Starting phenix.real_space_refine on Thu Jul 2 01:51:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cti_26991/07_2026/8cti_26991.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cti_26991/07_2026/8cti_26991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cti_26991/07_2026/8cti_26991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cti_26991/07_2026/8cti_26991.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8cti_26991/07_2026/8cti_26991.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cti_26991/07_2026/8cti_26991.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cti_26991/07_2026/8cti_26991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cti_26991/07_2026/8cti_26991.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 70 5.49 5 S 19 5.16 5 C 3114 2.51 5 N 916 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5297 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1658 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2131 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 3 Chain: "C" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1508 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 59} Time building chain proxies: 1.31, per 1000 atoms: 0.25 Number of scatterers: 5297 At special positions: 0 Unit cell: (69.3, 89.1, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 70 15.00 O 1178 8.00 N 916 7.00 C 3114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 148.3 milliseconds 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 890 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 8 sheets defined 19.2% alpha, 32.3% beta 23 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.927A pdb=" N GLU A 48 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 removed outlier: 3.641A pdb=" N VAL A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU A 93 " --> pdb=" O GLY A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 125 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 168 through 174 removed outlier: 4.012A pdb=" N LYS A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 174 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 Processing helix chain 'A' and resid 200 through 214 removed outlier: 3.775A pdb=" N HIS A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.742A pdb=" N LEU A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 138 removed outlier: 8.288A pdb=" N LEU A 137 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 105 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 102 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU A 79 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N PHE A 158 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA A 81 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU A 160 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 83 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR A 155 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N TYR A 195 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N MET A 157 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ILE A 197 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N PHE A 159 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY A 192 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE A 255 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 69 removed outlier: 4.233A pdb=" N ALA B 66 " --> pdb=" O THR B 79 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER B 97 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG B 89 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS B 95 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.587A pdb=" N ALA B 107 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASP B 125 " --> pdb=" O ASP B 121 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 142 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER B 128 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU B 140 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 153 removed outlier: 6.890A pdb=" N ALA B 163 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 151 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU B 161 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 172 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE B 169 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 183 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL B 171 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 196 removed outlier: 3.595A pdb=" N SER B 208 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU B 217 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN B 223 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 252 removed outlier: 3.682A pdb=" N ARG B 248 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 261 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS B 262 