Starting phenix.real_space_refine on Fri Aug 22 15:54:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbb_37419/08_2025/8wbb_37419_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbb_37419/08_2025/8wbb_37419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbb_37419/08_2025/8wbb_37419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbb_37419/08_2025/8wbb_37419.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbb_37419/08_2025/8wbb_37419_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbb_37419/08_2025/8wbb_37419_neut.cif" } resolution = 2.9 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= 0.167 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 3440 2.51 5 N 937 2.21 5 O 1030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5449 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2736 Classifications: {'peptide': 346} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 329} Chain breaks: 1 Chain: "a" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2713 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Time building chain proxies: 1.55, per 1000 atoms: 0.28 Number of scatterers: 5449 At special positions: 0 Unit cell: (87.55, 68.85, 113.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1030 8.00 N 937 7.00 C 3440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.04 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.37 Conformation dependent library (CDL) restraints added in 197.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1266 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 9 sheets defined 19.6% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 40 through 53 removed outlier: 3.634A pdb=" N SER A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.526A pdb=" N MET A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 71 " --> pdb=" O MET A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.533A pdb=" N LEU A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.561A pdb=" N ARG A 148 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 183 removed outlier: 4.021A pdb=" N LEU A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.500A pdb=" N HIS A 229 " --> pdb=" O PRO A 226 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.694A pdb=" N MET A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.524A pdb=" N ALA A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'a' and resid 40 through 53 removed outlier: 3.706A pdb=" N GLU a 51 " --> pdb=" O LEU a 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP a 52 " --> pdb=" O ASN a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 71 removed outlier: 3.539A pdb=" N ILE a 66 " --> pdb=" O ARG a 62 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET a 67 " --> pdb=" O LEU a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 71 through 82 removed outlier: 3.551A pdb=" N GLY a 82 " --> pdb=" O VAL a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.842A pdb=" N LEU a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.729A pdb=" N THR a 230 " --> pdb=" O LYS a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.527A pdb=" N ALA a 248 " --> pdb=" O LYS a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 removed outlier: 3.668A pdb=" N LEU a 270 " --> pdb=" O PRO a 267 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY a 271 " --> pdb=" O TRP a 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 267 through 271' Processing helix chain 'a' and resid 341 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 removed outlier: 4.326A pdb=" N LYS A 14 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA A 5 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 16 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS a 14 " --> pdb=" O ALA a 5 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE a 19 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.543A pdb=" N ASN A 166 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR A 158 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57 removed outlier: 6.735A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 4.750A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ILE A 212 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N SER A 205 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP a 201 " --> pdb=" O ALA a 215 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA a 215 " --> pdb=" O TRP a 201 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU a 203 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 6.071A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 32 through 35 removed outlier: 6.250A pdb=" N ASN a 166 " --> pdb=" O TYR a 158 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR a 158 " --> pdb=" O ASN a 166 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 56 through 57 removed outlier: 6.636A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.812A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL a 89 " --> pdb=" O ILE a 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.020A pdb=" N THR a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N CYS a 313 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 342 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: 0.66 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 911 1.31 - 1.44: 1564 1.44 - 1.57: 3057 1.57 - 1.70: 0 1.70 - 1.83: 60 Bond restraints: 5592 Sorted by residual: bond pdb=" C LEU a 42 " pdb=" O LEU a 42 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.19e-02 7.06e+03 2.39e+01 bond pdb=" CA LEU a 42 " pdb=" C LEU a 42 " ideal model delta sigma weight residual 1.524 1.472 0.053 1.29e-02 6.01e+03 1.66e+01 bond pdb=" CA ARG a 41 " pdb=" C ARG a 41 " ideal model delta sigma weight residual 1.522 1.466 0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" N ARG a 41 " pdb=" CA ARG a 41 " ideal model delta sigma weight residual 1.457 1.409 0.048 1.29e-02 6.01e+03 1.38e+01 bond pdb=" CA ALA a 40 " pdb=" CB ALA a 40 " ideal model delta sigma weight residual 1.537 1.491 0.046 1.38e-02 5.25e+03 1.13e+01 ... (remaining 5587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 7378 1.53 - 3.06: 152 3.06 - 4.59: 41 4.59 - 6.12: 12 6.12 - 7.66: 5 Bond angle restraints: 7588 Sorted by residual: angle pdb=" N ARG a 41 " pdb=" CA ARG a 41 " pdb=" C ARG a 41 " ideal model delta sigma weight residual 112.90 105.24 7.66 1.31e+00 5.83e-01 3.41e+01 angle pdb=" CA MET a 162 " pdb=" CB MET a 162 " pdb=" CG MET a 162 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA LYS a 11 " pdb=" CB LYS a 11 " pdb=" CG LYS a 11 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" N ALA a 40 " pdb=" CA ALA a 40 " pdb=" CB ALA a 40 " ideal model delta sigma weight residual 110.90 106.46 4.44 1.33e+00 5.65e-01 1.11e+01 angle pdb=" C LYS a 11 " pdb=" N GLU a 12 " pdb=" CA GLU a 12 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 ... (remaining 7583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2742 17.96 - 35.93: 408 35.93 - 53.89: 126 53.89 - 71.85: 25 71.85 - 89.82: 12 Dihedral angle restraints: 3313 sinusoidal: 1344 harmonic: 1969 Sorted by residual: dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 316 " pdb=" CB CYS A 316 " ideal model delta sinusoidal sigma weight residual 93.00 169.63 -76.63 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS a 55 " pdb=" SG CYS a 55 " pdb=" SG CYS a 143 " pdb=" CB CYS a 143 " ideal model delta sinusoidal sigma weight residual -86.00 -154.99 68.99 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS A 4 " pdb=" SG CYS A 4 " pdb=" SG CYS A 15 " pdb=" CB CYS A 15 " ideal model delta sinusoidal sigma weight residual 93.00 54.68 38.32 1 1.00e+01 1.00e-02 2.07e+01 ... (remaining 3310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 445 0.029 - 0.058: 247 0.058 - 0.087: 60 0.087 - 0.115: 47 0.115 - 0.144: 9 Chirality restraints: 808 Sorted by residual: chirality pdb=" CA ILE a 22 " pdb=" N ILE a 22 " pdb=" C ILE a 22 " pdb=" CB ILE a 22 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE A 22 " pdb=" N ILE A 22 " pdb=" C ILE A 22 " pdb=" CB ILE A 22 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE a 243 " pdb=" N ILE a 243 " pdb=" C ILE a 243 " pdb=" CB ILE a 243 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 805 not shown) Planarity restraints: 967 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN a 35 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO a 36 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO a 36 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO a 36 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET a 162 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C MET a 162 " -0.031 2.00e-02 2.50e+03 pdb=" O MET a 162 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE a 163 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS a 280 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO a 281 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO a 281 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO a 281 " -0.021 5.00e-02 4.00e+02 ... (remaining 964 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 599 2.75 - 3.29: 4700 3.29 - 3.83: 8466 3.83 - 4.36: 10523 4.36 - 4.90: 18925 Nonbonded interactions: 43213 Sorted by model distance: nonbonded pdb=" OG SER A 59 " pdb=" OD2 ASP A 136 " model vdw 2.213 3.040 nonbonded pdb=" OG SER a 38 " pdb=" O LYS a 116 " model vdw 2.230 3.040 nonbonded pdb=" NZ LYS a 33 " pdb=" OE1 GLN a 