Starting phenix.real_space_refine on Thu Jun 5 06:13:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbb_37419/06_2025/8wbb_37419_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbb_37419/06_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_37419/06_2025/8wbb_37419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbb_37419/06_2025/8wbb_37419.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbb_37419/06_2025/8wbb_37419_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbb_37419/06_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-5710/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: 4.27, per 1000 atoms: 0.78 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: 1.32 Conformation dependent library (CDL) restraints added in 680.9 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: 0.71 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: 1.63 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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: 1.170 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: 0.040 Set scattering table: 0.070 Process input model: 17.940 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- 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 : 0.728 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: 1.1247 time to fit residues: 99.1802 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 : 0.641 ------------------------------------------------------------------------------- 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: 0.3054 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 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 : 0.638 Fit side-chains REVERT: A 327 ASP cc_start: 0.8285 (m-30) cc_final: 0.8057 (m-30) REVERT: a 62 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.6330 (mpt180) REVERT: a 75 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8014 (mp) REVERT: a 147 ARG cc_start: 0.8093 (mtp85) cc_final: 0.7741 (mtm-85) REVERT: a 162 MET cc_start: 0.3951 (tpp) cc_final: 0.3671 (tpp) REVERT: a 192 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8047 (mtpp) REVERT: a 306 LYS cc_start: 0.8158 (pttt) cc_final: 0.7888 (pttp) outliers start: 29 outliers final: 13 residues processed: 93 average time/residue: 0.9355 time to fit residues: 92.0094 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 : 0.587 ------------------------------------------------------------------------------- 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: 9.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3735 r_free = 0.3735 target = 0.155559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114921 restraints weight = 5408.485| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.11 r_work: 0.3058 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5601 Z= 0.103 Angle : 0.531 5.563 7606 Z= 0.273 Chirality : 0.042 0.170 808 Planarity : 0.003 0.038 967 Dihedral : 4.873 48.192 737 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 : 5.56 % Allowed : 27.99 % 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: -1.31 (0.31), residues: 681 helix: 0.83 (0.66), residues: 73 sheet: -1.02 (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 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 133) hydrogen bonds : angle 5.40340 ( 342) SS BOND : bond 0.00333 ( 9) SS BOND : angle 0.91191 ( 18) covalent geometry : bond 0.00245 ( 5592) covalent geometry : angle 0.52940 ( 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 103 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8300 (m-30) cc_final: 0.7997 (m-30) REVERT: a 147 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7769 (mtm-85) REVERT: a 162 MET cc_start: 0.4025 (tpp) cc_final: 0.3656 (tpp) REVERT: a 192 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8075 (mtpp) REVERT: a 306 LYS cc_start: 0.8239 (pttt) cc_final: 0.7938 (pttp) REVERT: a 310 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7464 (mp10) outliers start: 33 outliers final: 15 residues processed: 95 average time/residue: 0.9394 time to fit residues: 94.6271 Evaluate side-chains 78 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.151888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111211 restraints weight = 5551.277| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.10 r_work: 0.3004 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1410 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= 0.153 Angle : 0.577 6.263 7606 Z= 0.296 Chirality : 0.044 0.172 808 Planarity : 0.004 0.037 967 Dihedral : 4.615 35.267 733 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.40 % Allowed : 28.84 % Favored : 65.77 % 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: -1.34 (0.30), residues: 681 helix: 0.94 (0.66), residues: 73 sheet: -1.13 (0.45), residues: 131 loop : -1.16 (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 323 