Starting phenix.real_space_refine on Thu Jul 24 06:03:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0l_24108/07_2025/7n0l_24108.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0l_24108/07_2025/7n0l_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_24108/07_2025/7n0l_24108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0l_24108/07_2025/7n0l_24108.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0l_24108/07_2025/7n0l_24108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0l_24108/07_2025/7n0l_24108.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, '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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, '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: 4.00, per 1000 atoms: 0.76 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: 1.36 Conformation dependent library (CDL) restraints added in 573.7 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: 0.51 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: 1.46 Time building geometry restraints manager: 1.57 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: 0.03 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: 1.230 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.020 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:15.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP B 192 HIS 0.002 0.001 HIS B 283 PHE 0.007 0.001 PHE A 235 TYR 0.007 0.001 TYR A 239 ARG 0.002 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.29318 ( 359) hydrogen bonds : angle 10.93533 ( 1077) covalent geometry : bond 0.00940 ( 5412) covalent geometry : angle 0.87905 ( 7328) *********************** 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 : 0.599 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: 0.7613 (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: 1.0156 time to fit residues: 130.9389 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 : 0.579 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.141179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107810 restraints weight = 6888.675| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.62 r_work: 0.3268 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5412 Z= 0.134 Angle : 0.573 5.583 7328 Z= 0.300 Chirality : 0.039 0.142 784 Planarity : 0.005 0.031 894 Dihedral : 13.171 77.934 847 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 7.75 % Allowed : 20.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.28), residues: 614 helix: -1.64 (0.19), residues: 532 sheet: None (None), residues: 0 loop : -2.18 (0.55), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 192 HIS 0.004 0.001 HIS B 283 PHE 0.018 0.001 PHE A 333 TYR 0.010 0.001 TYR B 240 ARG 0.007 0.001 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 359) hydrogen bonds : angle 4.86992 ( 1077) covalent geometry : bond 0.00279 ( 5412) covalent geometry : angle 0.57338 ( 7328) *********************** 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 126 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 84 time to evaluate : 0.612 Fit side-chains REVERT: A 28 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6878 (tp30) REVERT: A 39 GLU cc_start: 0.7798 (pp20) cc_final: 0.7146 (pp20) REVERT: A 84 GLU cc_start: 0.7241 (tp30) cc_final: 0.6795 (tp30) REVERT: A 239 TYR cc_start: 0.7292 (m-80) cc_final: 0.6654 (t80) REVERT: A 327 ARG cc_start: 0.8121 (ttm170) cc_final: 0.7500 (mtt180) REVERT: B 39 GLU cc_start: 0.7794 (pp20) cc_final: 0.7142 (pp20) REVERT: B 84 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7023 (tp30) REVERT: B 214 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8339 (mt) REVERT: B 239 TYR cc_start: 0.7278 (m-80) cc_final: 0.6636 (t80) REVERT: B 327 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7502 (mtt180) outliers start: 42 outliers final: 18 residues processed: 123 average time/residue: 1.2172 time to fit residues: 155.8800 Evaluate side-chains 92 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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 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 98 GLU 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 37 optimal weight: 0.0270 chunk 56 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7838 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.142103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108573 restraints weight = 7019.886| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.67 