35 " model vdw 2.267 3.120 nonbonded pdb=" O ASP A 23 " pdb=" OG1 THR A 27 " model vdw 2.277 3.040 nonbonded pdb=" NH1 ARG A 172 " pdb=" OG SER A 176 " model vdw 2.312 3.120 ... (remaining 43208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 118 or resid 128 through 352)) selection = chain 'a' } 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: 1.850 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.320 Find NCS groups from input model: 0.080 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.004 0.058 5601 Z= 0.203 Angle : 0.623 7.655 7606 Z= 0.328 Chirality : 0.043 0.144 808 Planarity : 0.004 0.049 967 Dihedral : 19.177 89.816 2020 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.58 % Favored : 94.27 % Rotamer: Outliers : 0.51 % Allowed : 30.69 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.79 (0.30), residues: 681 helix: -0.39 (0.66), residues: 71 sheet: -1.27 (0.47), residues: 121 loop : -1.35 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 62 TYR 0.010 0.001 TYR a 256 PHE 0.013 0.002 PHE A 20 TRP 0.007 0.001 TRP A 150 HIS 0.003 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5592) covalent geometry : angle 0.61970 ( 7588) SS BOND : bond 0.00354 ( 9) SS BOND : angle 1.42951 ( 18) hydrogen bonds : bond 0.27243 ( 133) hydrogen bonds : angle 9.40424 ( 342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.235 Fit side-chains REVERT: a 147 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7461 (mtm-85) REVERT: a 306 LYS cc_start: 0.8096 (pttt) cc_final: 0.7860 (pttp) outliers start: 3 outliers final: 3 residues processed: 84 average time/residue: 0.5329 time to fit residues: 46.8245 Evaluate side-chains 72 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 62 ARG Chi-restraints excluded: chain a residue 322 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.0980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.0270 chunk 27 optimal weight: 0.0470 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 84 HIS A 208 GLN A 293 HIS a 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115087 restraints weight = 5495.457| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.14 r_work: 0.3055 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5601 Z= 0.103 Angle : 0.552 5.880 7606 Z= 0.285 Chirality : 0.043 0.161 808 Planarity : 0.004 0.037 967 Dihedral : 5.181 46.402 741 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.58 % Favored : 94.27 % Rotamer: Outliers : 5.23 % Allowed : 27.99 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.49 (0.31), residues: 681 helix: 0.41 (0.68), residues: 72 sheet: -1.15 (0.46), residues: 133 loop : -1.21 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 62 TYR 0.008 0.001 TYR a 256 PHE 0.011 0.001 PHE a 20 TRP 0.007 0.001 TRP A 150 HIS 0.003 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 5592) covalent geometry : angle 0.55047 ( 7588) SS BOND : bond 0.00247 ( 9) SS BOND : angle 0.93604 ( 18) hydrogen bonds : bond 0.04263 ( 133) hydrogen bonds : angle 6.05128 ( 342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.216 Fit side-chains REVERT: A 327 ASP cc_start: 0.8331 (m-30) cc_final: 0.8117 (m-30) REVERT: a 62 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.6471 (mpt180) REVERT: a 147 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7728 (mtm-85) REVERT: a 192 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8048 (mtpp) REVERT: a 306 LYS cc_start: 0.8158 (pttt) cc_final: 0.7892 (pttp) outliers start: 31 outliers final: 13 residues processed: 98 average time/residue: 0.4336 time to fit residues: 44.7761 Evaluate side-chains 78 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 62 ARG Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 57 optimal weight: 0.0070 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.155419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.114843 restraints weight = 5431.708| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.10 r_work: 0.3061 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5601 Z= 0.106 Angle : 0.535 5.516 7606 Z= 0.276 Chirality : 0.043 0.174 808 Planarity : 0.003 0.038 967 Dihedral : 4.884 48.009 737 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.73 % Allowed : 27.82 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.29 (0.31), residues: 681 helix: 0.81 (0.66), residues: 73 sheet: -1.03 (0.46), residues: 131 loop : -1.12 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 62 TYR 0.009 0.001 TYR a 256 PHE 0.009 0.001 PHE a 277 TRP 0.007 0.001 TRP A 150 HIS 0.003 0.000 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 5592) covalent geometry : angle 0.53377 ( 7588) SS BOND : bond 0.00209 ( 9) SS BOND : angle 0.88365 ( 