Starting phenix.real_space_refine on Thu Sep 10 23:41:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cti_26991/09_2026/8cti_26991.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cti_26991/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cti_26991/09_2026/8cti_26991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cti_26991/09_2026/8cti_26991.map" model { file = "/net/cci-nas-00/data/ceres_data/8cti_26991/09_2026/8cti_26991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cti_26991/09_2026/8cti_26991.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8cti_26991/09_2026/8cti_26991.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cti_26991/09_2026/8cti_26991.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 71} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 59} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.17, per 1000 atoms: 0.22 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: 0.94 Conformation dependent library (CDL) restraints added in 151.1 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: 0.67 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: 0.98 Time building geometry restraints manager: 0.64 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 - 16.09: 2580 16.09 - 32.18: 320 32.18 - 48.27: 129 48.27 - 64.36: 92 64.36 - 80.45: 19 Dihedral angle restraints: 3140 sinusoidal: 1769 harmonic: 1371 Sorted by residual: dihedral pdb=" C4' C C 16 " pdb=" C3' C C 16 " pdb=" C2' C C 16 " pdb=" C1' C C 16 " ideal model delta sinusoidal sigma weight residual 36.35 -36.92 73.27 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' G C 17 " pdb=" C3' G C 17 " pdb=" C2' G C 17 " pdb=" C1' G C 17 " ideal model delta sinusoidal sigma weight residual 36.34 -36.89 73.23 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' A C 58 " pdb=" C3' A C 58 " pdb=" C2' A C 58 " pdb=" C1' A C 58 " ideal model delta sinusoidal sigma weight residual 36.34 -35.85 72.19 1 3.10e+00 1.04e-01 6.93e+02 ... (remaining 3137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 727 0.058 - 0.115: 104 0.115 - 0.173: 15 0.173 - 0.231: 37 0.231 - 0.288: 56 Chirality restraints: 939 Sorted by residual: chirality pdb=" C2' U C 20 " pdb=" C3' U C 20 " pdb=" O2' U C 20 " pdb=" C1' U C 20 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' C C 16 " pdb=" C3' C C 16 " pdb=" O2' C C 16 " pdb=" C1' C C 16 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" P U C 19 " pdb=" OP1 U C 19 " pdb=" OP2 U C 19 " pdb=" O5' U C 19 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (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: 2.330 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.390 Find NCS groups from input model: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- 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= 0.351 Angle : 0.936 31.069 7883 Z= 0.473 Chirality : 0.085 0.288 939 Planarity : 0.005 0.075 740 Dihedral : 19.093 80.446 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 0.01150 / 0.35 ( 5565) covalent geometry : angle 0.93556 / 0.47 ( 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 : 0.165 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.0532 time to fit residues: 3.7475 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 : 0.161 ------------------------------------------------------------------------------- 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: 7.9990 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: 9.9990 chunk 53 optimal weight: 4.9990 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 = 0.4696 r_free = 0.4696 target = 0.202859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.143640 restraints weight = 7559.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.147633 restraints weight = 4829.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.150210 restraints weight = 3709.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.151815 restraints weight = 3151.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.152596 restraints weight = 2857.021| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 5565 Z= 0.262 Angle : 1.055 14.733 7883 Z= 0.453 Chirality : 0.080 0.796 939 Planarity : 0.005 0.037 740 Dihedral : 16.904 166.546 1363 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.41 % Allowed : 20.19 % Favored : 76.40 % 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: -1.15 (0.39), residues: 459 helix: -0.38 (0.57), residues: 70 sheet: -0.31 (0.42), residues: 163 loop : -1.16 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 17 TYR 0.016 0.002 TYR B 218 PHE 0.021 0.003 PHE A 149 TRP 0.010 0.002 TRP B 252 HIS 0.006 0.002 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.26 ( 5565) covalent geometry : angle 1.05518 / 0.45 ( 7883) hydrogen bonds : bond 0.04700 / 2.81 ( 182) hydrogen bonds : angle 5.83604 / 3.90 ( 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 63 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.100 Fit side-chains REVERT: A 79 GLU cc_start: 0.7927 (mp0) cc_final: 0.7509 (mp0) REVERT: B 70 SER cc_start: 0.4940 (p) cc_final: 0.4729 (t) REVERT: B 133 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7725 (tm-30) outliers start: 14 outliers final: 9 residues processed: 60 average time/residue: 0.0443 time to fit residues: 4.0361 Evaluate side-chains 53 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.158 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 0.0170 chunk 42 optimal weight: 5.