Starting phenix.real_space_refine on Tue Feb 3 17:01:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0l_24108/02_2026/7n0l_24108.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0l_24108/02_2026/7n0l_24108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n0l_24108/02_2026/7n0l_24108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0l_24108/02_2026/7n0l_24108.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0l_24108/02_2026/7n0l_24108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0l_24108/02_2026/7n0l_24108.cif" } resolution = 2.8 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= 0.004 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 6 5.49 5 S 34 5.16 5 C 3460 2.51 5 N 868 2.21 5 O 902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5270 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2587 Classifications: {'peptide': 313} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2587 Classifications: {'peptide': 313} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.58, per 1000 atoms: 0.30 Number of scatterers: 5270 At special positions: 0 Unit cell: (101.97, 89.61, 88.58, 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 34 16.00 P 6 15.00 O 902 8.00 N 868 7.00 C 3460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 404.7 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 84.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 removed outlier: 3.728A pdb=" N TRP A 16 " --> pdb=" O CYS A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 67 removed outlier: 3.724A pdb=" N LYS A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 51 " --> pdb=" O CYS A 47 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.944A pdb=" N GLU A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.516A pdb=" N LEU A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 154 removed outlier: 3.504A pdb=" N LYS A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 185 removed outlier: 3.601A pdb=" N ASN A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 206 removed outlier: 3.816A pdb=" N VAL A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 250 removed outlier: 4.952A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 3.603A pdb=" N TRP A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 296 removed outlier: 3.691A pdb=" N GLY A 282 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 312 through 335 removed outlier: 3.911A pdb=" N ARG A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS A 334 " --> pdb=" O HIS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 21 removed outlier: 3.626A pdb=" N TRP B 16 " --> pdb=" O CYS B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 67 removed outlier: 3.765A pdb=" N LYS B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 51 " --> pdb=" O CYS B 47 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 83 through 98 removed outlier: 3.868A pdb=" N GLU B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.517A pdb=" N LEU B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 removed outlier: 3.506A pdb=" N LYS B 126 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 158 through 185 removed outlier: 3.601A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 206 removed outlier: 3.815A pdb=" N VAL B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA B 197 " --> pdb=" O TRP B 193 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 249 removed outlier: 4.954A pdb=" N ASN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLN B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 234 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 removed outlier: 3.607A pdb=" N TRP B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 296 removed outlier: 3.692A pdb=" N GLY B 282 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 293 " --> pdb=" O ASN B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 312 through 335 removed outlier: 3.930A pdb=" N ARG B 327 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS B 334 " --> pdb=" O HIS B 330 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1077 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: 