r_work: 0.3274 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5412 Z= 0.121 Angle : 0.533 5.956 7328 Z= 0.274 Chirality : 0.039 0.158 784 Planarity : 0.004 0.031 894 Dihedral : 10.940 81.324 821 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 6.83 % Allowed : 23.43 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.32), residues: 614 helix: -0.33 (0.21), residues: 530 sheet: None (None), residues: 0 loop : -0.47 (0.80), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 192 HIS 0.003 0.001 HIS A 283 PHE 0.021 0.001 PHE B 333 TYR 0.009 0.001 TYR A 133 ARG 0.006 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 359) hydrogen bonds : angle 4.21757 ( 1077) covalent geometry : bond 0.00254 ( 5412) covalent geometry : angle 0.53275 ( 7328) *********************** 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 123 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 0.495 Fit side-chains REVERT: A 39 GLU cc_start: 0.7754 (pp20) cc_final: 0.7126 (pp20) REVERT: A 84 GLU cc_start: 0.7180 (tp30) cc_final: 0.6724 (tp30) REVERT: A 87 MET cc_start: 0.7068 (ppp) cc_final: 0.6545 (ppp) REVERT: A 111 LEU cc_start: 0.8637 (mt) cc_final: 0.8362 (mt) REVERT: A 135 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7753 (mttm) REVERT: A 188 ARG cc_start: 0.8282 (mmt90) cc_final: 0.7764 (mtp180) REVERT: A 237 GLN cc_start: 0.8591 (mt0) cc_final: 0.8371 (mt0) REVERT: A 239 TYR cc_start: 0.7089 (m-80) cc_final: 0.6738 (t80) REVERT: A 241 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7871 (tp-100) REVERT: A 327 ARG cc_start: 0.8086 (ttm170) cc_final: 0.7412 (mtt180) REVERT: B 31 ARG cc_start: 0.7717 (mtm110) cc_final: 0.6852 (mmm160) REVERT: B 66 LYS cc_start: 0.7611 (ptmm) cc_final: 0.7172 (tppp) REVERT: B 84 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7083 (tp30) REVERT: B 87 MET cc_start: 0.7081 (ppp) cc_final: 0.6362 (ppp) REVERT: B 111 LEU cc_start: 0.8631 (mt) cc_final: 0.8377 (mt) REVERT: B 135 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7745 (mttm) REVERT: B 188 ARG cc_start: 0.8254 (mmt90) cc_final: 0.7717 (mtp180) REVERT: B 239 TYR cc_start: 0.7099 (m-80) cc_final: 0.6769 (t80) REVERT: B 327 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7418 (mtt180) outliers start: 37 outliers final: 15 residues processed: 118 average time/residue: 1.2101 time to fit residues: 148.7562 Evaluate side-chains 94 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 A residue 299 ASP 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 245 LEU Chi-restraints excluded: chain B residue 299 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3803 r_free = 0.3803 target = 0.143399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111636 restraints weight = 7294.502| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.64 r_work: 0.3288 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2634 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= 0.117 Angle : 0.518 6.111 7328 Z= 0.263 Chirality : 0.039 0.170 784 Planarity : 0.003 0.030 894 Dihedral : 9.742 84.350 815 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 4.24 % Allowed : 25.83 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.34), residues: 614 helix: 0.44 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.28 (0.82), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 192 HIS 0.002 0.001 HIS B 283 PHE 0.022 0.001 PHE A 333 TYR 0.009 0.001 TYR A 133 ARG 0.004 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 359) hydrogen bonds : angle 3.98978 ( 1077) covalent geometry : bond 0.00249 ( 5412) covalent geometry : angle 0.51798 ( 7328) *********************** 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 101 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.573 Fit side-chains REVERT: A 28 GLU cc_start: 0.7497 (tp30) cc_final: 0.7156 (tp30) REVERT: A 39 GLU cc_start: 0.7781 (pp20) cc_final: 0.7194 (pp20) REVERT: A 66 LYS cc_start: 0.7940 (ttpp) cc_final: 0.7701 (ptmm) REVERT: A 84 GLU cc_start: 0.7227 (tp30) cc_final: 0.6710 (tp30) REVERT: A 111 LEU cc_start: 0.8584 (mt) cc_final: 0.8364 (mt) REVERT: A 135 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7702 (mttm) REVERT: A 188 ARG cc_start: 0.8277 (mmt90) cc_final: 0.7771 (mtp180) REVERT: A 239 TYR cc_start: 0.7030 (m-80) cc_final: 0.6705 (t80) REVERT: A 241 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7800 (tp-100) REVERT: A 246 TYR cc_start: 0.8424 (m-80) cc_final: 