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 GLN ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.207578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.159705 restraints weight = 7463.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.162380 restraints weight = 6667.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.164088 restraints weight = 5066.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.168379 restraints weight = 3641.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.168623 restraints weight = 2942.281| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5565 Z= 0.145 Angle : 0.803 10.744 7883 Z= 0.348 Chirality : 0.067 0.595 939 Planarity : 0.004 0.039 740 Dihedral : 16.553 170.765 1363 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.41 % Allowed : 22.14 % Favored : 74.45 % 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: 0.13 (0.58), residues: 70 sheet: -0.12 (0.41), residues: 168 loop : -1.20 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 17 TYR 0.009 0.001 TYR B 218 PHE 0.017 0.002 PHE A 211 TRP 0.011 0.001 TRP B 216 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 5565) covalent geometry : angle 0.80270 / 0.35 ( 7883) hydrogen bonds : bond 0.03873 / 2.41 ( 182) hydrogen bonds : angle 5.18089 / 3.46 ( 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 71 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.109 Fit side-chains REVERT: A 143 LYS cc_start: 0.7794 (ptpt) cc_final: 0.7438 (pttp) REVERT: A 151 LYS cc_start: 0.6586 (tptm) cc_final: 0.6382 (tptm) REVERT: A 211 PHE cc_start: 0.5342 (OUTLIER) cc_final: 0.3997 (t80) REVERT: B 133 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 187 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5829 (m170) outliers start: 14 outliers final: 9 residues processed: 67 average time/residue: 0.0501 time to fit residues: 4.8679 Evaluate side-chains 60 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4699 r_free = 0.4699 target = 0.203031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.154895 restraints weight = 7492.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.156928 restraints weight = 6838.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.158124 restraints weight = 6159.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.161394 restraints weight = 4257.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.161478 restraints weight = 3680.691| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5565 Z= 0.168 Angle : 0.812 11.794 7883 Z= 0.354 Chirality : 0.067 0.619 939 Planarity : 0.004 0.039 740 Dihedral : 16.596 168.628 1363 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.11 % Allowed : 21.41 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.86 (0.39), residues: 459 helix: 0.26 (0.58), residues: 70 sheet: -0.00 (0.42), residues: 166 loop : -1.25 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 36 TYR 0.010 0.001 TYR A 37 PHE 0.015 0.002 PHE A 256 TRP 0.012 0.002 TRP A 206 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 5565) covalent geometry : angle 0.81207 / 0.35 ( 7883) hydrogen bonds : bond 0.04029 / 2.57 ( 182) hydrogen bonds : angle 5.21372 / 3.51 ( 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 71 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.140 Fit side-chains REVERT: A 37 TYR cc_start: 0.6569 (p90) cc_final: 0.6334 (p90) REVERT: A 79 GLU cc_start: 0.8013 (mp0) cc_final: 0.7758 (mp0) REVERT: A 137 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5898 (mt) REVERT: A 211 PHE cc_start: 0.5347 (OUTLIER) cc_final: 0.3938 (t80) REVERT: B 133 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 187 HIS cc_start: 0.6382 (OUTLIER) cc_final: 0.6100 (m170) REVERT: B 244 PHE cc_start: 0.2967 (m-80) cc_final: 0.2761 (m-10) outliers start: 21 outliers final: 14 residues processed: 66 average time/residue: 0.0589 time to fit residues: 5.4311 Evaluate side-chains 60 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 173 TRP Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP 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 164 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: 0.8980 chunk 41 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.4645 r_free = 0.4645 target = 0.196689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.147703 restraints weight = 7695.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.151716 restraints weight = 8040.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.152806 restraints weight = 5632.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.156938 restraints weight = 3947.