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL B 267 " --> pdb=" O CYS B 262 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL B 268 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN B 285 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE B 270 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 297 removed outlier: 3.701A pdb=" N ASP B 294 " --> pdb=" O LEU B 306 " (cutoff:3.500A) 123 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 0.68 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.00: 1 1.00 - 1.22: 8 1.22 - 1.44: 2670 1.44 - 1.66: 2861 1.66 - 1.87: 25 Bond restraints: 5565 Sorted by residual: bond pdb=" CG PRO B 134 " pdb=" CD PRO B 134 " ideal model delta sigma weight residual 1.503 0.783 0.720 3.40e-02 8.65e+02 4.49e+02 bond pdb=" CB PRO B 134 " pdb=" CG PRO B 134 " ideal model delta sigma weight residual 1.492 1.874 -0.382 5.00e-02 4.00e+02 5.83e+01 bond pdb=" N PRO B 134 " pdb=" CD PRO B 134 " ideal model delta sigma weight residual 1.473 1.561 -0.088 1.40e-02 5.10e+03 3.93e+01 bond pdb=" CA PRO B 134 " pdb=" CB PRO B 134 " ideal model delta sigma weight residual 1.534 1.482 0.051 1.49e-02 4.50e+03 1.19e+01 bond pdb=" CB ASP A 45 " pdb=" CG ASP A 45 " ideal model delta sigma weight residual 1.516 1.553 -0.037 2.50e-02 1.60e+03 2.24e+00 ... (remaining 5560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.21: 7869 6.21 - 12.43: 11 12.43 - 18.64: 1 18.64 - 24.86: 1 24.86 - 31.07: 1 Bond angle restraints: 7883 Sorted by residual: angle pdb=" N PRO B 134 " pdb=" CD PRO B 134 " pdb=" CG PRO B 134 " ideal model delta sigma weight residual 103.20 72.13 31.07 1.50e+00 4.44e-01 4.29e+02 angle pdb=" CA PRO B 134 " pdb=" CB PRO B 134 " pdb=" CG PRO B 134 " ideal model delta sigma weight residual 104.50 85.59 18.91 1.90e+00 2.77e-01 9.91e+01 angle pdb=" N PRO B 134 " pdb=" CA PRO B 134 " pdb=" CB PRO B 134 " ideal model delta sigma weight residual 103.33 94.12 9.21 1.10e+00 8.26e-01 7.01e+01 angle pdb=" CA PRO B 134 " pdb=" N PRO B 134 " pdb=" CD PRO B 134 " ideal model delta sigma weight residual 112.00 105.45 6.55 1.40e+00 5.10e-01 2.19e+01 angle pdb=" CB PRO B 134 " pdb=" CG PRO B 134 " pdb=" CD PRO B 134 " ideal model delta sigma weight residual 106.10 91.98 14.12 3.20e+00 9.77e-02 1.95e+01 ... (remaining 7878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 2850 22.15 - 44.30: 231 44.30 - 66.45: 53 66.45 - 88.60: 5 88.60 - 110.75: 1 Dihedral angle restraints: 3140 sinusoidal: 1769 harmonic: 1371 Sorted by residual: dihedral pdb=" O4' U C 19 " pdb=" C1' U C 19 " pdb=" N1 U C 19 " pdb=" C2 U C 19 " ideal model delta sinusoidal sigma weight residual 200.00 89.25 110.75 1 1.50e+01 4.44e-03 5.78e+01 dihedral pdb=" O4' C C 16 " pdb=" C1' C C 16 " pdb=" N1 C C 16 " pdb=" C2 C C 16 " ideal model delta sinusoidal sigma weight residual -128.00 -55.71 -72.29 1 1.70e+01 3.46e-03 2.31e+01 dihedral pdb=" O4' A C 7 " pdb=" C1' A C 7 " pdb=" N9 A C 7 " pdb=" C4 A C 7 " ideal model delta sinusoidal sigma weight residual -106.00 -170.80 64.80 1 1.70e+01 3.46e-03 1.91e+01 ... (remaining 3137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 750 0.043 - 0.085: 123 0.085 - 0.128: 59 0.128 - 0.170: 6 0.170 - 0.213: 1 Chirality restraints: 939 Sorted by residual: chirality pdb=" CA ASP A 45 " pdb=" N ASP A 45 " pdb=" C ASP A 45 " pdb=" CB ASP A 45 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA GLN A 117 " pdb=" N GLN A 117 " pdb=" C GLN A 117 " pdb=" CB GLN A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.01e-01 chirality pdb=" CG LEU B 149 " pdb=" CB LEU B 149 " pdb=" CD1 LEU B 149 " pdb=" CD2 LEU B 149 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 936 not shown) Planarity restraints: 740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 133 " 0.053 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO B 134 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 134 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 134 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 118 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" CG ASP A 118 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 118 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 118 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 133 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C GLU B 133 " 0.035 2.00e-02 2.50e+03 pdb=" O GLU B 133 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO B 134 " -0.012 2.00e-02 2.50e+03 ... (remaining 737 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 300 2.71 - 3.26: 4875 3.26 - 3.81: 9539 3.81 - 4.35: 11728 4.35 - 4.90: 17905 Nonbonded interactions: 44347 Sorted by model distance: nonbonded pdb=" O2' G C 17 " pdb=" N2 G C 57 " model vdw 2.164 3.120 nonbonded pdb=" O GLY A 89 " pdb=" OG SER A 237 " model vdw 2.245 3.040 nonbonded