0.8190 (m-80) REVERT: A 327 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7416 (mtt180) REVERT: B 31 ARG cc_start: 0.7591 (mtm110) cc_final: 0.6825 (mmm160) REVERT: B 135 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7686 (mttm) REVERT: B 188 ARG cc_start: 0.8242 (mmt90) cc_final: 0.7724 (mtp180) REVERT: B 239 TYR cc_start: 0.6983 (m-80) cc_final: 0.6643 (t80) REVERT: B 327 ARG cc_start: 0.8086 (ttm170) cc_final: 0.7412 (mtt180) outliers start: 23 outliers final: 11 residues processed: 100 average time/residue: 1.2438 time to fit residues: 129.6343 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 : 0.626 ------------------------------------------------------------------------------- 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 A residue 299 ASP Chi-restraints excluded: chain B residue 40 LEU 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 Chi-restraints excluded: chain B residue 299 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.0010 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.145715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113709 restraints weight = 7268.071| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.69 r_work: 0.3293 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2896 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= 0.105 Angle : 0.489 6.179 7328 Z= 0.249 Chirality : 0.038 0.174 784 Planarity : 0.003 0.028 894 Dihedral : 9.232 85.954 808 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.06 % Allowed : 27.31 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.34), residues: 614 helix: 1.00 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.16 (0.82), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 192 HIS 0.002 0.001 HIS B 283 PHE 0.024 0.001 PHE A 333 TYR 0.010 0.001 TYR A 133 ARG 0.003 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 359) hydrogen bonds : angle 3.81330 ( 1077) covalent geometry : bond 0.00216 ( 5412) covalent geometry : angle 0.48945 ( 7328) *********************** 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 102 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.595 Fit side-chains REVERT: A 28 GLU cc_start: 0.7346 (tp30) cc_final: 0.7105 (tp30) REVERT: A 84 GLU cc_start: 0.7253 (tp30) cc_final: 0.6924 (tp30) REVERT: A 93 LEU cc_start: 0.6747 (tp) cc_final: 0.6387 (mt) REVERT: A 135 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7714 (mttm) REVERT: A 188 ARG cc_start: 0.8246 (mmt90) cc_final: 0.7747 (mtp180) REVERT: A 239 TYR cc_start: 0.6928 (m-80) cc_final: 0.6676 (t80) REVERT: A 246 TYR cc_start: 0.8297 (m-80) cc_final: 0.8017 (m-80) REVERT: A 327 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7463 (mtt180) REVERT: B 31 ARG cc_start: 0.7454 (mtm110) cc_final: 0.6805 (mmm160) REVERT: B 87 MET cc_start: 0.7183 (ppp) cc_final: 0.6756 (pp-130) REVERT: B 135 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7683 (mttm) REVERT: B 188 ARG cc_start: 0.8227 (mmt90) cc_final: 0.7721 (mtp180) REVERT: B 239 TYR cc_start: 0.6937 (m-80) cc_final: 0.6670 (t80) REVERT: B 327 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7467 (mtt180) outliers start: 22 outliers final: 9 residues processed: 100 average time/residue: 1.2733 time to fit residues: 132.5642 Evaluate side-chains 85 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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 242 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3814 r_free = 0.3814 target = 0.144681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.112291 restraints weight = 7163.564| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.70 r_work: 0.3269 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5412 Z= 0.124 Angle : 0.531 8.866 7328 Z= 0.263 Chirality : 0.040 0.186 784 Planarity : 0.003 0.028 894 Dihedral : 9.365 86.734 808 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.51 % Allowed : 27.86 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.33), residues: 614 helix: 1.23 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.15 (0.70), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 192 HIS 0.002 0.001 HIS B 30 PHE 0.025 0.001 PHE A 333 TYR 0.009 0.001 TYR A 133 ARG 0.003 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 359) hydrogen bonds : angle 3.80835 ( 1077) covalent geometry : bond 0.00269 ( 5412) covalent geometry : angle 0.53124 ( 7328) *********************** 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 