18) hydrogen bonds : bond 0.03636 ( 133) hydrogen bonds : angle 5.42341 ( 342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8286 (m-30) cc_final: 0.7973 (m-30) REVERT: a 75 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8040 (mp) REVERT: a 147 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7729 (mtm-85) REVERT: a 192 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8067 (mtpp) REVERT: a 306 LYS cc_start: 0.8218 (pttt) cc_final: 0.7911 (pttp) REVERT: a 310 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7443 (mp10) outliers start: 34 outliers final: 17 residues processed: 101 average time/residue: 0.4312 time to fit residues: 46.0728 Evaluate side-chains 85 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 67 MET Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Chi-restraints excluded: chain a residue 329 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 60 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS a 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.155620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.114714 restraints weight = 5441.493| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.10 r_work: 0.3023 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5601 Z= 0.109 Angle : 0.532 5.672 7606 Z= 0.273 Chirality : 0.043 0.170 808 Planarity : 0.003 0.037 967 Dihedral : 4.359 35.626 733 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.06 % Allowed : 29.85 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.20 (0.31), residues: 681 helix: 1.08 (0.66), residues: 73 sheet: -1.06 (0.45), residues: 131 loop : -1.06 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.009 0.001 TYR a 256 PHE 0.009 0.001 PHE a 277 TRP 0.007 0.001 TRP A 150 HIS 0.003 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5592) covalent geometry : angle 0.53106 ( 7588) SS BOND : bond 0.00242 ( 9) SS BOND : angle 0.89536 ( 18) hydrogen bonds : bond 0.03411 ( 133) hydrogen bonds : angle 5.20146 ( 342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8248 (m-30) cc_final: 0.7952 (m-30) REVERT: a 147 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7778 (mtm-85) REVERT: a 192 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.8058 (mtpp) REVERT: a 306 LYS cc_start: 0.8205 (pttt) cc_final: 0.7868 (ptmt) REVERT: a 310 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7420 (mp10) outliers start: 30 outliers final: 19 residues processed: 95 average time/residue: 0.3660 time to fit residues: 37.0795 Evaluate side-chains 87 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 50 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS a 48 ASN a 181 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.148944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.109880 restraints weight = 5594.860| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.09 r_work: 0.2952 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 5601 Z= 0.280 Angle : 0.696 7.511 7606 Z= 0.354 Chirality : 0.049 0.168 808 Planarity : 0.004 0.038 967 Dihedral : 5.111 34.018 733 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 5.56 % Allowed : 29.68 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.50 (0.30), residues: 681 helix: 0.71 (0.66), residues: 75 sheet: -1.33 (0.43), residues: 144 loop : -1.21 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG a 257 TYR 0.014 0.002 TYR a 256 PHE 0.015 0.002 PHE A 323 TRP 0.013 0.002 TRP A 210 HIS 0.007 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00699 ( 5592) covalent geometry : angle 0.69271 ( 7588) SS BOND : bond 0.00418 ( 9) SS BOND : angle 1.53144 ( 18) hydrogen bonds : bond 0.05200 ( 133) hydrogen bonds : angle 5.71493 ( 342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.224 Fit side-chains REVERT: A 66 ILE cc_start: 0.8593 (mt) cc_final: 0.8347 (mt) REVERT: A 85 ASP cc_start: 0.7518 (t0) cc_final: 0.7147 (p0) REVERT: A 327 ASP cc_start: 0.8493 (m-30) cc_final: 0.8254 (m-30) REVERT: a 13 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6492 (tp) REVERT: a 20 PHE cc_start: 0.8483 (t80) cc_final: 0.8235 (t80) REVERT: a 147 ARG cc_start: 0.8376 (mtp85) cc_final: 0.7991 (mtm-85) REVERT: a 192 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8111 (mtpp) REVERT: a 310 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7565 (mp10) outliers start: 33 outliers final: 20 residues processed: 89 average time/residue: 0.3911 time to fit residues: 37.0013 Evaluate side-chains 83 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.167970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.129230 restraints weight = 5336.831| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.15 r_work: 0.3302 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5601 