TYR 0.010 0.001 TYR a 256 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 133) hydrogen bonds : angle 5.41301 ( 342) SS BOND : bond 0.00297 ( 9) SS BOND : angle 1.09153 ( 18) covalent geometry : bond 0.00378 ( 5592) covalent geometry : angle 0.57486 ( 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 100 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 327 ASP cc_start: 0.8331 (m-30) cc_final: 0.8054 (m-30) REVERT: a 147 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7937 (mtm-85) REVERT: a 162 MET cc_start: 0.4090 (tpp) cc_final: 0.3678 (tpp) REVERT: a 192 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8084 (mtpp) REVERT: a 306 LYS cc_start: 0.8125 (pttt) cc_final: 0.7872 (ptmt) REVERT: a 310 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7519 (mp10) outliers start: 32 outliers final: 17 residues processed: 92 average time/residue: 0.7914 time to fit residues: 77.6930 Evaluate side-chains 84 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 65 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.150103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.110297 restraints weight = 5500.578| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.27 r_work: 0.2947 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5601 Z= 0.223 Angle : 0.642 6.871 7606 Z= 0.328 Chirality : 0.047 0.193 808 Planarity : 0.004 0.037 967 Dihedral : 4.942 34.782 733 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.56 % Allowed : 28.33 % Favored : 66.10 % 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: -1.48 (0.30), residues: 681 helix: 0.74 (0.66), residues: 75 sheet: -1.28 (0.44), residues: 136 loop : -1.23 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.006 0.001 HIS a 254 PHE 0.013 0.002 PHE A 323 TYR 0.013 0.002 TYR a 256 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 133) hydrogen bonds : angle 5.58726 ( 342) SS BOND : bond 0.00394 ( 9) SS BOND : angle 1.40252 ( 18) covalent geometry : bond 0.00553 ( 5592) covalent geometry : angle 0.63946 ( 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 95 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.653 Fit side-chains REVERT: A 85 ASP cc_start: 0.7482 (t0) cc_final: 0.7103 (p0) REVERT: A 245 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8486 (ttmm) REVERT: A 327 ASP cc_start: 0.8436 (m-30) cc_final: 0.8171 (m-30) REVERT: a 13 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6478 (tp) REVERT: a 75 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8106 (mp) REVERT: a 147 ARG cc_start: 0.8374 (mtp85) cc_final: 0.8006 (mtm-85) REVERT: a 162 MET cc_start: 0.3990 (tpp) cc_final: 0.3595 (tpp) REVERT: a 192 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8123 (mtpp) REVERT: a 306 LYS cc_start: 0.8016 (pttt) cc_final: 0.7815 (ptmt) REVERT: a 310 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7519 (mp10) outliers start: 33 outliers final: 19 residues processed: 89 average time/residue: 0.9195 time to fit residues: 86.8440 Evaluate side-chains 86 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.166287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.127718 restraints weight = 5305.953| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.14 r_work: 0.3252 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5601 Z= 0.148 Angle : 0.577 6.795 7606 Z= 0.294 Chirality : 0.044 0.179 808 Planarity : 0.004 0.037 967 Dihedral : 4.714 35.537 733 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 5.23 % Allowed : 28.50 % 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 (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: -1.45 (0.30), residues: 681 helix: 1.05 (0.66), residues: 73 sheet: -1.26 (0.44), residues: 131 loop : -1.25 (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 0.012 0.002 PHE A 323 TYR 0.011 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 133) hydrogen bonds : angle 5.37044 ( 342) SS BOND : bond 0.00332 ( 9) SS BOND : angle 1.46996 ( 18) covalent geometry : bond 0.00364 ( 5592) covalent geometry : angle 0.57279 ( 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 93 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.706 Fit side-chains REVERT: A 85 ASP cc_start: 0.7418 (t0) cc_final: 0.7061 (p0) REVERT: A 245 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8451 (ttmm) REVERT: a 13 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6466 (tp) REVERT: a 147 ARG cc_start: 0.8340 (mtp85) cc_final: 0.7952 (mtm-85) REVERT: a 162 MET cc_start: 0.3823 (tpp) cc_final: 0.3433 (tpp) REVERT: a 192 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8127 (mtpp) REVERT: a 306 LYS cc_start: 0.8038 (pttt) cc_final: 0.7760 (ptmt) REVERT: a 310 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7485 (mp10) outliers start: 31 outliers final: 19 residues processed: 90 average time/residue: 0.8714 time to fit residues: 