96 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.751 Fit side-chains REVERT: A 28 GLU cc_start: 0.7396 (tp30) cc_final: 0.7146 (tp30) REVERT: A 84 GLU cc_start: 0.7459 (tp30) cc_final: 0.6974 (tp30) REVERT: A 93 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6461 (mt) REVERT: A 135 LYS cc_start: 0.7986 (mtpt) cc_final: 0.7655 (mttm) REVERT: A 188 ARG cc_start: 0.8296 (mmt90) cc_final: 0.7749 (mtp180) REVERT: A 239 TYR cc_start: 0.6993 (m-80) cc_final: 0.6642 (t80) REVERT: A 241 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7757 (tp-100) REVERT: A 246 TYR cc_start: 0.8375 (m-80) cc_final: 0.8138 (m-80) REVERT: A 327 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7418 (mtt180) REVERT: B 31 ARG cc_start: 0.7419 (mtm110) cc_final: 0.6780 (mmm160) REVERT: B 59 GLN cc_start: 0.7949 (mt0) cc_final: 0.7603 (mm110) REVERT: B 87 MET cc_start: 0.7136 (ppp) cc_final: 0.6714 (pp-130) REVERT: B 135 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7648 (mttm) REVERT: B 188 ARG cc_start: 0.8272 (mmt90) cc_final: 0.7709 (mtp180) REVERT: B 239 TYR cc_start: 0.6971 (m-80) cc_final: 0.6624 (t80) REVERT: B 327 ARG cc_start: 0.8081 (ttm170) cc_final: 0.7399 (mtt180) outliers start: 19 outliers final: 9 residues processed: 93 average time/residue: 1.3298 time to fit residues: 128.7808 Evaluate side-chains 88 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.145049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113002 restraints weight = 7093.990| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.63 r_work: 0.3310 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3113 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 : 0.503 7.976 7328 Z= 0.251 Chirality : 0.039 0.195 784 Planarity : 0.003 0.027 894 Dihedral : 9.160 87.802 808 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.77 % Allowed : 29.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.33), residues: 614 helix: 1.55 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.17 (0.67), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 192 HIS 0.002 0.001 HIS A 30 PHE 0.025 0.001 PHE A 333 TYR 0.010 0.001 TYR A 133 ARG 0.003 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 359) hydrogen bonds : angle 3.72940 ( 1077) covalent geometry : bond 0.00221 ( 5412) covalent geometry : angle 0.50275 ( 7328) *********************** 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 93 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.542 Fit side-chains REVERT: A 28 GLU cc_start: 0.7269 (tp30) cc_final: 0.7031 (tp30) REVERT: A 59 GLN cc_start: 0.7901 (mt0) cc_final: 0.7679 (mm110) REVERT: A 77 MET cc_start: 0.5243 (mpt) cc_final: 0.4747 (tmt) REVERT: A 84 GLU cc_start: 0.7374 (tp30) cc_final: 0.6780 (tp30) REVERT: A 87 MET cc_start: 0.7458 (ptp) cc_final: 0.7086 (ppp) REVERT: A 93 LEU cc_start: 0.6836 (OUTLIER) cc_final: 0.6464 (mt) REVERT: A 135 LYS cc_start: 0.8053 (mtpt) cc_final: 0.7749 (mttm) REVERT: A 138 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8230 (tp) REVERT: A 188 ARG cc_start: 0.8260 (mmt90) cc_final: 0.7800 (mtp180) REVERT: A 239 TYR cc_start: 0.6982 (m-80) cc_final: 0.6712 (t80) REVERT: A 246 TYR cc_start: 0.8365 (m-80) cc_final: 0.8118 (m-80) REVERT: A 327 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7483 (mtt180) REVERT: B 31 ARG cc_start: 0.7364 (mtm110) cc_final: 0.6616 (mmm-85) REVERT: B 59 GLN cc_start: 0.7925 (mt0) cc_final: 0.7611 (mm110) REVERT: B 87 MET cc_start: 0.7095 (ppp) cc_final: 0.6683 (pp-130) REVERT: B 135 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7746 (mttm) REVERT: B 188 ARG cc_start: 0.8231 (mmt90) cc_final: 0.7773 (mtp180) REVERT: B 239 TYR cc_start: 0.6951 (m-80) cc_final: 0.6680 (t80) REVERT: B 327 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7456 (mtt180) outliers start: 15 outliers final: 9 residues processed: 91 average time/residue: 1.2628 time to fit residues: 119.7402 Evaluate side-chains 88 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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 242 SER Chi-restraints excluded: chain B residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 36 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.146041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113940 restraints weight = 7191.266| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.67 r_work: 0.3297 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3145 