Starting phenix.real_space_refine on Fri Aug 22 15:28:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9im0_60678/08_2025/9im0_60678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9im0_60678/08_2025/9im0_60678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9im0_60678/08_2025/9im0_60678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9im0_60678/08_2025/9im0_60678.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9im0_60678/08_2025/9im0_60678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9im0_60678/08_2025/9im0_60678.map" } resolution = 2.95 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= 0.008 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3 5.49 5 S 31 5.16 5 C 3126 2.51 5 N 855 2.21 5 O 948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4964 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1828 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "O" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 650 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "A" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2454 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 2 Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2178 SG CYS O 282 66.597 45.226 20.262 1.00 70.05 S ATOM 2197 SG CYS O 285 65.310 41.858 18.744 1.00 79.92 S ATOM 2431 SG CYS O 314 62.747 44.487 19.719 1.00 80.27 S Time building chain proxies: 1.49, per 1000 atoms: 0.30 Number of scatterers: 4964 At special positions: 0 Unit cell: (112.64, 101.2, 63.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 31 16.00 P 3 15.00 O 948 8.00 N 855 7.00 C 3126 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 188.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN O 801 " pdb="ZN ZN O 801 " - pdb=" NE2 HIS O 290 " pdb="ZN ZN O 801 " - pdb=" SG CYS O 285 " pdb="ZN ZN O 801 " - pdb=" SG CYS O 314 " pdb="ZN ZN O 801 " - pdb=" SG CYS O 282 " Number of angles added : 3 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1192 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 9 sheets defined 33.5% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'D' and resid 20 through 26 removed outlier: 3.580A pdb=" N GLN D 25 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 Processing helix chain 'D' and resid 78 through 104 Processing helix chain 'D' and resid 108 through 119 removed outlier: 4.018A pdb=" N ASN D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 161 removed outlier: 4.584A pdb=" N ARG D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 170 through 174 removed outlier: 4.001A pdb=" N VAL D 173 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.506A pdb=" N ASP D 206 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU D 208 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'O' and resid 242 through 254 Processing helix chain 'A' and resid 36 through 47 removed outlier: 4.533A pdb=" N GLU A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 104 removed outlier: 3.540A pdb=" N ILE A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 144 through 150 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.726A pdb=" N SER A 168 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 removed outlier: 3.917A pdb=" N LEU A 208 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.544A pdb=" N SER A 242 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A 243 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 244 " --> pdb=" O ILE A 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 244' Processing helix chain 'A' and resid 245 through 254 removed outlier: 3.825A pdb=" N PHE A 254 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.000A pdb=" N ASN A 262 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 263 " --> pdb=" O ASN A 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 310 through 314 Processing sheet with id=AA1, first strand: chain 'D' and resid 32 through 35 Processing sheet with id=AA2, first strand: chain 'D' and resid 64 through 73 removed outlier: 10.917A pdb=" N VAL D 65 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ASP D 139 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE D 67 " --> pdb=" O PHE D 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 64 through 73 removed outlier: 10.917A pdb=" N VAL D 65 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ASP D 139 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE D 67 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TYR D 219 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP D 139 " --> pdb=" O TYR D 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=AA5, first strand: chain 'O' and resid 294 through 299 removed outlier: 3.702A pdb=" N LYS O 317 " --> pdb=" O ILE O 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 32 through 35 removed outlier: 4.088A pdb=" N PHE A 12 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 64 through 71 removed outlier: 11.155A pdb=" N VAL A 65 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N ASP A 139 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ILE A 67 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 219 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 141 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 221 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 143 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'A' and resid 294 through 299 173 hydrogen bonds defined for protein. 