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.156951 restraints weight = 3250.411| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5565 Z= 0.256 Angle : 0.899 11.886 7883 Z= 0.400 Chirality : 0.070 0.631 939 Planarity : 0.005 0.039 740 Dihedral : 16.882 169.699 1363 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 8.52 % Allowed : 18.49 % Favored : 72.99 % 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: -1.19 (0.38), residues: 459 helix: 0.21 (0.59), residues: 66 sheet: -0.41 (0.41), residues: 172 loop : -1.37 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 119 TYR 0.013 0.002 TYR A 186 PHE 0.022 0.003 PHE B 190 TRP 0.014 0.002 TRP A 206 HIS 0.006 0.002 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.26 ( 5565) covalent geometry : angle 0.89923 / 0.40 ( 7883) hydrogen bonds : bond 0.05034 / 3.26 ( 182) hydrogen bonds : angle 5.78387 / 3.97 ( 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 89 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 54 time to evaluate : 0.167 Fit side-chains REVERT: A 117 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: A 132 GLN cc_start: 0.2750 (OUTLIER) cc_final: 0.2203 (mm-40) REVERT: A 137 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5963 (mt) REVERT: A 138 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.4557 (tmt170) REVERT: A 211 PHE cc_start: 0.5834 (OUTLIER) cc_final: 0.4314 (t80) REVERT: B 133 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 244 PHE cc_start: 0.3043 (m-80) cc_final: 0.2832 (m-10) outliers start: 35 outliers final: 21 residues processed: 81 average time/residue: 0.0639 time to fit residues: 7.1197 Evaluate side-chains 74 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.162 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 132 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 176 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 78 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 164 ASP 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: 2.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 5 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 = 0.4670 r_free = 0.4670 target = 0.199034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.147301 restraints weight = 7645.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.150379 restraints weight = 6048.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.151313 restraints weight = 5519.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.152614 restraints weight = 3743.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.153047 restraints weight = 3460.284| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5565 Z= 0.155 Angle : 0.801 10.969 7883 Z= 0.355 Chirality : 0.063 0.431 939 Planarity : 0.004 0.036 740 Dihedral : 16.824 170.696 1363 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.35 % Allowed : 24.33 % Favored : 70.32 % 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: 0.48 (0.60), residues: 66 sheet: -0.52 (0.40), residues: 184 loop : -1.14 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.023 0.002 TYR A 115 PHE 0.016 0.002 PHE A 211 TRP 0.013 0.001 TRP B 216 HIS 0.008 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 5565) covalent geometry : angle 0.80051 / 0.36 ( 7883) hydrogen bonds : bond 0.04099 / 2.68 ( 182) hydrogen bonds : angle 5.28283 / 3.57 ( 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 74 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.159 Fit side-chains REVERT: A 79 GLU cc_start: 0.7860 (mp0) cc_final: 0.7512 (mp0) REVERT: A 132 GLN cc_start: 0.2444 (OUTLIER) cc_final: 0.1942 (mm-40) REVERT: A 137 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.5847 (mt) REVERT: A 211 PHE cc_start: 0.5860 (OUTLIER) cc_final: 0.4228 (t80) REVERT: B 133 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 244 PHE cc_start: 0.3108 (m-80) cc_final: 0.2907 (m-10) REVERT: B 277 ARG cc_start: 0.8224 (tpt170) cc_final: 0.7770 (tpp80) REVERT: B 307 GLN cc_start: 0.4407 (pm20) cc_final: 0.4168 (pm20) outliers start: 22 outliers final: 14 residues processed: 69 average time/residue: 0.0631 time to fit residues: 5.8956 Evaluate side-chains 63 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 132 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 A residue 211 PHE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP 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 146 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 260 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: 10.0000 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.207192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.158087 restraints weight = 7297.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.158016 restraints weight = 6467.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.159806 restraints weight = 5834.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.161519 restraints weight = 3775.