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= 0.109 Angle : 0.504 7.554 7328 Z= 0.252 Chirality : 0.039 0.200 784 Planarity : 0.003 0.027 894 Dihedral : 9.133 88.488 808 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.34), residues: 614 helix: 1.76 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.77 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 192 HIS 0.002 0.001 HIS B 30 PHE 0.026 0.001 PHE A 333 TYR 0.010 0.001 TYR A 133 ARG 0.002 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 359) hydrogen bonds : angle 3.69133 ( 1077) covalent geometry : bond 0.00230 ( 5412) covalent geometry : angle 0.50421 ( 7328) *********************** 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 94 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.567 Fit side-chains REVERT: A 28 GLU cc_start: 0.7269 (tp30) cc_final: 0.7033 (tp30) REVERT: A 77 MET cc_start: 0.5376 (mpt) cc_final: 0.5000 (tmt) REVERT: A 84 GLU cc_start: 0.7274 (tp30) cc_final: 0.6835 (tp30) REVERT: A 87 MET cc_start: 0.7454 (ptp) cc_final: 0.7002 (ppp) REVERT: A 93 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6433 (mt) REVERT: A 135 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7755 (mttm) REVERT: A 138 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8287 (tp) REVERT: A 188 ARG cc_start: 0.8244 (mmt90) cc_final: 0.7792 (mtp180) REVERT: A 239 TYR cc_start: 0.6997 (m-80) cc_final: 0.6735 (t80) REVERT: A 241 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7781 (tp-100) REVERT: A 246 TYR cc_start: 0.8350 (m-80) cc_final: 0.8051 (m-80) REVERT: A 327 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7474 (mtt180) REVERT: B 31 ARG cc_start: 0.7371 (mtm110) cc_final: 0.6470 (mmm-85) REVERT: B 87 MET cc_start: 0.7279 (ppp) cc_final: 0.6887 (pp-130) REVERT: B 135 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7754 (mttm) REVERT: B 188 ARG cc_start: 0.8215 (mmt90) cc_final: 0.7711 (mtp180) REVERT: B 239 TYR cc_start: 0.6975 (m-80) cc_final: 0.6690 (t80) REVERT: B 327 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7445 (mtt180) outliers start: 17 outliers final: 10 residues processed: 92 average time/residue: 1.2717 time to fit residues: 121.7674 Evaluate side-chains 87 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 26 ILE 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 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 61 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 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 = 0.3823 r_free = 0.3823 target = 0.145212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.113267 restraints weight = 7143.134| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.63 r_work: 0.3300 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5412 Z= 0.113 Angle : 0.520 7.789 7328 Z= 0.260 Chirality : 0.039 0.197 784 Planarity : 0.003 0.026 894 Dihedral : 9.130 88.851 808 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 : 2.77 % Allowed : 29.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.34), residues: 614 helix: 1.88 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.78 (0.69), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 192 HIS 0.002 0.001 HIS B 30 PHE 0.026 0.001 PHE A 333 TYR 0.010 0.001 TYR A 133 ARG 0.002 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 359) hydrogen bonds : angle 3.69077 ( 1077) covalent geometry : bond 0.00242 ( 5412) covalent geometry : angle 0.51987 ( 7328) *********************** 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 91 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.573 Fit side-chains REVERT: A 28 GLU cc_start: 0.7266 (tp30) cc_final: 0.7031 (tp30) REVERT: A 77 MET cc_start: 0.5526 (mpt) cc_final: 0.5187 (tmt) REVERT: A 84 GLU cc_start: 0.7241 (tp30) cc_final: 0.6894 (tp30) REVERT: A 87 MET cc_start: 0.7475 (ptp) cc_final: 0.7033 (ppp) REVERT: A 93 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6442 (mt) REVERT: A 135 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7735 (mttm) REVERT: A 138 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8296 (tp) REVERT: A 188 ARG cc_start: 0.8245 (mmt90) cc_final: 0.7728 (mtp180) REVERT: A 239 TYR cc_start: 0.6980 (m-80) cc_final: 0.6708 (t80) REVERT: A 241 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7800 (tp-100) REVERT: A 246 TYR cc_start: 0.8334 (m-80) cc_final: 0.7985 (m-80) REVERT: A 327 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7463 (mtt180) REVERT: B 31 ARG cc_start: 