83.3210 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 : 0.642 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.166968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.128637 restraints weight = 5293.342| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.06 r_work: 0.3298 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5601 Z= 0.131 Angle : 0.555 6.159 7606 Z= 0.284 Chirality : 0.043 0.175 808 Planarity : 0.003 0.037 967 Dihedral : 4.576 35.810 733 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.55 % Allowed : 29.51 % 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: -1.39 (0.30), residues: 681 helix: 1.16 (0.65), residues: 73 sheet: -1.33 (0.44), residues: 136 loop : -1.18 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 150 HIS 0.003 0.001 HIS a 254 PHE 0.010 0.001 PHE A 323 TYR 0.010 0.001 TYR a 256 ARG 0.002 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 133) hydrogen bonds : angle 5.23338 ( 342) SS BOND : bond 0.00358 ( 9) SS BOND : angle 1.34748 ( 18) covalent geometry : bond 0.00319 ( 5592) covalent geometry : angle 0.55177 ( 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 92 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.612 Fit side-chains REVERT: A 85 ASP cc_start: 0.7423 (t0) cc_final: 0.7051 (p0) REVERT: A 94 LYS cc_start: 0.8179 (tttt) cc_final: 0.7494 (mptm) REVERT: a 13 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6503 (tp) REVERT: a 87 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8425 (p) REVERT: a 147 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8005 (mtm-85) REVERT: a 162 MET cc_start: 0.3750 (tpp) cc_final: 0.3312 (tpp) REVERT: a 192 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8072 (mtpp) REVERT: a 306 LYS cc_start: 0.8049 (pttt) cc_final: 0.7783 (ptmt) REVERT: a 310 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7475 (mp10) outliers start: 27 outliers final: 19 residues processed: 87 average time/residue: 0.8450 time to fit residues: 78.2869 Evaluate side-chains 87 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 13 LEU 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 228 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: 0.5980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 24 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 = 0.3958 r_free = 0.3958 target = 0.168282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.129937 restraints weight = 5335.061| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.10 r_work: 0.3297 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1816 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 : 0.526 5.999 7606 Z= 0.270 Chirality : 0.042 0.168 808 Planarity : 0.003 0.036 967 Dihedral : 4.397 35.730 733 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.55 % Allowed : 28.67 % 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: -1.27 (0.30), residues: 681 helix: 1.40 (0.65), residues: 73 sheet: -1.23 (0.44), residues: 131 loop : -1.14 (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 0.009 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 0.03175 ( 133) hydrogen bonds : angle 5.03935 ( 342) SS BOND : bond 0.00327 ( 9) SS BOND : angle 1.09411 ( 18) covalent geometry : bond 0.00247 ( 5592) covalent geometry : angle 0.52401 ( 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 93 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.638 Fit side-chains REVERT: A 94 LYS cc_start: 0.8230 (tttt) cc_final: 0.7485 (mptm) REVERT: A 245 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8436 (ttmm) REVERT: a 13 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6472 (tp) REVERT: a 76 ASN cc_start: 0.8331 (m-40) cc_final: 0.8084 (m-40) REVERT: a 87 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8404 (p) REVERT: a 147 ARG cc_start: 0.8306 (mtp85) cc_final: 0.7917 (mtm-85) REVERT: a 162 MET cc_start: 0.3643 (tpp) cc_final: 0.3247 (tpp) REVERT: a 192 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8069 (mtpp) REVERT: a 306 LYS cc_start: 0.8057 (pttt) cc_final: 0.7783 (ptmt) REVERT: a 310 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7460 (mp10) outliers start: 27 outliers final: 17 residues processed: 89 average time/residue: 0.8881 time to fit residues: 83.8559 Evaluate side-chains 87 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 13 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.163071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125440 restraints weight = 5349.655| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.06 r_work: 0.3205 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 5601 Z= 0.267 Angle : 0.682 7.935 7606 Z= 0.344 Chirality : 0.049 0.171 808 Planarity : 0.004 0.038 967 Dihedral : 5.015 34.585 733 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.38 % Allowed : 28.67 % Favored : 66.95 % 