Z= 0.107 Angle : 0.542 6.806 7606 Z= 0.277 Chirality : 0.043 0.181 808 Planarity : 0.003 0.036 967 Dihedral : 4.561 35.779 733 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.89 % Allowed : 29.51 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.34 (0.30), residues: 681 helix: 1.16 (0.66), residues: 73 sheet: -1.22 (0.45), residues: 131 loop : -1.17 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.009 0.001 TYR a 256 PHE 0.011 0.001 PHE A 323 TRP 0.008 0.001 TRP A 150 HIS 0.003 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 5592) covalent geometry : angle 0.53890 ( 7588) SS BOND : bond 0.00330 ( 9) SS BOND : angle 1.24202 ( 18) hydrogen bonds : bond 0.03357 ( 133) hydrogen bonds : angle 5.23750 ( 342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.234 Fit side-chains REVERT: A 85 ASP cc_start: 0.7441 (t0) cc_final: 0.7080 (p0) REVERT: a 147 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7902 (mtm-85) REVERT: a 192 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8107 (mtpp) REVERT: a 310 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7437 (mp10) outliers start: 29 outliers final: 17 residues processed: 91 average time/residue: 0.4585 time to fit residues: 44.1200 Evaluate side-chains 83 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 67 MET Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 0.0670 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 208 GLN A 293 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126183 restraints weight = 5432.749| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.16 r_work: 0.3255 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5601 Z= 0.195 Angle : 0.613 6.278 7606 Z= 0.312 Chirality : 0.046 0.182 808 Planarity : 0.004 0.037 967 Dihedral : 4.830 35.262 733 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.89 % Allowed : 29.17 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.46 (0.30), residues: 681 helix: 1.01 (0.65), residues: 75 sheet: -1.60 (0.41), residues: 152 loop : -1.10 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.012 0.001 TYR a 256 PHE 0.013 0.002 PHE A 323 TRP 0.008 0.001 TRP A 210 HIS 0.005 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 5592) covalent geometry : angle 0.60857 ( 7588) SS BOND : bond 0.00405 ( 9) SS BOND : angle 1.58241 ( 18) hydrogen bonds : bond 0.04240 ( 133) hydrogen bonds : angle 5.41154 ( 342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.225 Fit side-chains REVERT: A 85 ASP cc_start: 0.7439 (t0) cc_final: 0.7060 (p0) REVERT: a 147 ARG cc_start: 0.8349 (mtp85) cc_final: 0.7949 (mtm-85) REVERT: a 192 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8120 (mtpp) REVERT: a 310 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7521 (mp10) outliers start: 29 outliers final: 20 residues processed: 86 average time/residue: 0.4379 time to fit residues: 39.9777 Evaluate side-chains 84 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.128078 restraints weight = 5394.196| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.09 r_work: 0.3221 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5601 Z= 0.167 Angle : 0.588 6.220 7606 Z= 0.300 Chirality : 0.045 0.182 808 Planarity : 0.004 0.036 967 Dihedral : 4.747 35.561 733 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.55 % Allowed : 29.17 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.45 (0.31), residues: 681 helix: 1.22 (0.66), residues: 73 sheet: -1.59 (0.41), residues: 154 loop : -1.12 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.012 0.001 TYR a 256 PHE 0.012 0.002 PHE A 323 TRP 0.008 0.001 TRP A 150 HIS 0.004 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 5592) covalent geometry : angle 0.58472 ( 7588) SS BOND : bond 0.00393 ( 9) SS BOND : angle 1.46037 ( 18) hydrogen bonds : bond 0.03954 ( 133) hydrogen bonds : angle 5.33667 ( 342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.217 Fit side-chains REVERT: A 85 ASP cc_start: 0.7457 (t0) cc_final: 0.7045 (p0) REVERT: A 94 LYS cc_start: 0.8270 (tttt) cc_final: 0.7491 (mptm) REVERT: A 245 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8583 (tttp) REVERT: a 87 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8422 (p) REVERT: a 147 ARG cc_start: 0.8361 (mtp85) cc_final: 0.7967 (mtm-85) REVERT: a 192 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8168 (mtpp) REVERT: a 310 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7515 (mp10) outliers start: 27 outliers final: 19 residues processed: 86 average time/residue: 0.4281 time to fit residues: 39.0827 Evaluate side-chains 86 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 184 MET Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 