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.162303 restraints weight = 3377.315| |-----------------------------------------------------------------------------| r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.5374 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= 0.132 Angle : 0.743 9.779 7883 Z= 0.329 Chirality : 0.059 0.373 939 Planarity : 0.004 0.037 740 Dihedral : 16.765 172.309 1363 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.84 % Allowed : 23.60 % Favored : 70.56 % 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: -0.83 (0.38), residues: 459 helix: 0.68 (0.58), residues: 70 sheet: -0.22 (0.40), residues: 174 loop : -1.19 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 138 TYR 0.027 0.001 TYR A 115 PHE 0.017 0.001 PHE A 211 TRP 0.008 0.001 TRP B 216 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 5565) covalent geometry : angle 0.74261 / 0.33 ( 7883) hydrogen bonds : bond 0.03817 / 2.58 ( 182) hydrogen bonds : angle 5.08906 / 3.41 ( 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 71 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.138 Fit side-chains REVERT: A 79 GLU cc_start: 0.7668 (mp0) cc_final: 0.7204 (mp0) REVERT: A 117 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: A 132 GLN cc_start: 0.2414 (OUTLIER) cc_final: 0.1846 (mm-40) REVERT: A 137 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6040 (mt) REVERT: A 211 PHE cc_start: 0.5610 (OUTLIER) cc_final: 0.4001 (t80) REVERT: B 133 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7494 (tm-30) REVERT: B 164 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6517 (p0) REVERT: B 244 PHE cc_start: 0.3043 (m-80) cc_final: 0.2831 (m-10) REVERT: B 307 GLN cc_start: 0.4654 (pm20) cc_final: 0.4421 (pm20) outliers start: 24 outliers final: 14 residues processed: 67 average time/residue: 0.0489 time to fit residues: 4.6620 Evaluate side-chains 65 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE 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 199 THR 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: 0.8980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.199807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.148587 restraints weight = 7251.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.150212 restraints weight = 6501.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.151813 restraints weight = 5956.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.153121 restraints weight = 4053.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.153927 restraints weight = 3774.733| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.5787 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= 0.192 Angle : 0.808 9.296 7883 Z= 0.364 Chirality : 0.060 0.381 939 Planarity : 0.005 0.040 740 Dihedral : 16.691 171.543 1363 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 7.06 % Allowed : 22.87 % 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: -0.93 (0.39), residues: 459 helix: 0.76 (0.60), residues: 66 sheet: -0.50 (0.40), residues: 174 loop : -1.08 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 277 TYR 0.009 0.001 TYR A 186 PHE 0.027 0.002 PHE A 252 TRP 0.021 0.002 TRP A 206 HIS 0.005 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 5565) covalent geometry : angle 0.80760 / 0.36 ( 7883) hydrogen bonds : bond 0.04144 / 2.73 ( 182) hydrogen bonds : angle 5.38919 / 3.67 ( 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 79 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 0.160 Fit side-chains REVERT: A 79 GLU cc_start: 0.7765 (mp0) cc_final: 0.7470 (mp0) REVERT: A 117 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: A 132 GLN cc_start: 0.2499 (OUTLIER) cc_final: 0.1881 (mm-40) REVERT: A 137 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6176 (mt) REVERT: A 211 PHE cc_start: 0.5894 (OUTLIER) cc_final: 0.4178 (t80) REVERT: B 133 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7517 (tm-30) REVERT: B 307 GLN cc_start: 0.4973 (pm20) cc_final: 0.4747 (pm20) outliers start: 29 outliers final: 22 residues processed: 72 average time/residue: 0.0495 time to fit residues: 5.0892 Evaluate side-chains 71 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 45 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 81 ASP 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 164 ASP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 228 HIS 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: 1.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 228 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.200236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.150746 restraints weight = 7368.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.150049 restraints weight = 7209.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.151850 restraints weight = 6528.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.153222 restraints weight = 4432.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.154133 restraints weight = 3981.436| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5565 Z= 0.190 Angle : 0.798 9.101 7883 Z= 0.362 Chirality : 0.059 0.383 939 Planarity : 0.005 0.041 740 Dihedral : 16.700 171.711 1363 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.84 % Allowed : 24.57 % Favored : 69.59 % 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: -1.02 (0.38), residues: 459 helix: 0.64 (0.61), residues: 66 sheet: -0.50 (0.40), residues: 171 loop : -1.17 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 277 TYR 0.009 0.001 TYR A 150 PHE 0.023 0.002 PHE A 252 TRP 0.016 0.001 TRP A 206 HIS 0.006 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 5565) covalent geometry : angle 0.79823 / 0.36 ( 7883) hydrogen bonds : bond 0.04182 / 2.79 ( 182) hydrogen bonds : angle 5.43701 / 3.70 ( 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 