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: -1.54 (0.30), residues: 681 helix: 0.98 (0.65), residues: 75 sheet: -1.50 (0.41), residues: 154 loop : -1.23 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 210 HIS 0.007 0.001 HIS a 254 PHE 0.016 0.002 PHE A 323 TYR 0.013 0.002 TYR a 256 ARG 0.003 0.000 ARG a 257 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 133) hydrogen bonds : angle 5.53337 ( 342) SS BOND : bond 0.00483 ( 9) SS BOND : angle 1.74204 ( 18) covalent geometry : bond 0.00665 ( 5592) covalent geometry : angle 0.67726 ( 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 91 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.634 Fit side-chains REVERT: A 85 ASP cc_start: 0.7432 (t0) cc_final: 0.7072 (p0) REVERT: A 94 LYS cc_start: 0.8212 (tttt) cc_final: 0.7488 (mptm) REVERT: A 245 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8472 (ttmm) REVERT: a 13 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6519 (tp) REVERT: a 147 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8063 (mtm-85) REVERT: a 162 MET cc_start: 0.3868 (tpp) cc_final: 0.3448 (tpp) REVERT: a 192 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8149 (mtpp) REVERT: a 306 LYS cc_start: 0.8011 (pttt) cc_final: 0.7751 (ptmt) REVERT: a 310 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7555 (mp10) outliers start: 26 outliers final: 19 residues processed: 86 average time/residue: 0.8661 time to fit residues: 79.1973 Evaluate side-chains 85 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 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 = 0.3950 r_free = 0.3950 target = 0.167566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.129400 restraints weight = 5321.204| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.11 r_work: 0.3249 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5601 Z= 0.106 Angle : 0.552 8.194 7606 Z= 0.280 Chirality : 0.043 0.171 808 Planarity : 0.003 0.036 967 Dihedral : 4.497 35.783 733 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.54 % Allowed : 29.51 % Favored : 66.95 % 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: -1.36 (0.30), residues: 681 helix: 1.38 (0.65), residues: 73 sheet: -1.31 (0.43), residues: 138 loop : -1.20 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.002 0.001 HIS A 254 PHE 0.010 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 0.03244 ( 133) hydrogen bonds : angle 5.11201 ( 342) SS BOND : bond 0.00323 ( 9) SS BOND : angle 1.13638 ( 18) covalent geometry : bond 0.00250 ( 5592) covalent geometry : angle 0.55021 ( 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 91 residues out of total 593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.642 Fit side-chains REVERT: A 85 ASP cc_start: 0.7491 (t0) cc_final: 0.7129 (p0) REVERT: A 94 LYS cc_start: 0.8252 (tttt) cc_final: 0.7487 (mptm) REVERT: A 245 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8481 (ttmm) REVERT: a 13 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6524 (tp) REVERT: a 87 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8427 (p) REVERT: a 147 ARG cc_start: 0.8402 (mtp85) cc_final: 0.8022 (mtm-85) REVERT: a 162 MET cc_start: 0.3646 (tpp) cc_final: 0.3178 (tpp) REVERT: a 306 LYS cc_start: 0.8046 (pttt) cc_final: 0.7764 (ptmt) REVERT: a 310 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7407 (mp10) outliers start: 21 outliers final: 16 residues processed: 88 average time/residue: 0.8585 time to fit residues: 80.6498 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 : 0.699 ------------------------------------------------------------------------------- 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 13 LEU 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: 8.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.164223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126880 restraints weight = 5410.223| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.06 r_work: 0.3210 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5601 Z= 0.199 Angle : 0.629 8.053 7606 Z= 0.318 Chirality : 0.046 0.169 808 Planarity : 0.004 0.037 967 Dihedral : 4.808 35.191 733 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.54 % Allowed : 29.68 % 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: -1.47 (0.31), residues: 681 helix: 1.17 (0.65), residues: 75 sheet: -1.59 (0.40), residues: 159 loop : -1.13 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 150 HIS 0.006 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 294 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 133) hydrogen bonds : angle 5.35618 ( 342) SS BOND : bond 0.00399 ( 9) SS BOND : angle 1.45391 ( 18) covalent geometry : bond 0.00494 ( 5592) covalent geometry : angle 0.62579 ( 7588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4440.28 seconds wall clock time: 76 minutes 51.54 seconds (4611.54 seconds total)