pdb=" O LYS A 143 " pdb=" NZ LYS B 168 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG A 258 " pdb=" O ILE A 259 " model vdw 2.274 3.120 nonbonded pdb=" O ASP A 45 " pdb=" OD1 ASP A 45 " model vdw 2.286 3.040 ... (remaining 44342 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 2.370 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.830 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 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 : 0.011 0.720 5565 Z= 0.345 Angle : 0.792 31.069 7883 Z= 0.439 Chirality : 0.040 0.213 939 Planarity : 0.005 0.075 740 Dihedral : 15.409 110.750 2250 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.49 % Allowed : 22.87 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.38), residues: 459 helix: -1.33 (0.55), residues: 69 sheet: -0.36 (0.42), residues: 162 loop : -1.28 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 17 TYR 0.019 0.001 TYR B 38 PHE 0.016 0.002 PHE A 256 TRP 0.022 0.002 TRP A 206 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.01142 / 0.34 ( 5565) covalent geometry : angle 0.79237 / 0.44 ( 7883) hydrogen bonds : bond 0.20344 / 13.05 ( 182) hydrogen bonds : angle 7.92195 / 5.16 ( 430) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.124 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.0525 time to fit residues: 3.6639 Evaluate side-chains 38 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.202426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.154605 restraints weight = 7590.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.154919 restraints weight = 7248.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.156599 restraints weight = 6467.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.160947 restraints weight = 4320.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.161275 restraints weight = 3391.674| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5565 Z= 0.247 Angle : 0.713 8.421 7883 Z= 0.362 Chirality : 0.043 0.167 939 Planarity : 0.005 0.037 740 Dihedral : 11.839 103.208 1363 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.89 % Allowed : 19.22 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.39), residues: 459 helix: -0.37 (0.57), residues: 70 sheet: -0.22 (0.42), residues: 161 loop : -1.25 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 17 TYR 0.017 0.002 TYR B 218 PHE 0.020 0.003 PHE B 190 TRP 0.011 0.002 TRP A 173 HIS 0.006 0.002 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 ( 5565) covalent geometry : angle 0.71253 / 0.36 ( 7883) hydrogen bonds : bond 0.04402 / 2.75 ( 182) hydrogen bonds : angle 5.88240 / 3.93 ( 430) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.100 Fit side-chains REVERT: A 79 GLU cc_start: 0.7894 (mp0) cc_final: 0.7545 (mp0) REVERT: A 211 PHE cc_start: 0.5038 (OUTLIER) cc_final: 0.4807 (t80) REVERT: B 70 SER cc_start: 0.4859 (p) cc_final: 0.4636 (t) REVERT: B 133 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7672 (tm-30) outliers start: 16 outliers final: 9 residues processed: 61 average time/residue: 0.0365 time to fit residues: 3.3564 Evaluate side-chains 56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.204147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.151875 restraints weight = 7507.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.154885 restraints weight = 5637.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.155751 restraints weight = 5346.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.155937 restraints weight = 3703.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.156917 restraints weight = 3570.640| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5565 Z= 0.130 Angle : 0.552 8.629 7883 Z= 0.280 Chirality : 0.038 0.143 939 Planarity : 0.004 0.034 740 Dihedral : 11.375 100.760 1363 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.14 % Allowed : 20.92 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.39), residues: 459 helix: 0.13 (0.58), residues: 70 sheet: -0.20 (0.40), residues: 176 loop : -1.17 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 17 TYR 0.009 0.001 TYR B 218 PHE 0.022 0.002 PHE B 36 TRP 0.011 0.001 TRP B 216 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 5565) covalent geometry : angle 0.55197 / 0.28 ( 7883) hydrogen bonds : bond 0.03826 / 2.38 ( 182) hydrogen bonds : angle 5.26107 / 3.51 ( 430) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.157 Fit side-chains REVERT: A 79 GLU cc_start: 0.7891 (mp0) cc_final: 0.7392 (mp0) REVERT: A 137 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5707 (mt) REVERT: A 143 LYS cc_start: 0.7750 (ptpt) cc_final: 0.7422 (pttp) REVERT: A 211 PHE cc_start: 0.5118 (OUTLIER) cc_final: 0.4668 (t80) REVERT: B 133 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 187 HIS cc_start: 0.6232 (OUTLIER) cc_final: 0.5956 (m170) outliers start: 17 outliers final: 11 residues processed: 70 average time/residue: 0.0569 time to fit residues: 5.6176 Evaluate side-chains 64 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.200836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.153652 restraints weight = 7486.