1.00 Time building geometry restraints manager: 0.71 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: 784 1.30 - 1.43: 1602 1.43 - 1.55: 2960 1.55 - 1.68: 14 1.68 - 1.81: 52 Bond restraints: 5412 Sorted by residual: bond pdb=" C1B COA B 401 " pdb=" O4B COA B 401 " ideal model delta sigma weight residual 1.418 1.630 -0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C1B COA A 401 " pdb=" O4B COA A 401 " ideal model delta sigma weight residual 1.418 1.629 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C1B COA B 401 " pdb=" C2B COA B 401 " ideal model delta sigma weight residual 1.533 1.339 0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C1B COA A 401 " pdb=" C2B COA A 401 " ideal model delta sigma weight residual 1.533 1.340 0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" C4B COA A 401 " pdb=" O4B COA A 401 " ideal model delta sigma weight residual 1.453 1.308 0.145 2.00e-02 2.50e+03 5.26e+01 ... (remaining 5407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 7211 2.77 - 5.55: 83 5.55 - 8.32: 20 8.32 - 11.10: 4 11.10 - 13.87: 10 Bond angle restraints: 7328 Sorted by residual: angle pdb=" N1A COA B 401 " pdb=" C6A COA B 401 " pdb=" N6A COA B 401 " ideal model delta sigma weight residual 119.19 105.32 13.87 3.00e+00 1.11e-01 2.14e+01 angle pdb=" N1A COA A 401 " pdb=" C6A COA A 401 " pdb=" N6A COA A 401 " ideal model delta sigma weight residual 119.19 105.33 13.86 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C1B COA A 401 " pdb=" N9A COA A 401 " pdb=" C4A COA A 401 " ideal model delta sigma weight residual 129.16 116.15 13.01 3.00e+00 1.11e-01 1.88e+01 angle pdb=" C1B COA B 401 " pdb=" N9A COA B 401 " pdb=" C4A COA B 401 " ideal model delta sigma weight residual 129.16 116.19 12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C5A COA A 401 " pdb=" C6A COA A 401 " pdb=" N6A COA A 401 " ideal model delta sigma weight residual 122.68 134.33 -11.65 3.00e+00 1.11e-01 1.51e+01 ... (remaining 7323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 2544 16.12 - 32.24: 445 32.24 - 48.36: 136 48.36 - 64.48: 53 64.48 - 80.60: 14 Dihedral angle restraints: 3192 sinusoidal: 1354 harmonic: 1838 Sorted by residual: dihedral pdb=" CA ASN A 185 " pdb=" C ASN A 185 " pdb=" N GLY A 186 " pdb=" CA GLY A 186 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASN B 185 " pdb=" C ASN B 185 " pdb=" N GLY B 186 " pdb=" CA GLY B 186 " ideal model delta harmonic sigma weight residual 180.00 163.56 16.44 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA MET B 309 " pdb=" C MET B 309 " pdb=" N CYS B 310 " pdb=" CA CYS B 310 " ideal model delta harmonic sigma weight residual 180.00 164.22 15.78 0 5.00e+00 4.00e-02 9.96e+00 ... (remaining 3189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 383 0.024 - 0.049: 253 0.049 - 0.073: 116 0.073 - 0.098: 27 0.098 - 0.122: 5 Chirality restraints: 784 Sorted by residual: chirality pdb=" C1B COA A 401 " pdb=" C2B COA A 401 " pdb=" N9A COA A 401 " pdb=" O4B COA A 401 " both_signs ideal model delta sigma weight residual False 2.35 2.47 -0.12 2.00e-01 2.50e+01 3.72e-01 chirality pdb=" C1B COA B 401 " pdb=" C2B COA B 401 " pdb=" N9A COA B 401 " pdb=" O4B COA B 401 " both_signs ideal model delta sigma weight residual False 2.35 2.47 -0.12 2.00e-01 2.50e+01 3.68e-01 chirality pdb=" CA PRO B 300 " pdb=" N PRO B 300 " pdb=" C PRO B 300 " pdb=" CB PRO B 300 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.56e-01 ... (remaining 781 not shown) Planarity restraints: 894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 69 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 70 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 69 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 70 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 70 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 70 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 312 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO B 313 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.016 5.00e-02 4.00e+02 ... (remaining 891 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 223 2.73 - 3.27: 5457 3.27 - 3.81: 8674 3.81 - 4.36: 11578 4.36 - 4.90: 18490 Nonbonded interactions: 44422 Sorted by model distance: nonbonded pdb=" O GLN A 44 " pdb=" OG1 THR A 48 " model vdw 2.185 3.040 nonbonded pdb=" O GLN B 44 " pdb=" OG1 THR B 48 " model vdw 2.189 3.040 nonbonded pdb=" O LEU B 37 " pdb=" OG1 THR B 41 " model vdw 2.239 3.040 nonbonded pdb=" O LEU A 37 " pdb=" OG1 THR A 41 " model vdw 2.242 3.040 nonbonded pdb=" OE2 GLU A 28 " pdb=" NH2 ARG A 31 " model vdw 2.287 3.120 ... (remaining 44417 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.710 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.040 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 0.212 5412 Z= 0.464 Angle : 0.879 13.871 7328 Z= 0.376 Chirality : 0.037 0.122 784 Planarity : 0.003 0.045 894 Dihedral : 19.626 80.604 2004 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 9.23 % Allowed : 20.30 % Favored : 70.48 % 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: -6.10 (0.22), residues: 614 helix: -3.82 (0.14), residues: 530 sheet: None (None), residues: 0 loop : -3.06 (0.55), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 57 TYR 0.007 0.001 TYR A 239 PHE 0.007 0.001 PHE A 235 TRP 0.015 0.001 TRP B 192 HIS 0.002 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00940 ( 5412) covalent geometry : angle 0.87905 ( 7328) hydrogen bonds : bond 0.29318 ( 359) hydrogen bonds : angle 10.93533 ( 1077) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 73 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 39 GLU cc_start: 0.7926 (pp20) cc_final: 0.7366 (pp20) REVERT: A 77 MET cc_start: 0.5173 (mpt) cc_final: 0.4909 (mpt) REVERT: A 87 MET cc_start: 0.6170 (ppp) cc_final: 0.5926 (ppp) REVERT: A 327 ARG cc_start: 0.7612 (ttm170) cc_final: 0.7369 (mtt180) REVERT: B 20 GLN cc_start: 0.6717 (pp30) cc_final: 0.6515 (tt0) REVERT: B 39 GLU cc_start: 0.7932 (pp20) cc_final: 0.7376 (pp20) REVERT: B 84 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6914 (tp30) REVERT: B 87 MET cc_start: 0.5988 (ppp) cc_final: 0.5775 (ppp) REVERT: B 327 ARG cc_start: 0.7611 (ttm170) cc_final: 0.7239 (mtt180) outliers start: 50 outliers final: 25 residues processed: 123 average time/residue: 0.4373 time to fit residues: 56.0962 Evaluate side-chains 101 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 304 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN A 334 HIS ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN B 156 ASN B 334 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108006 restraints weight = 7020.275| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.65 r_work: 0.3275 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5412 Z= 0.134 Angle : 0.569 5.602 7328 Z= 0.299 Chirality : 0.038 0.144 784 Planarity : 0.005 0.031 894 Dihedral : 12.988 78.121 847 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 7.56 % Allowed : 20.30 % Favored : 72.14 % 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: -2.88 (0.28), residues: 614 helix: -1.63 (0.19), residues: 532 sheet: None (None), residues: 0 loop : -2.16 (0.55), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 188 TYR 0.010 0.001 TYR B 240 PHE 0.018 0.001 PHE A 333 TRP 0.022 0.001 TRP B 192 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5412) covalent geometry : angle 0.56949 ( 7328) hydrogen bonds : bond 0.04757 ( 359) hydrogen bonds : angle 4.83484 ( 1077) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.212 Fit side-chains REVERT: A 28 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6890 (tp30) REVERT: A 39 GLU cc_start: 0.7831 (pp20) cc_final: 0.7147 (pp20) REVERT: A 84 GLU cc_start: 0.7231 (tp30) cc_final: 0.6783 (tp30) REVERT: A 214 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8334 (mt) REVERT: A 239 TYR cc_start: 0.7276 (m-80) cc_final: 0.6671 (t80) REVERT: A 327 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7507 (mtt180) REVERT: B 39 GLU cc_start: 0.7794 (pp20) cc_final: 0.7132 (pp20) REVERT: B 84 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7083 (tp30) REVERT: B 135 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7753 (mttm) REVERT: B 214 