74 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.169 Fit side-chains REVERT: A 79 GLU cc_start: 0.7729 (mp0) cc_final: 0.7436 (mp0) REVERT: A 117 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8458 (pm20) REVERT: A 132 GLN cc_start: 0.2576 (OUTLIER) cc_final: 0.1913 (mm-40) REVERT: A 137 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6133 (mt) REVERT: A 211 PHE cc_start: 0.5962 (OUTLIER) cc_final: 0.4238 (t80) REVERT: B 133 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7518 (tm-30) REVERT: B 254 GLN cc_start: 0.7606 (tt0) cc_final: 0.7212 (tm-30) REVERT: B 307 GLN cc_start: 0.5066 (pm20) cc_final: 0.4799 (pm20) outliers start: 24 outliers final: 19 residues processed: 69 average time/residue: 0.0570 time to fit residues: 5.6141 Evaluate side-chains 75 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 132 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 A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 69 PHE Chi-restraints excluded: chain B residue 81 ASP 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 162 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 228 HIS 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: 6.9990 chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.0050 chunk 43 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 = 0.4680 r_free = 0.4680 target = 0.203027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.152087 restraints weight = 7346.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.153889 restraints weight = 6613.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.155221 restraints weight = 5859.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.155919 restraints weight = 3756.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.156595 restraints weight = 3554.294| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5565 Z= 0.139 Angle : 0.761 8.896 7883 Z= 0.345 Chirality : 0.058 0.387 939 Planarity : 0.004 0.040 740 Dihedral : 16.598 172.441 1363 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.11 % Allowed : 26.03 % Favored : 68.86 % 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: -0.89 (0.38), residues: 459 helix: 0.73 (0.60), residues: 66 sheet: -0.39 (0.40), residues: 166 loop : -1.10 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 277 TYR 0.008 0.001 TYR A 150 PHE 0.022 0.002 PHE A 252 TRP 0.017 0.001 TRP A 206 HIS 0.011 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 5565) covalent geometry : angle 0.76136 / 0.35 ( 7883) hydrogen bonds : bond 0.03697 / 2.47 ( 182) hydrogen bonds : angle 5.22033 / 3.54 ( 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: 21 poor density : 49 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7688 (mp0) cc_final: 0.7339 (mp0) REVERT: A 117 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8430 (pm20) REVERT: A 132 GLN cc_start: 0.2475 (OUTLIER) cc_final: 0.1846 (mm-40) REVERT: A 211 PHE cc_start: 0.5835 (OUTLIER) cc_final: 0.4067 (t80) REVERT: B 133 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7468 (tm-30) REVERT: B 307 GLN cc_start: 0.5169 (pm20) cc_final: 0.4884 (pm20) outliers start: 21 outliers final: 16 residues processed: 66 average time/residue: 0.0611 time to fit residues: 5.7294 Evaluate side-chains 66 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 104 LEU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 171 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain B residue 64 ILE 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 151 VAL Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 228 HIS 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: 0.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 0.0010 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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 = 0.4679 r_free = 0.4679 target = 0.202784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.154087 restraints weight = 7305.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.154771 restraints weight = 7000.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.156357 restraints weight = 6223.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.157326 restraints weight = 4189.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.158361 restraints weight = 3738.121| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5565 Z= 0.144 Angle : 0.754 7.987 7883 Z= 0.343 Chirality : 0.058 0.394 939 Planarity : 0.004 0.040 740 Dihedral : 16.522 173.264 1363 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.38 % Allowed : 26.03 % Favored : 69.59 % 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: -0.80 (0.39), residues: 459 helix: 0.79 (0.61), residues: 66 sheet: -0.38 (0.39), residues: 174 loop : -0.99 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 277 TYR 0.008 0.001 TYR A 150 PHE 0.020 0.002 PHE A 252 TRP 0.016 0.001 TRP A 206 HIS 0.004 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 5565) covalent geometry : angle 0.75386 / 0.34 ( 7883) hydrogen bonds : bond 0.03675 / 2.45 ( 182) hydrogen bonds : angle 5.22108 / 3.54 ( 430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1111.64 seconds wall clock time: 20 minutes 14.19 seconds (1214.19 seconds total)