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.157119 restraints weight = 7938.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.158641 restraints weight = 5852.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.162801 restraints weight = 4043.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.163273 restraints weight = 3205.668| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5565 Z= 0.187 Angle : 0.605 8.946 7883 Z= 0.308 Chirality : 0.040 0.151 939 Planarity : 0.004 0.037 740 Dihedral : 11.235 95.082 1363 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.35 % Allowed : 22.38 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.39), residues: 459 helix: 0.20 (0.58), residues: 70 sheet: -0.16 (0.41), residues: 168 loop : -1.31 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.011 0.002 TYR A 37 PHE 0.030 0.002 PHE A 217 TRP 0.010 0.002 TRP A 206 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 ( 5565) covalent geometry : angle 0.60521 / 0.31 ( 7883) hydrogen bonds : bond 0.04045 / 2.56 ( 182) hydrogen bonds : angle 5.48122 / 3.72 ( 430) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.165 Fit side-chains REVERT: A 79 GLU cc_start: 0.7855 (mp0) cc_final: 0.7317 (mp0) REVERT: A 117 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8494 (pm20) REVERT: A 137 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5914 (mt) REVERT: B 133 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7798 (tm-30) REVERT: B 187 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.6359 (m170) outliers start: 22 outliers final: 13 residues processed: 70 average time/residue: 0.0589 time to fit residues: 5.7131 Evaluate side-chains 60 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4814 r_free = 0.4814 target = 0.211984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.164937 restraints weight = 7818.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.167365 restraints weight = 9348.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.168870 restraints weight = 6912.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.172933 restraints weight = 4497.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.173035 restraints weight = 3684.924| |-----------------------------------------------------------------------------| r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5565 Z= 0.181 Angle : 0.597 9.290 7883 Z= 0.305 Chirality : 0.040 0.171 939 Planarity : 0.005 0.042 740 Dihedral : 11.112 88.777 1363 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 5.60 % Allowed : 21.17 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.39), residues: 459 helix: 0.60 (0.59), residues: 66 sheet: -0.51 (0.39), residues: 183 loop : -1.27 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 17 TYR 0.013 0.002 TYR B 218 PHE 0.015 0.002 PHE A 256 TRP 0.017 0.002 TRP A 206 HIS 0.005 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 ( 5565) covalent geometry : angle 0.59713 / 0.30 ( 7883) hydrogen bonds : bond 0.03939 / 2.48 ( 182) hydrogen bonds : angle 5.38605 / 3.67 ( 430) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.159 Fit side-chains REVERT: A 79 GLU cc_start: 0.7631 (mp0) cc_final: 0.7208 (mp0) REVERT: A 117 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8322 (pm20) REVERT: A 137 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6095 (mt) REVERT: A 138 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.4408 (tmt170) REVERT: A 143 LYS cc_start: 0.7445 (ptpp) cc_final: 0.7143 (pttp) REVERT: A 151 LYS cc_start: 0.7073 (tptm) cc_final: 0.6569 (tttm) REVERT: B 133 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 187 HIS cc_start: 0.6876 (OUTLIER) cc_final: 0.6674 (m170) outliers start: 23 outliers final: 13 residues processed: 74 average time/residue: 0.0576 time to fit residues: 5.7422 Evaluate side-chains 71 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.213226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.162447 restraints weight = 7713.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.168816 restraints weight = 8138.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.169628 restraints weight = 4647.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.170035 restraints weight = 3996.