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8338 (mt) REVERT: B 239 TYR cc_start: 0.7257 (m-80) cc_final: 0.6662 (t80) REVERT: B 327 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7503 (mtt180) outliers start: 41 outliers final: 17 residues processed: 121 average time/residue: 0.4680 time to fit residues: 58.7926 Evaluate side-chains 95 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107669 restraints weight = 7037.961| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.64 r_work: 0.3271 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5412 Z= 0.129 Angle : 0.543 5.969 7328 Z= 0.279 Chirality : 0.039 0.165 784 Planarity : 0.004 0.032 894 Dihedral : 10.824 82.502 818 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 6.64 % Allowed : 23.06 % Favored : 70.30 % 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: -0.72 (0.32), residues: 614 helix: -0.30 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -0.52 (0.79), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.009 0.001 TYR B 238 PHE 0.021 0.001 PHE B 333 TRP 0.020 0.001 TRP A 192 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5412) covalent geometry : angle 0.54329 ( 7328) hydrogen bonds : bond 0.04136 ( 359) hydrogen bonds : angle 4.22509 ( 1077) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.200 Fit side-chains REVERT: A 39 GLU cc_start: 0.7740 (pp20) cc_final: 0.7123 (pp20) REVERT: A 84 GLU cc_start: 0.7167 (tp30) cc_final: 0.6605 (tp30) REVERT: A 135 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7748 (mttm) REVERT: A 188 ARG cc_start: 0.8268 (mmt90) cc_final: 0.7748 (mtp180) REVERT: A 239 TYR cc_start: 0.7150 (m-80) cc_final: 0.6706 (t80) REVERT: A 241 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7886 (tp-100) REVERT: A 246 TYR cc_start: 0.8460 (m-80) cc_final: 0.8189 (m-80) REVERT: A 327 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7391 (mtt180) REVERT: B 31 ARG cc_start: 0.7718 (mtm110) cc_final: 0.6837 (mmm160) REVERT: B 39 GLU cc_start: 0.7744 (pp20) cc_final: 0.7125 (pp20) REVERT: B 84 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7130 (tp30) REVERT: B 87 MET cc_start: 0.7129 (ppp) cc_final: 0.6369 (ppp) REVERT: B 121 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8636 (mt) REVERT: B 135 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7726 (mttm) REVERT: B 188 ARG cc_start: 0.8253 (mmt90) cc_final: 0.7724 (mtp180) REVERT: B 239 TYR cc_start: 0.7120 (m-80) cc_final: 0.6750 (t80) REVERT: B 327 ARG cc_start: 0.8142 (ttm170) cc_final: 0.7458 (mtt180) outliers start: 36 outliers final: 13 residues processed: 118 average time/residue: 0.5795 time to fit residues: 70.8937 Evaluate side-chains 93 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 19 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 1 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.144368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112155 restraints weight = 7138.423| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.67 r_work: 0.3277 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5412 Z= 0.116 Angle : 0.517 6.136 7328 Z= 0.263 Chirality : 0.039 0.166 784 Planarity : 0.003 0.030 894 Dihedral : 9.753 84.715 815 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 4.98 % Allowed : 24.35 % Favored : 70.66 % 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: 0.43 (0.34), residues: 614 helix: 0.50 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.34 (0.81), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 188 TYR 0.009 0.001 TYR A 133 PHE 0.021 0.001 PHE A 333 TRP 0.019 0.001 TRP B 192 HIS 0.002 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5412) covalent geometry : angle 0.51701 ( 7328) hydrogen bonds : bond 0.03816 ( 359) hydrogen bonds : angle 3.99424 ( 1077) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.148 Fit side-chains REVERT: A 28 GLU cc_start: 0.7450 (tp30) cc_final: 0.7158 (tp30) REVERT: A 39 GLU cc_start: 0.7778 (pp20) cc_final: 0.7184 (pp20) REVERT: A 66 LYS cc_start: 0.7941 (ttpp) cc_final: 0.7704 (ptmm) REVERT: A 84 GLU cc_start: 0.7230 (tp30) cc_final: 0.6855 (tp30) REVERT: A 87 MET cc_start: 