450 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.77 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1643 1.35 - 1.46: 1130 1.46 - 1.58: 2241 1.58 - 1.70: 4 1.70 - 1.82: 43 Bond restraints: 5061 Sorted by residual: bond pdb=" C VAL A 231 " pdb=" N PRO A 232 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.68e+00 bond pdb=" CB ASN A 216 " pdb=" CG ASN A 216 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.67e+00 bond pdb=" CA ASN A 216 " pdb=" CB ASN A 216 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.54e-02 4.22e+03 1.54e+00 bond pdb=" CB LYS O 286 " pdb=" CG LYS O 286 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.41e+00 bond pdb=" CB ASP A 70 " pdb=" CG ASP A 70 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.04e+00 ... (remaining 5056 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 6753 1.99 - 3.98: 90 3.98 - 5.97: 16 5.97 - 7.96: 1 7.96 - 9.95: 1 Bond angle restraints: 6861 Sorted by residual: angle pdb=" CA LEU A 274 " pdb=" CB LEU A 274 " pdb=" CG LEU A 274 " ideal model delta sigma weight residual 116.30 126.25 -9.95 3.50e+00 8.16e-02 8.08e+00 angle pdb=" C ILE A 241 " pdb=" N SER A 242 " pdb=" CA SER A 242 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 6.98e+00 angle pdb=" CB LYS O 286 " pdb=" CG LYS O 286 " pdb=" CD LYS O 286 " ideal model delta sigma weight residual 111.30 117.15 -5.85 2.30e+00 1.89e-01 6.48e+00 angle pdb=" N PRO D 199 " pdb=" CA PRO D 199 " pdb=" C PRO D 199 " ideal model delta sigma weight residual 110.70 113.76 -3.06 1.22e+00 6.72e-01 6.29e+00 angle pdb=" CA ASN A 216 " pdb=" CB ASN A 216 " pdb=" CG ASN A 216 " ideal model delta sigma weight residual 112.60 115.10 -2.50 1.00e+00 1.00e+00 6.23e+00 ... (remaining 6856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 2795 17.97 - 35.94: 266 35.94 - 53.91: 37 53.91 - 71.88: 9 71.88 - 89.84: 4 Dihedral angle restraints: 3111 sinusoidal: 1294 harmonic: 1817 Sorted by residual: dihedral pdb=" CA MET A 150 " pdb=" C MET A 150 " pdb=" N LYS A 151 " pdb=" CA LYS A 151 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ARG A 288 " pdb=" C ARG A 288 " pdb=" N SER A 289 " pdb=" CA SER A 289 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA PHE A 240 " pdb=" C PHE A 240 " pdb=" N ILE A 241 " pdb=" CA ILE A 241 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 489 0.033 - 0.065: 188 0.065 - 0.098: 65 0.098 - 0.130: 40 0.130 - 0.163: 3 Chirality restraints: 785 Sorted by residual: chirality pdb=" CA ASN A 216 " pdb=" N ASN A 216 " pdb=" C ASN A 216 " pdb=" CB ASN A 216 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA ILE A 303 " pdb=" N ILE A 303 " pdb=" C ILE A 303 " pdb=" CB ILE A 303 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL A 231 " pdb=" N VAL A 231 " pdb=" C VAL A 231 " pdb=" CB VAL A 231 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 782 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 221 " -0.012 2.00e-02 2.50e+03 1.45e-02 3.66e+00 pdb=" CG PHE A 221 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 221 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 221 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 221 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 221 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 221 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 120 " -0.008 2.00e-02 2.50e+03 1.31e-02 3.01e+00 pdb=" CG PHE A 120 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A 120 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 120 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 120 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 120 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 120 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 199 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO D 200 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 200 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 200 " 0.024 5.00e-02 4.00e+02 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 972 2.78 - 3.31: 4567 3.31 - 3.84: 7537 3.84 - 4.37: 8311 4.37 - 4.90: 14656 Nonbonded interactions: 36043 Sorted by model distance: nonbonded pdb=" OG SER A 115 " pdb=" O ASP A 139 " model vdw 2.250 3.040 nonbonded pdb=" O ASN D 217 " pdb=" ND2 ASN D 217 " model vdw 2.251 3.120 nonbonded pdb=" N GLU D 49 " pdb=" OE1 GLU D 49 " model vdw 2.258 3.120 nonbonded pdb=" OD1 ASN O 256 " pdb=" OG1 THR O 280 " model vdw 2.288 3.040 nonbonded pdb=" O ARG A 99 " pdb=" OG1 THR A 103 " model vdw 2.290 3.040 ... (remaining 36038 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.520 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:10.