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.170803 restraints weight = 3842.731| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5565 Z= 0.207 Angle : 0.627 9.384 7883 Z= 0.320 Chirality : 0.041 0.154 939 Planarity : 0.005 0.043 740 Dihedral : 11.167 86.551 1363 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 6.33 % Allowed : 22.38 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.39), residues: 459 helix: 0.37 (0.60), residues: 66 sheet: -0.55 (0.41), residues: 175 loop : -1.37 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 17 TYR 0.009 0.002 TYR A 186 PHE 0.016 0.002 PHE B 69 TRP 0.008 0.001 TRP A 46 HIS 0.005 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 ( 5565) covalent geometry : angle 0.62662 / 0.32 ( 7883) hydrogen bonds : bond 0.04376 / 2.78 ( 182) hydrogen bonds : angle 5.58994 / 3.85 ( 430) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.167 Fit side-chains REVERT: A 79 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: A 137 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6214 (mt) REVERT: A 143 LYS cc_start: 0.7428 (ptpp) cc_final: 0.7222 (pttp) REVERT: B 133 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7665 (tm-30) REVERT: B 277 ARG cc_start: 0.7766 (tpt170) cc_final: 0.7550 (tpp-160) outliers start: 26 outliers final: 20 residues processed: 76 average time/residue: 0.0621 time to fit residues: 6.5401 Evaluate side-chains 76 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 228 HIS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 34 optimal weight: 0.0670 chunk 38 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.206141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.156524 restraints weight = 7568.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.159840 restraints weight = 8388.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.161429 restraints weight = 6119.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.164452 restraints weight = 4343.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.164605 restraints weight = 3984.604| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5565 Z= 0.134 Angle : 0.567 9.995 7883 Z= 0.291 Chirality : 0.038 0.148 939 Planarity : 0.004 0.039 740 Dihedral : 10.938 86.325 1363 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.14 % Allowed : 25.06 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.39), residues: 459 helix: 0.61 (0.60), residues: 66 sheet: -0.51 (0.40), residues: 181 loop : -1.20 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.007 0.001 TYR A 150 PHE 0.016 0.002 PHE B 251 TRP 0.008 0.001 TRP A 206 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 5565) covalent geometry : angle 0.56658 / 0.29 ( 7883) hydrogen bonds : bond 0.03526 / 2.21 ( 182) hydrogen bonds : angle 5.28061 / 3.59 ( 430) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.174 Fit side-chains REVERT: A 79 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 143 LYS cc_start: 0.7311 (ptpp) cc_final: 0.7106 (pttp) REVERT: B 133 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7544 (tm-30) outliers start: 17 outliers final: 13 residues processed: 68 average time/residue: 0.0629 time to fit residues: 5.9358 Evaluate side-chains 66 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.209159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.159889 restraints weight = 7718.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.162181 restraints weight = 7898.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.163506 restraints weight = 6769.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.167626 restraints weight = 4759.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.167700 restraints weight = 3984.308| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5565 Z= 0.150 Angle : 0.593 9.358 7883 Z= 0.307 Chirality : 0.039 0.184 939 Planarity : 0.005 0.062 740 Dihedral : 10.897 85.007 1363 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.62 % Allowed : 25.55 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.39), residues: 459 helix: 0.77 (0.61), residues: 66 sheet: -0.43 (0.40), residues: 171 loop : -1.14 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 277 TYR 0.007 0.001 TYR A 150 PHE 0.015 0.002 PHE B 251 TRP 0.007 0.001 TRP B 252 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 5565) covalent geometry : angle 0.59307 / 0.31 ( 7883) hydrogen bonds : bond 0.03604 / 2.27 ( 182) hydrogen bonds : angle 5.32952 / 3.62 ( 430) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 117 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8166 (pm20) REVERT: A 137 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6228 (mt) REVERT: B 133 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7514 (tm-30) REVERT: B 226 CYS cc_start: 0.5361 (t) cc_final: 0.5077 (p) outliers start: 19 outliers final: 15 residues processed: 72 average time/residue: 0.0526 time to fit residues: 5.3909 Evaluate side-chains 72 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 50 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.210209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.161188 restraints weight = 7693.