0.7097 (ppp) cc_final: 0.6533 (ppp) REVERT: A 135 LYS cc_start: 0.8051 (mtpt) cc_final: 0.7720 (mttm) REVERT: A 188 ARG cc_start: 0.8292 (mmt90) cc_final: 0.7781 (mtp180) REVERT: A 239 TYR cc_start: 0.7045 (m-80) cc_final: 0.6723 (t80) REVERT: A 241 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7806 (tp-100) REVERT: A 246 TYR cc_start: 0.8419 (m-80) cc_final: 0.8075 (m-80) REVERT: A 327 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7423 (mtt180) REVERT: B 31 ARG cc_start: 0.7559 (mtm110) cc_final: 0.6812 (mmm160) REVERT: B 87 MET cc_start: 0.7144 (ppp) cc_final: 0.6457 (ppp) REVERT: B 135 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7696 (mttm) REVERT: B 188 ARG cc_start: 0.8251 (mmt90) cc_final: 0.7731 (mtp180) REVERT: B 239 TYR cc_start: 0.6994 (m-80) cc_final: 0.6672 (t80) REVERT: B 327 ARG cc_start: 0.8070 (ttm170) cc_final: 0.7389 (mtt180) outliers start: 27 outliers final: 10 residues processed: 103 average time/residue: 0.5295 time to fit residues: 56.6869 Evaluate side-chains 87 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113353 restraints weight = 7381.726| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.72 r_work: 0.3282 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5412 Z= 0.112 Angle : 0.505 6.204 7328 Z= 0.256 Chirality : 0.039 0.175 784 Planarity : 0.003 0.029 894 Dihedral : 9.372 86.037 808 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.69 % Allowed : 27.49 % Favored : 68.82 % 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: 1.14 (0.34), residues: 614 helix: 1.01 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.32 (0.81), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.009 0.001 TYR A 133 PHE 0.024 0.001 PHE A 333 TRP 0.018 0.001 TRP B 192 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5412) covalent geometry : angle 0.50510 ( 7328) hydrogen bonds : bond 0.03695 ( 359) hydrogen bonds : angle 3.84466 ( 1077) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.200 Fit side-chains REVERT: A 28 GLU cc_start: 0.7413 (tp30) cc_final: 0.7160 (tp30) REVERT: A 84 GLU cc_start: 0.7265 (tp30) cc_final: 0.6935 (tp30) REVERT: A 93 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6400 (mt) REVERT: A 135 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7631 (mttm) REVERT: A 188 ARG cc_start: 0.8278 (mmt90) cc_final: 0.7742 (mtp180) REVERT: A 239 TYR cc_start: 0.6953 (m-80) cc_final: 0.6627 (t80) REVERT: A 241 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7712 (tp-100) REVERT: A 246 TYR cc_start: 0.8333 (m-80) cc_final: 0.7988 (m-80) REVERT: A 327 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7373 (mtt180) REVERT: B 31 ARG cc_start: 0.7421 (mtm110) cc_final: 0.6539 (mmm-85) REVERT: B 87 MET cc_start: 0.7187 (ppp) cc_final: 0.6754 (pp-130) REVERT: B 135 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7603 (mttm) REVERT: B 188 ARG cc_start: 0.8238 (mmt90) cc_final: 0.7693 (mtp180) REVERT: B 239 TYR cc_start: 0.6888 (m-80) cc_final: 0.6564 (t80) REVERT: B 327 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7405 (mtt180) outliers start: 20 outliers final: 8 residues processed: 97 average time/residue: 0.5304 time to fit residues: 53.5316 Evaluate side-chains 88 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 chunk 42 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 49 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.0524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.144507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111944 restraints weight = 7282.377| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.69 r_work: 0.3273 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5412 Z= 0.126 Angle : 0.532 8.947 7328 Z= 0.265 Chirality : 0.040 0.188 784 Planarity : 0.003 0.028 894 Dihedral : 9.422 86.543 808 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.51 % Allowed : 28.04 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.33), residues: 614 helix: 1.16 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.18 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.009 0.001 TYR A 133 PHE 0.025 0.001 PHE A 333 TRP 0.018 