0.7330 (mtm110) cc_final: 0.6465 (mmm-85) REVERT: B 87 MET cc_start: 0.7246 (ppp) cc_final: 0.6847 (pp-130) REVERT: B 135 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7729 (mttm) REVERT: B 188 ARG cc_start: 0.8219 (mmt90) cc_final: 0.7703 (mtp180) REVERT: B 239 TYR cc_start: 0.6933 (m-80) cc_final: 0.6660 (t80) REVERT: B 327 ARG cc_start: 0.8109 (ttm170) cc_final: 0.7432 (mtt180) outliers start: 15 outliers final: 10 residues processed: 89 average time/residue: 1.3533 time to fit residues: 125.2759 Evaluate side-chains 87 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 26 ILE 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 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 16 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 58 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.145990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.113520 restraints weight = 7142.689| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.67 r_work: 0.3293 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3234 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= 0.108 Angle : 0.503 7.041 7328 Z= 0.251 Chirality : 0.039 0.195 784 Planarity : 0.003 0.026 894 Dihedral : 9.074 89.302 808 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.58 % Allowed : 29.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.34), residues: 614 helix: 1.96 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.56 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 192 HIS 0.002 0.001 HIS B 30 PHE 0.027 0.001 PHE A 333 TYR 0.010 0.001 TYR A 133 ARG 0.002 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 359) hydrogen bonds : angle 3.66718 ( 1077) covalent geometry : bond 0.00228 ( 5412) covalent geometry : angle 0.50338 ( 7328) ********************** 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 90 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.605 Fit side-chains REVERT: A 28 GLU cc_start: 0.7303 (tp30) cc_final: 0.7073 (tp30) REVERT: A 77 MET cc_start: 0.5434 (mpt) cc_final: 0.5212 (tmt) REVERT: A 84 GLU cc_start: 0.7079 (tp30) cc_final: 0.6758 (tp30) REVERT: A 87 MET cc_start: 0.7612 (ptp) cc_final: 0.7199 (ppp) REVERT: A 93 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6454 (mt) REVERT: A 135 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7706 (mttm) REVERT: A 138 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8268 (tp) REVERT: A 188 ARG cc_start: 0.8256 (mmt90) cc_final: 0.7719 (mtp180) REVERT: A 239 TYR cc_start: 0.6961 (m-80) cc_final: 0.6698 (t80) REVERT: A 246 TYR cc_start: 0.8319 (m-80) cc_final: 0.7953 (m-80) REVERT: A 327 ARG cc_start: 0.8035 (ttm170) cc_final: 0.7439 (mtt180) REVERT: B 87 MET cc_start: 0.7302 (ppp) cc_final: 0.6906 (pp-130) REVERT: B 135 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7686 (mttm) REVERT: B 188 ARG cc_start: 0.8259 (mmt90) cc_final: 0.7711 (mtp180) REVERT: B 239 TYR cc_start: 0.6892 (m-80) cc_final: 0.6647 (t80) REVERT: B 327 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7397 (mtt180) outliers start: 14 outliers final: 11 residues processed: 88 average time/residue: 1.2666 time to fit residues: 116.3641 Evaluate side-chains 87 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 26 ILE 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 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 21 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.143961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111459 restraints weight = 7095.296| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.63 r_work: 0.3280 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5412 Z= 0.117 Angle : 0.515 6.918 7328 Z= 0.257 Chirality : 0.040 0.191 784 Planarity : 0.003 0.035 894 Dihedral : 9.156 89.361 808 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 : 2.40 % Allowed : 29.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.34), residues: 614 helix: 1.96 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.47 (0.71), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 192 HIS 0.004 0.001 HIS B 30 PHE 0.027 0.001 PHE A 333 TYR 0.010 0.001 TYR A 133 ARG 0.008 0.000 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 359) hydrogen bonds : angle 3.69688 ( 1077) covalent geometry : bond 0.00252 ( 5412) covalent geometry : angle 0.51466 ( 7328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4439.47 seconds wall clock time: 76 minutes 15.17 seconds (4575.17 seconds total)