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.163978 restraints weight = 8536.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.165769 restraints weight = 6281.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.168308 restraints weight = 4272.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.168836 restraints weight = 4081.799| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5565 Z= 0.143 Angle : 0.595 9.192 7883 Z= 0.309 Chirality : 0.039 0.178 939 Planarity : 0.005 0.060 740 Dihedral : 10.862 84.606 1363 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.14 % Allowed : 26.03 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.39), residues: 459 helix: 0.73 (0.61), residues: 66 sheet: -0.29 (0.40), residues: 167 loop : -1.23 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 277 TYR 0.007 0.001 TYR A 150 PHE 0.016 0.002 PHE B 251 TRP 0.005 0.001 TRP B 252 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 5565) covalent geometry : angle 0.59470 / 0.31 ( 7883) hydrogen bonds : bond 0.03544 / 2.25 ( 182) hydrogen bonds : angle 5.30559 / 3.58 ( 430) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: A 117 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: A 137 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6179 (mt) REVERT: B 133 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7495 (tm-30) outliers start: 17 outliers final: 14 residues processed: 66 average time/residue: 0.0501 time to fit residues: 4.7490 Evaluate side-chains 68 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.208898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.159610 restraints weight = 7732.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.162405 restraints weight = 8470.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.163834 restraints weight = 6802.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.165050 restraints weight = 4481.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.165943 restraints weight = 4294.279| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5565 Z= 0.148 Angle : 0.599 9.481 7883 Z= 0.310 Chirality : 0.039 0.189 939 Planarity : 0.005 0.059 740 Dihedral : 10.859 84.440 1363 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.14 % Allowed : 26.52 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.39), residues: 459 helix: 0.57 (0.60), residues: 66 sheet: -0.28 (0.40), residues: 164 loop : -1.20 (0.42), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.008 0.001 TYR A 150 PHE 0.015 0.002 PHE B 251 TRP 0.006 0.001 TRP B 252 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 5565) covalent geometry : angle 0.59892 / 0.31 ( 7883) hydrogen bonds : bond 0.03622 / 2.27 ( 182) hydrogen bonds : angle 5.29436 / 3.61 ( 430) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 918 Ramachandran restraints generated. 459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.116 Fit side-chains REVERT: A 79 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: B 71 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5654 (tptt) REVERT: B 133 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7516 (tm-30) outliers start: 17 outliers final: 14 residues processed: 65 average time/residue: 0.0448 time to fit residues: 4.1125 Evaluate side-chains 67 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 260 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.207932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.159283 restraints weight = 7723.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.162153 restraints weight = 8932.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.163815 restraints weight = 6674.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.164882 restraints weight = 4472.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.165448 restraints weight = 4331.793| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5565 Z= 0.161 Angle : 0.611 8.299 7883 Z= 0.315 Chirality : 0.039 0.175 939 Planarity : 0.005 0.061 740 Dihedral : 10.919 85.110 1363 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.14 % Allowed : 25.79 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.39), residues: 459 helix: 0.40 (0.58), residues: 66 sheet: -0.37 (0.40), residues: 164 loop : -1.22 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.009 0.001 TYR B 269 PHE 0.016 0.002 PHE B 251 TRP 0.007 0.001 TRP B 252 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 5565) covalent geometry : angle 0.61100 / 0.32 ( 7883) hydrogen bonds : bond 0.03709 / 2.35 ( 182) hydrogen bonds : angle 5.46791 / 3.73 ( 430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 992.23 seconds wall clock time: 17 minutes 50.31 seconds (1070.31 seconds total)