0.001 TRP B 192 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 5412) covalent geometry : angle 0.53159 ( 7328) hydrogen bonds : bond 0.03767 ( 359) hydrogen bonds : angle 3.83084 ( 1077) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.194 Fit side-chains REVERT: A 28 GLU cc_start: 0.7418 (tp30) cc_final: 0.7168 (tp30) REVERT: A 84 GLU cc_start: 0.7413 (tp30) cc_final: 0.6908 (tp30) REVERT: A 93 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6449 (mt) REVERT: A 135 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7670 (mttm) REVERT: A 188 ARG cc_start: 0.8304 (mmt90) cc_final: 0.7750 (mtp180) REVERT: A 239 TYR cc_start: 0.7043 (m-80) cc_final: 0.6664 (t80) REVERT: A 241 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7768 (tp-100) REVERT: A 246 TYR cc_start: 0.8311 (m-80) cc_final: 0.8015 (m-80) REVERT: A 327 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7413 (mtt180) REVERT: B 31 ARG cc_start: 0.7490 (mtm110) cc_final: 0.6762 (mmm160) REVERT: B 87 MET cc_start: 0.7136 (ppp) cc_final: 0.6685 (pp-130) REVERT: B 88 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7384 (mttm) REVERT: B 135 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7639 (mttm) REVERT: B 188 ARG cc_start: 0.8271 (mmt90) cc_final: 0.7704 (mtp180) REVERT: B 239 TYR cc_start: 0.7002 (m-80) cc_final: 0.6636 (t80) REVERT: B 327 ARG cc_start: 0.8088 (ttm170) cc_final: 0.7398 (mtt180) outliers start: 19 outliers final: 9 residues processed: 94 average time/residue: 0.5036 time to fit residues: 49.2113 Evaluate side-chains 89 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.146272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113858 restraints weight = 7187.758| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.68 r_work: 0.3294 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5412 Z= 0.106 Angle : 0.507 7.981 7328 Z= 0.251 Chirality : 0.039 0.195 784 Planarity : 0.003 0.028 894 Dihedral : 9.174 87.961 808 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.14 % Allowed : 28.78 % Favored : 68.08 % 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: 1.87 (0.34), residues: 614 helix: 1.53 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -0.29 (0.77), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 188 TYR 0.010 0.001 TYR A 133 PHE 0.026 0.001 PHE A 333 TRP 0.018 0.001 TRP B 192 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 5412) covalent geometry : angle 0.50670 ( 7328) hydrogen bonds : bond 0.03576 ( 359) hydrogen bonds : angle 3.73803 ( 1077) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.122 Fit side-chains REVERT: A 28 GLU cc_start: 0.7313 (tp30) cc_final: 0.7069 (tp30) REVERT: A 59 GLN cc_start: 0.7889 (mt0) cc_final: 0.7639 (mm110) REVERT: A 77 MET cc_start: 0.5064 (mpt) cc_final: 0.4750 (mpt) REVERT: A 84 GLU cc_start: 0.7373 (tp30) cc_final: 0.6767 (tp30) REVERT: A 87 MET cc_start: 0.7445 (ptp) cc_final: 0.7094 (ppp) REVERT: A 93 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6398 (mt) REVERT: A 135 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7671 (mttm) REVERT: A 138 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8202 (tp) REVERT: A 188 ARG cc_start: 0.8232 (mmt90) cc_final: 0.7754 (mtp180) REVERT: A 239 TYR cc_start: 0.6921 (m-80) cc_final: 0.6629 (t80) REVERT: A 246 TYR cc_start: 0.8330 (m-80) cc_final: 0.8011 (m-80) REVERT: A 327 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7421 (mtt180) REVERT: B 31 ARG cc_start: 0.7367 (mtm110) cc_final: 0.6572 (mmm-85) REVERT: B 59 GLN cc_start: 0.7942 (mt0) cc_final: 0.7652 (mm110) REVERT: B 87 MET cc_start: 0.7137 (ppp) cc_final: 0.6709 (pp-130) REVERT: B 88 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7380 (mttm) REVERT: B 135 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7645 (mttm) REVERT: B 188 ARG cc_start: 0.8214 (mmt90) cc_final: 0.7726 (mtp180) REVERT: B 239 TYR cc_start: 0.6904 (m-80) cc_final: 0.6603 (t80) REVERT: B 327 ARG cc_start: 0.8084 (ttm170) cc_final: 0.7405 (mtt180) outliers start: 17 outliers final: 9 residues processed: 92 average time/residue: 0.5747 time to fit residues: 54.8938 Evaluate