.054 1339 Dihedral : 11.318 175.682 1374 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Rotamer: Outliers : 1.09 % Allowed : 12.45 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.28), residues: 955 helix: 2.39 (0.27), residues: 367 sheet: 0.36 (0.38), residues: 188 loop : 0.40 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 621 TYR 0.010 0.001 TYR A 996 PHE 0.014 0.001 PHE A 826 TRP 0.011 0.001 TRP A 448 HIS 0.002 0.000 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 ( 7953) covalent geometry : angle 0.47730 / 0.24 (10858) SS BOND : bond 0.00241 / 0.16 ( 3) SS BOND : angle 0.99752 / 0.61 ( 6) hydrogen bonds : bond 0.03293 / 2.21 ( 375) hydrogen bonds : angle 4.62064 / 3.35 ( 1041) Misc. bond : bond 0.00046 / 0.03 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1910 Ramachandran restraints generated. 955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.223 Fit side-chains REVERT: A 256 GLU cc_start: 0.7146 (tt0) cc_final: 0.6631 (pp20) REVERT: A 339 MET cc_start: 0.9036 (mmm) cc_final: 0.8833 (mmp) REVERT: A 484 LYS cc_start: 0.8231 (tppt) cc_final: 0.7869 (tttp) REVERT: A 495 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7202 (mt-10) REVERT: A 521 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6891 (tt0) REVERT: A 550 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7781 (mtpp) REVERT: A 568 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7917 (mtpp) REVERT: A 570 GLU cc_start: 0.7999 (tt0) cc_final: 0.7536 (tt0) REVERT: A 621 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7789 (mtm-85) REVERT: A 624 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7733 (ttp80) REVERT: A 734 ASP cc_start: 0.8348 (p0) cc_final: 0.8138 (p0) REVERT: A 774 MET cc_start: 0.7904 (ttm) cc_final: 0.6420 (mpt) REVERT: A 781 GLU cc_start: 0.8007 (pt0) cc_final: 0.7283 (mm-30) REVERT: A 837 GLN cc_start: 0.8016 (mt0) cc_final: 0.7774 (mt0) REVERT: A 903 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 994 ILE cc_start: 0.8053 (mm) cc_final: 0.7410 (tt) REVERT: A 1013 ARG cc_start: 0.7315 (ttm170) cc_final: 0.6139 (ttp-170) REVERT: A 1073 PHE cc_start: 0.7692 (m-10) cc_final: 0.7372 (m-10) REVERT: A 1076 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7726 (mmm) REVERT: A 1079 ILE cc_start: 0.8345 (mm) cc_final: 0.8120 (mt) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.4948 time to fit residues: 56.1935 Evaluate side-chains 104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 704 MET Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 1059 SER Chi-restraints excluded: chain A residue 1076 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 ASN A 758 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.133736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099831 restraints weight = 9144.276| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.10 r_work: 0.3148 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7962 Z= 0.130 Angle : 0.498 6.861 10864 Z= 0.252 Chirality : 0.041 0.131 1282 Planarity : 0.004 0.054 1339 Dihedral : 11.361 176.721 1374 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.57 % Favored : 98.32 % Rotamer: Outliers : 1.09 % Allowed : 12.70 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.28), residues: 955 helix: 2.35 (0.27), residues: 365 sheet: 0.44 (0.38), residues: 186 loop : 0.47 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 621 TYR 0.012 0.001 TYR A 996 PHE 0.019 0.001 PHE A 826 TRP 0.009 0.001 TRP A 448 HIS 0.003 0.000 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7953) covalent geometry : angle 0.49731 / 0.25 (10858) SS BOND : bond 0.00260 / 0.17 ( 3) SS BOND : angle 1.11440 / 0.69 ( 6) hydrogen bonds : bond 0.03498 / 2.35 ( 375) hydrogen bonds : angle 4.65934 / 3.38 ( 1041) Misc. bond : bond 0.00057 / 0.04 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2613.63 seconds wall clock time: 45 minutes 7.46 seconds (2707.46 seconds total)