310 GLN Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 55 optimal weight: 0.2980 chunk 48 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.169797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.131627 restraints weight = 5344.139| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.07 r_work: 0.3314 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.002 0.019 5601 Z= 0.086 Angle : 0.526 8.472 7606 Z= 0.267 Chirality : 0.042 0.172 808 Planarity : 0.003 0.036 967 Dihedral : 4.320 36.196 733 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.04 % Allowed : 30.52 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.23 (0.31), residues: 681 helix: 1.48 (0.64), residues: 73 sheet: -1.25 (0.44), residues: 131 loop : -1.10 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.008 0.001 TYR a 256 PHE 0.009 0.001 PHE A 277 TRP 0.008 0.001 TRP A 150 HIS 0.002 0.000 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 5592) covalent geometry : angle 0.52419 ( 7588) SS BOND : bond 0.00298 ( 9) SS BOND : angle 0.97782 ( 18) hydrogen bonds : bond 0.02945 ( 133) hydrogen bonds : angle 4.96426 ( 342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.219 Fit side-chains REVERT: A 1 ASP cc_start: 0.8022 (m-30) cc_final: 0.7652 (m-30) REVERT: A 94 LYS cc_start: 0.8236 (tttt) cc_final: 0.7485 (mptm) REVERT: a 76 ASN cc_start: 0.8297 (m-40) cc_final: 0.7996 (m-40) REVERT: a 87 THR cc_start: 0.8656 (OUTLIER) cc_final: 0.8397 (p) REVERT: a 147 ARG cc_start: 0.8308 (mtp85) cc_final: 0.7919 (mtm-85) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.4308 time to fit residues: 39.7870 Evaluate side-chains 84 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127418 restraints weight = 5392.073| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.25 r_work: 0.3263 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5601 Z= 0.150 Angle : 0.584 8.155 7606 Z= 0.297 Chirality : 0.044 0.172 808 Planarity : 0.004 0.036 967 Dihedral : 4.577 35.260 733 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.87 % Allowed : 30.86 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.33 (0.31), residues: 681 helix: 1.51 (0.65), residues: 73 sheet: -1.55 (0.41), residues: 154 loop : -1.06 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.011 0.001 TYR a 256 PHE 0.010 0.002 PHE A 323 TRP 0.008 0.001 TRP A 150 HIS 0.004 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5592) covalent geometry : angle 0.58169 ( 7588) SS BOND : bond 0.00349 ( 9) SS BOND : angle 1.26736 ( 18) hydrogen bonds : bond 0.03683 ( 133) hydrogen bonds : angle 5.18407 ( 342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1362 Ramachandran restraints generated. 681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.226 Fit side-chains REVERT: A 85 ASP cc_start: 0.7493 (t0) cc_final: 0.7103 (p0) REVERT: A 94 LYS cc_start: 0.8215 (tttt) cc_final: 0.7492 (mptm) REVERT: A 245 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8540 (tttp) REVERT: a 87 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8407 (p) REVERT: a 147 ARG cc_start: 0.8340 (mtp85) cc_final: 0.7953 (mtm-85) outliers start: 17 outliers final: 15 residues processed: 82 average time/residue: 0.4343 time to fit residues: 37.7972 Evaluate side-chains 83 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain a residue 2 THR Chi-restraints excluded: chain a residue 8 TRP Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 75 LEU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 209 THR Chi-restraints excluded: chain a residue 284 THR Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 327 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.126994 restraints weight = 5394.030| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.24 r_work: 0.3259 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5601 Z= 0.167 Angle : 0.605 8.086 7606 Z= 0.307 Chirality : 0.045 0.181 808 Planarity : 0.004 0.037 967 Dihedral : 4.699 35.072 733 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.54 % Allowed : 30.02 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.41 (0.31), residues: 681 helix: 1.27 (0.64), residues: 75 sheet: -1.58 (0.40), residues: 159 loop : -1.08 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.011 0.001 TYR a 256 PHE 0.011 0.002 PHE A 323 TRP 0.008 0.001 TRP A 150 HIS 0.004 0.001 HIS a 254 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 5592) covalent geometry : angle 0.60198 ( 7588) SS BOND : bond 0.00357 ( 9) SS BOND : angle 1.37126 ( 18) hydrogen bonds : bond 0.03922 ( 133) hydrogen bonds : angle 5.27270 ( 342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.39 seconds wall clock time: 37 minutes 50.64 seconds (2270.64 seconds total)