side-chains 90 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.143231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110629 restraints weight = 7239.558| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.68 r_work: 0.3249 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5412 Z= 0.161 Angle : 0.577 8.996 7328 Z= 0.285 Chirality : 0.042 0.197 784 Planarity : 0.003 0.028 894 Dihedral : 9.652 87.052 808 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.51 % Allowed : 28.60 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.33), residues: 614 helix: 1.38 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.13 (0.71), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 90 TYR 0.009 0.001 TYR A 238 PHE 0.025 0.001 PHE A 333 TRP 0.018 0.002 TRP B 192 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 5412) covalent geometry : angle 0.57656 ( 7328) hydrogen bonds : bond 0.03989 ( 359) hydrogen bonds : angle 3.89354 ( 1077) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.227 Fit side-chains REVERT: A 28 GLU cc_start: 0.7451 (tp30) cc_final: 0.7201 (tp30) REVERT: A 39 GLU cc_start: 0.7798 (pp20) cc_final: 0.7303 (pp20) REVERT: A 77 MET cc_start: 0.5350 (mpt) cc_final: 0.4883 (tmt) REVERT: A 84 GLU cc_start: 0.7316 (tp30) cc_final: 0.6893 (tp30) REVERT: A 87 MET cc_start: 0.7520 (ptp) cc_final: 0.7075 (ppp) REVERT: A 135 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7770 (mttm) REVERT: A 239 TYR cc_start: 0.7200 (m-80) cc_final: 0.6630 (t80) REVERT: A 241 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7810 (tp-100) REVERT: A 246 TYR cc_start: 0.8380 (m-80) cc_final: 0.8092 (m-80) REVERT: A 327 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7468 (mtt180) REVERT: B 39 GLU cc_start: 0.7811 (pp20) cc_final: 0.7310 (pp20) REVERT: B 59 GLN cc_start: 0.7937 (mt0) cc_final: 0.7632 (mm110) REVERT: B 87 MET cc_start: 0.7124 (ppp) cc_final: 0.6670 (pp-130) REVERT: B 88 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7356 (mttm) REVERT: B 135 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7737 (mttm) REVERT: B 188 ARG cc_start: 0.8322 (mmt90) cc_final: 0.7747 (mtp180) REVERT: B 239 TYR cc_start: 0.7177 (m-80) cc_final: 0.6683 (t80) REVERT: B 241 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7758 (tp-100) REVERT: B 327 ARG cc_start: 0.8138 (ttm170) cc_final: 0.7450 (mtt180) outliers start: 19 outliers final: 11 residues processed: 93 average time/residue: 0.6273 time to fit residues: 60.4015 Evaluate side-chains 89 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 55 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.145972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113604 restraints weight = 7199.442| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.67 r_work: 0.3290 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5412 Z= 0.110 Angle : 0.527 7.720 7328 Z= 0.260 Chirality : 0.039 0.202 784 Planarity : 0.003 0.028 894 Dihedral : 9.220 88.140 808 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.32 % Allowed : 28.97 % Favored : 67.71 % 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: 2.05 (0.34), residues: 614 helix: 1.71 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.77 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 188 TYR 0.010 0.001 TYR A 133 PHE 0.025 0.001 PHE A 333 TRP 0.018 0.001 TRP A 192 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 5412) covalent geometry : angle 0.52700 ( 7328) hydrogen bonds : bond 0.03624 ( 359) hydrogen bonds : angle 3.75172 ( 1077) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.194 Fit side-chains REVERT: A 28 GLU cc_start: 0.7340 (tp30) cc_final: 0.7083 (tp30) REVERT: A 81 GLN cc_start: 0.6521 (OUTLIER) cc_final: 0.6264 (pp30) REVERT: A 84 GLU cc_start: 0.7288 (tp30) cc_final: 0.6959 (tp30) REVERT: A 87 MET cc_start: 0.7537 (ptp) cc_final: 0.7104 (ppp) REVERT: A 135 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7681 (mttm) REVERT: A 188 ARG cc_start: 0.8269 (mmt90) cc_final: 0.7713 (mtp180) REVERT: A 239 TYR cc_start: 0.7015 (m-80) cc_final: 0.6681 (t80) REVERT: A 246 TYR cc_start: 0.8344 (m-80) cc_final: 0.8021 (m-80) REVERT: A 327 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7361 (mtt180) REVERT: B 87 MET cc_start: 0.7143 (ppp) cc_final: 0.6714 (pp-130) REVERT: B 88 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7374 (mttm) REVERT: B 135 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7672 (mttm) REVERT: B 188 ARG cc_start: 0.8276 (mmt90) cc_final: 0.7697 (mtp180) REVERT: B 239 TYR cc_start: 0.6951 (m-80) cc_final: 0.6606 (t80) REVERT: B 327 ARG cc_start: 0.8049 (ttm170) cc_final: 0.7358 (mtt180) outliers start: 18 outliers final: 12 residues processed: 92 average time/residue: 0.4419 time to fit residues: 42.2772 Evaluate side-chains 87 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.144792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.111913 restraints weight = 7160.260| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.68 r_work: 0.3255 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5412 Z= 0.132 Angle : 0.546 7.243 7328 Z= 0.270 Chirality : 0.041 0.204 784 Planarity : 0.003 0.028 894 Dihedral : 9.363 87.577 808 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.95 % Allowed : 28.97 % Favored : 68.08 % 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: 2.04 (0.34), residues: 614 helix: 1.68 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.57 (0.73), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 31 TYR 0.009 0.001 TYR A 133 PHE 0.026 0.001 PHE A 333 TRP 0.018 0.001 TRP A 192 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 5412) covalent geometry : angle 0.54623 ( 7328) hydrogen bonds : bond 0.03778 ( 359) hydrogen bonds : angle 3.78801 ( 1077) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.185 Fit side-chains REVERT: A 28 GLU cc_start: 0.7405 (tp30) cc_final: 0.7146 (tp30) REVERT: A 84 GLU cc_start: 0.7293 (tp30) cc_final: 0.6964 (tp30) REVERT: A 87 MET cc_start: 0.7636 (ptp) cc_final: 0.7213 (ppp) REVERT: A 135 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7669 (mttm) REVERT: A 138 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8271 (tp) REVERT: A 188 ARG cc_start: 0.8311 (mmt90) cc_final: 0.7724 (mtp180) REVERT: A 239 TYR cc_start: 0.7040 (m-80) cc_final: 0.6629 (t80) REVERT: A 241 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7744 (tp-100) REVERT: A 246 TYR cc_start: 0.8330 (m-80) cc_final: 0.8031 (m-80) REVERT: A 327 ARG cc_start: 0.8059 (ttm170) cc_final: 0.7363 (mtt180) REVERT: B 39 GLU cc_start: 0.7823 (pp20) cc_final: 0.7291 (pp20) REVERT: B 87 MET cc_start: 0.7195 (ppp) cc_final: 0.6749 (pp-130) REVERT: B 88 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7378 (mttm) REVERT: B 135 LYS cc_start: 0.7979 (mtpt) cc_final: 0.7605 (mttm) REVERT: B 188 ARG cc_start: 0.8283 (mmt90) cc_final: 0.7686 (mtp180) REVERT: B 239 TYR cc_start: 0.7000 (m-80) cc_final: 0.6589 (t80) REVERT: B 327 ARG cc_start: 0.8049 (ttm170) cc_final: 0.7347 (mtt180) outliers start: 16 outliers final: 11 residues processed: 88 average time/residue: 0.6247 time to fit residues: 56.9566 Evaluate side-chains 89 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 88 LYS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111274 restraints weight = 7170.275| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.66 r_work: 0.3257 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5412 Z= 0.146 Angle : 0.570 7.423 7328 Z= 0.283 Chirality : 0.042 0.217 784 Planarity : 0.003 0.028 894 Dihedral : 9.483 87.225 808 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.14 % Allowed : 29.15 % Favored : 67.71 % 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: 1.98 (0.34), residues: 614 helix: 1.63 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.53 (0.73), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 90 TYR 0.010 0.001 TYR B 238 PHE 0.026 0.001 PHE A 333 TRP 0.017 0.001 TRP A 192 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5412) covalent geometry : angle 0.57015 ( 7328) hydrogen bonds : bond 0.03863 ( 359) hydrogen bonds : angle 3.81710 ( 1077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.44 seconds wall clock time: 33 minutes 11.75 seconds (1991.75 seconds total)