Starting phenix.real_space_refine on Sat May 10 06:41:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbb_37419/05_2025/8wbb_37419_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbb_37419/05_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_37419/05_2025/8wbb_37419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbb_37419/05_2025/8wbb_37419.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbb_37419/05_2025/8wbb_37419_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbb_37419/05_2025/8wbb_37419_neut.cif" } resolution = 2.9 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= 0.167 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 4.41, per 1000 atoms: 0.81 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: 1.41 Conformation dependent library (CDL) restraints added in 707.0 milliseconds 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: 0.81 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: 1.75 Time building geometry restraints manager: 1.66 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: 0.980 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.360 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.390 ------------------------------------------------------------------------------- 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 : 8.88 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 (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: -1.79 (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 TRP 0.007 0.001 TRP A 150 HIS 0.003 0.001 HIS a 254 PHE 0.013 0.002 PHE A 20 TYR 0.010 0.001 TYR a 256 ARG 0.006 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.27243 ( 133) hydrogen bonds : angle 9.40424 ( 342) SS BOND : bond 0.00354 ( 9) SS BOND : angle 1.42951 ( 18) covalent geometry : bond 0.00368 ( 5592) covalent geometry : angle 0.61970 ( 7588) *********************** 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 : 0.646 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: 1.0729 time to fit residues: 94.8312 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 : 0.627 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.155588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114975 restraints weight = 5430.731| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.13 r_work: 0.3053 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5601 Z= 0.106 Angle : 0.556 5.876 7606 Z= 0.288 Chirality : 0.043 0.161 808 Planarity : 0.004 0.038 967 Dihedral : 5.200 47.332 741 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.98 % Rotamer: Outliers : 4.89 % Allowed : 28.33 % 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 (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: -1.49 (0.31), residues: 681 helix: 0.50 (0.68), residues: 71 sheet: -1.15 (0.46), residues: 133 loop : -1.22 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 150 HIS 0.003 0.001 HIS a 254 PHE 0.011 0.001 PHE a 20 TYR 0.008 0.001 TYR a 256 ARG 0.005 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 133) hydrogen bonds : angle 5.99958 ( 342) SS BOND : bond 0.00255 ( 9) SS BOND : angle 0.97469 ( 18) covalent geometry : bond 0.00250 ( 5592) covalent geometry : angle 0.55476 ( 7588) *********************** 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 99 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.574 Fit side-chains REVERT: A 327 ASP cc_start: 0.8284 (m-30) cc_final: 0.8058 (m-30) REVERT: a 62 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6323 (mpt180) REVERT: a 75 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8022 (mp) REVERT: a 147 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7740 (mtm-85) REVERT: a 162 MET cc_start: 0.3965 (tpp) cc_final: 0.3684 (tpp) REVERT: a 192 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.8047 (mtpp) REVERT: a 306 LYS cc_start: 0.8158 (pttt) cc_final: 0.7890 (pttp) outliers start: 29 outliers final: 13 residues processed: 93 average time/residue: 0.9201 time to fit residues: 90.6644 Evaluate side-chains 82 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 327 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.157269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.117045 restraints weight = 5372.282| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.05 r_work: 0.3051 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5601 Z= 0.100 Angle : 0.528 5.518 7606 Z= 0.272 Chirality : 0.042 0.171 808 Planarity : 0.003 0.038 967 Dihedral : 4.861 48.237 737 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.55 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 (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: -1.30 (0.31), residues: 681 helix: 0.83 (0.66), residues: 73 sheet: -1.01 (0.46), residues: 131 loop : -1.14 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 150 HIS 0.003 0.000 HIS a 254 PHE 0.009 0.001 PHE a 277 TYR 0.008 0.001 TYR a 256 ARG 0.004 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 133) hydrogen bonds : angle 5.39877 ( 342) SS BOND : bond 0.00401 ( 9) SS BOND : angle 0.90117 ( 18) covalent geometry : bond 0.00238 ( 5592) covalent geometry : angle 0.52639 ( 7588) *********************** 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 104 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 70 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8280 (m-30) cc_final: 0.7981 (m-30) REVERT: a 147 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7738 (mtm-85) REVERT: a 162 MET cc_start: 0.4006 (tpp) cc_final: 0.3631 (tpp) REVERT: a 192 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8060 (mtpp) REVERT: a 306 LYS cc_start: 0.8222 (pttt) cc_final: 0.7919 (pttp) REVERT: a 310 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7440 (mp10) outliers start: 34 outliers final: 16 residues processed: 96 average time/residue: 0.8658 time to fit residues: 88.2221 Evaluate side-chains 79 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 98 SER Chi-restraints excluded: chain a residue 157 ASP 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 12 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 0.1980 chunk 1 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.152279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111478 restraints weight = 5540.809| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.10 r_work: 0.3009 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5601 Z= 0.144 Angle : 0.570 6.175 7606 Z= 0.292 Chirality : 0.044 0.173 808 Planarity : 0.004 0.037 967 Dihedral : 4.585 35.293 733 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.40 % Allowed : 29.01 % 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 (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: -1.32 (0.30), residues: 681 helix: 0.96 (0.66), residues: 73 sheet: -1.13 (0.45), residues: 131 loop : -1.15 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.004 0.001 HIS a 254 PHE 0.010 0.002 PHE a 277 TYR 0.010 0.001 TYR a 256 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 133) hydrogen bonds : angle 5.37949 ( 342) SS BOND : bond 0.00269 ( 9) SS BOND : angle 1.06268 ( 18) covalent geometry : bond 0.00353 ( 5592) covalent geometry : angle 0.56817 ( 7588) *********************** 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 101 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8330 (m-30) cc_final: 0.8048 (m-30) REVERT: a 147 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7923 (mtm-85) REVERT: a 162 MET cc_start: 0.4023 (tpp) cc_final: 0.3625 (tpp) REVERT: a 192 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8081 (mtpp) REVERT: a 306 LYS cc_start: 0.8123 (pttt) cc_final: 0.7870 (ptmt) REVERT: a 310 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7503 (mp10) outliers start: 32 outliers final: 20 residues processed: 91 average time/residue: 0.8005 time to fit residues: 77.7645 Evaluate side-chains 88 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 342 GLU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 a 181 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.162441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.124108 restraints weight = 5381.186| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.17 r_work: 0.3203 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 5601 Z= 0.318 Angle : 0.725 8.025 7606 Z= 0.368 Chirality : 0.050 0.175 808 Planarity : 0.004 0.038 967 Dihedral : 5.236 34.131 733 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 6.41 % Allowed : 27.99 % 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 (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: -1.59 (0.30), residues: 681 helix: 0.71 (0.68), residues: 73 sheet: -1.38 (0.43), residues: 144 loop : -1.29 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 210 HIS 0.007 0.001 HIS a 254 PHE 0.017 0.002 PHE A 323 TYR 0.014 0.002 TYR a 256 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.05487 ( 133) hydrogen bonds : angle 5.79722 ( 342) SS BOND : bond 0.00606 ( 9) SS BOND : angle 1.72532 ( 18) covalent geometry : bond 0.00795 ( 5592) covalent geometry : angle 0.72109 ( 7588) *********************** 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 101 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 63 time to evaluate : 0.588 Fit side-chains REVERT: A 85 ASP cc_start: 0.7403 (t0) cc_final: 0.7035 (p0) REVERT: A 245 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8497 (ttmm) REVERT: a 13 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6535 (tp) REVERT: a 20 PHE cc_start: 0.8445 (t80) cc_final: 0.8219 (t80) REVERT: a 75 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7922 (mp) REVERT: a 147 ARG cc_start: 0.8373 (mtp85) cc_final: 0.7973 (mtm-85) REVERT: a 162 MET cc_start: 0.3980 (tpp) cc_final: 0.3564 (tpp) REVERT: a 192 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8160 (mtpp) REVERT: a 306 LYS cc_start: 0.7984 (pttt) cc_final: 0.7709 (ptmt) REVERT: a 310 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7553 (mp10) outliers start: 38 outliers final: 20 residues processed: 94 average time/residue: 0.8864 time to fit residues: 88.4399 Evaluate side-chains 87 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 245 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 342 GLU 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 58 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.168533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.130020 restraints weight = 5306.355| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.19 r_work: 0.3306 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5601 Z= 0.100 Angle : 0.536 6.761 7606 Z= 0.275 Chirality : 0.042 0.175 808 Planarity : 0.003 0.036 967 Dihedral : 4.555 36.005 733 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.05 % Allowed : 30.02 % 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 (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: -1.40 (0.30), residues: 681 helix: 1.06 (0.66), residues: 73 sheet: -1.22 (0.45), residues: 131 loop : -1.22 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.003 0.001 HIS A 254 PHE 0.011 0.001 PHE A 323 TYR 0.009 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03286 ( 133) hydrogen bonds : angle 5.24122 ( 342) SS BOND : bond 0.00300 ( 9) SS BOND : angle 1.24618 ( 18) covalent geometry : bond 0.00235 ( 5592) covalent geometry : angle 0.53291 ( 7588) *********************** 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 89 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.627 Fit side-chains REVERT: A 66 ILE cc_start: 0.8413 (mt) cc_final: 0.8185 (mt) REVERT: A 85 ASP cc_start: 0.7392 (t0) cc_final: 0.7041 (p0) REVERT: a 147 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7920 (mtm-85) REVERT: a 162 MET cc_start: 0.3873 (tpp) cc_final: 0.3375 (tpp) REVERT: a 192 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8083 (mtpp) REVERT: a 306 LYS cc_start: 0.8070 (pttt) cc_final: 0.7800 (ptmt) REVERT: a 310 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7429 (mp10) outliers start: 24 outliers final: 13 residues processed: 86 average time/residue: 0.8280 time to fit residues: 75.9672 Evaluate side-chains 79 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 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 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 36 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.164521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.125819 restraints weight = 5321.129| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.14 r_work: 0.3251 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5601 Z= 0.205 Angle : 0.624 6.560 7606 Z= 0.318 Chirality : 0.046 0.178 808 Planarity : 0.004 0.037 967 Dihedral : 4.875 35.369 733 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.22 % Allowed : 29.34 % 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 (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: -1.53 (0.30), residues: 681 helix: 0.87 (0.66), residues: 75 sheet: -1.37 (0.43), residues: 136 loop : -1.28 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.005 0.001 HIS a 254 PHE 0.013 0.002 PHE A 323 TYR 0.012 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 133) hydrogen bonds : angle 5.46189 ( 342) SS BOND : bond 0.00437 ( 9) SS BOND : angle 1.68117 ( 18) covalent geometry : bond 0.00510 ( 5592) covalent geometry : angle 0.61925 ( 7588) *********************** 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 87 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.666 Fit side-chains REVERT: A 85 ASP cc_start: 0.7406 (t0) cc_final: 0.7041 (p0) REVERT: A 94 LYS cc_start: 0.8221 (tttt) cc_final: 0.7507 (mptm) REVERT: A 245 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8449 (ttmm) REVERT: a 147 ARG cc_start: 0.8380 (mtp85) cc_final: 0.7994 (mtm-85) REVERT: a 162 MET cc_start: 0.3912 (tpp) cc_final: 0.3517 (tpp) REVERT: a 192 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8136 (mtpp) REVERT: a 306 LYS cc_start: 0.8042 (pttt) cc_final: 0.7772 (ptmt) REVERT: a 310 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7543 (mp10) outliers start: 25 outliers final: 17 residues processed: 82 average time/residue: 0.9035 time to fit residues: 78.7660 Evaluate side-chains 82 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 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 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 157 ASP 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 17 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131101 restraints weight = 5315.862| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.17 r_work: 0.3305 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5601 Z= 0.092 Angle : 0.516 5.895 7606 Z= 0.266 Chirality : 0.042 0.165 808 Planarity : 0.003 0.036 967 Dihedral : 4.389 36.323 733 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.71 % Allowed : 29.68 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.30 (0.30), residues: 681 helix: 1.34 (0.66), residues: 73 sheet: -1.24 (0.45), residues: 131 loop : -1.15 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.003 0.001 HIS A 254 PHE 0.008 0.001 PHE A 277 TYR 0.009 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 133) hydrogen bonds : angle 5.07035 ( 342) SS BOND : bond 0.00306 ( 9) SS BOND : angle 1.07722 ( 18) covalent geometry : bond 0.00215 ( 5592) covalent geometry : angle 0.51409 ( 7588) *********************** 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 94 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.589 Fit side-chains REVERT: A 85 ASP cc_start: 0.7397 (t0) cc_final: 0.7026 (p0) REVERT: A 94 LYS cc_start: 0.8233 (tttt) cc_final: 0.7489 (mptm) REVERT: a 76 ASN cc_start: 0.8307 (m-40) cc_final: 0.8026 (m-40) REVERT: a 87 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8394 (p) REVERT: a 147 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7928 (mtm-85) REVERT: a 162 MET cc_start: 0.3635 (tpp) cc_final: 0.3184 (tpp) REVERT: a 306 LYS cc_start: 0.8051 (pttt) cc_final: 0.7787 (ptmt) REVERT: a 310 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7351 (mp10) outliers start: 22 outliers final: 16 residues processed: 91 average time/residue: 0.8576 time to fit residues: 83.0503 Evaluate side-chains 85 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 157 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.161211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122841 restraints weight = 5370.644| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.15 r_work: 0.3176 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 5601 Z= 0.376 Angle : 0.777 8.971 7606 Z= 0.392 Chirality : 0.053 0.187 808 Planarity : 0.004 0.038 967 Dihedral : 5.307 34.517 733 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.38 % Allowed : 28.84 % 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 (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: -1.67 (0.30), residues: 681 helix: 0.80 (0.66), residues: 73 sheet: -1.48 (0.42), residues: 151 loop : -1.34 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 210 HIS 0.009 0.002 HIS a 254 PHE 0.020 0.003 PHE A 323 TYR 0.015 0.002 TYR a 256 ARG 0.004 0.001 ARG a 257 Details of bonding type rmsd hydrogen bonds : bond 0.05723 ( 133) hydrogen bonds : angle 5.73593 ( 342) SS BOND : bond 0.00605 ( 9) SS BOND : angle 2.17662 ( 18) covalent geometry : bond 0.00941 ( 5592) covalent geometry : angle 0.77079 ( 7588) *********************** 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 89 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.647 Fit side-chains REVERT: A 85 ASP cc_start: 0.7445 (t0) cc_final: 0.7012 (p0) REVERT: A 94 LYS cc_start: 0.8271 (tttt) cc_final: 0.7444 (mptm) REVERT: a 75 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7891 (mp) REVERT: a 147 ARG cc_start: 0.8385 (mtp85) cc_final: 0.8044 (mtm-85) REVERT: a 162 MET cc_start: 0.3813 (tpp) cc_final: 0.3446 (tpp) REVERT: a 192 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8158 (mtpp) REVERT: a 306 LYS cc_start: 0.7959 (pttt) cc_final: 0.7671 (ptmt) REVERT: a 310 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7514 (mp10) outliers start: 26 outliers final: 18 residues processed: 84 average time/residue: 0.8965 time to fit residues: 79.9711 Evaluate side-chains 80 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.127017 restraints weight = 5326.910| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.18 r_work: 0.3275 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1861 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= 0.147 Angle : 0.595 8.132 7606 Z= 0.303 Chirality : 0.044 0.181 808 Planarity : 0.004 0.037 967 Dihedral : 4.792 35.829 733 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.37 % Allowed : 30.19 % 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 (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: -1.58 (0.30), residues: 681 helix: 1.00 (0.66), residues: 74 sheet: -1.63 (0.41), residues: 154 loop : -1.22 (0.26), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.004 0.001 HIS a 254 PHE 0.011 0.002 PHE a 277 TYR 0.010 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 133) hydrogen bonds : angle 5.33976 ( 342) SS BOND : bond 0.00379 ( 9) SS BOND : angle 1.39784 ( 18) covalent geometry : bond 0.00358 ( 5592) covalent geometry : angle 0.59225 ( 7588) ********************** 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 80 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.576 Fit side-chains REVERT: A 85 ASP cc_start: 0.7457 (t0) cc_final: 0.7058 (p0) REVERT: A 94 LYS cc_start: 0.8206 (tttt) cc_final: 0.7467 (mptm) REVERT: a 87 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8459 (p) REVERT: a 147 ARG cc_start: 0.8410 (mtp85) cc_final: 0.8028 (mtm-85) REVERT: a 162 MET cc_start: 0.3706 (tpp) cc_final: 0.3322 (tpp) REVERT: a 306 LYS cc_start: 0.8040 (pttt) cc_final: 0.7764 (ptmt) REVERT: a 310 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7457 (mp10) outliers start: 20 outliers final: 17 residues processed: 79 average time/residue: 0.8558 time to fit residues: 72.0077 Evaluate side-chains 80 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 98 SER Chi-restraints excluded: chain a residue 132 THR Chi-restraints excluded: chain a residue 157 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS a 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.167567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130147 restraints weight = 5384.937| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.08 r_work: 0.3293 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1898 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= 0.115 Angle : 0.556 8.122 7606 Z= 0.281 Chirality : 0.043 0.179 808 Planarity : 0.003 0.037 967 Dihedral : 4.535 36.428 733 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.54 % Allowed : 29.85 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.43 (0.30), residues: 681 helix: 1.45 (0.66), residues: 72 sheet: -1.36 (0.43), residues: 138 loop : -1.26 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.003 0.001 HIS a 254 PHE 0.009 0.001 PHE a 277 TYR 0.010 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03370 ( 133) hydrogen bonds : angle 5.11960 ( 342) SS BOND : bond 0.00308 ( 9) SS BOND : angle 1.15659 ( 18) covalent geometry : bond 0.00277 ( 5592) covalent geometry : angle 0.55350 ( 7588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4248.89 seconds wall clock time: 74 minutes 1.30 seconds (4441.30 seconds total)