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6923 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 : 0.002 0.036 5065 Z= 0.116 Angle : 0.577 9.948 6864 Z= 0.306 Chirality : 0.044 0.163 785 Planarity : 0.004 0.043 882 Dihedral : 14.167 89.844 1919 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.35 % Allowed : 11.11 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.36), residues: 599 helix: 0.69 (0.42), residues: 173 sheet: 0.54 (0.54), residues: 100 loop : -0.56 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 6 TYR 0.007 0.001 TYR A 62 PHE 0.033 0.002 PHE A 221 TRP 0.004 0.001 TRP A 236 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 5061) covalent geometry : angle 0.57352 ( 6861) hydrogen bonds : bond 0.18085 ( 166) hydrogen bonds : angle 5.31608 ( 450) metal coordination : bond 0.00622 ( 4) metal coordination : angle 3.24157 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.242 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 102 average time/residue: 0.5135 time to fit residues: 54.7368 Evaluate side-chains 98 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 253 ILE Chi-restraints excluded: chain A residue 241 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.0470 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.0010 chunk 25 optimal weight: 0.0980 chunk 58 optimal weight: 0.3980 overall best weight: 0.2284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.176054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155741 restraints weight = 7475.700| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.48 r_work: 0.3890 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5065 Z= 0.145 Angle : 0.573 7.828 6864 Z= 0.305 Chirality : 0.045 0.148 785 Planarity : 0.004 0.043 882 Dihedral : 8.082 87.532 704 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.23 % Allowed : 11.46 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.35), residues: 599 helix: 0.80 (0.41), residues: 174 sheet: 0.39 (0.57), residues: 91 loop : -0.78 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 6 TYR 0.009 0.001 TYR D 43 PHE 0.018 0.002 PHE A 100 TRP 0.005 0.001 TRP A 236 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5061) covalent geometry : angle 0.56892 ( 6861) hydrogen bonds : bond 0.04801 ( 166) hydrogen bonds : angle 4.40866 ( 450) metal coordination : bond 0.00657 ( 4) metal coordination : angle 3.29915 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.197 Fit side-chains REVERT: D 206 ASP cc_start: 0.7887 (m-30) cc_final: 0.7647 (m-30) REVERT: D 217 ASN cc_start: 0.7489 (t0) cc_final: 0.7273 (t0) outliers start: 7 outliers final: 6 residues processed: 96 average time/residue: 0.3700 time to fit residues: 37.7460 Evaluate side-chains 93 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain O residue 253 ILE Chi-restraints excluded: chain O residue 272 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 214 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 0.0870 chunk 1 optimal weight: 0.0670 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.171913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.151547 restraints weight = 7487.295| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.48 r_work: 0.3839 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5065 Z= 0.207 Angle : 0.633 8.141 6864 Z= 0.336 Chirality : 0.047 0.152 785 Planarity : 0.005 0.038 882 Dihedral : 7.718 86.617 702 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.01 % Favored : 92.82 % Rotamer: Outliers : 2.29 % Allowed : 13.76 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.34), residues: 599 helix: 0.29 (0.40), residues: 180 sheet: 0.14 (0.56), residues: 87 loop : -0.73 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.013 0.002 TYR D 43 PHE 0.041 0.003 PHE A 221 TRP 0.005 0.001 TRP A 236 HIS 0.008 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 5061) covalent geometry : angle 0.62738 ( 6861) hydrogen bonds : bond 0.06045 ( 166) hydrogen bonds : angle 4.55094 ( 450) metal coordination : bond 0.00722 ( 4) metal coordination : angle 4.01741 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.7782 (m110) cc_final: 0.7565 (m110) REVERT: A 54 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6842 (tt0) REVERT: A 310 ASN cc_start: 0.7600 (t0) cc_final: 0.7339 (t0) outliers start: 13 outliers final: 9 residues processed: 103 average time/residue: 0.4822 time to fit residues: 52.0532 Evaluate side-chains 105 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain O residue 253 ILE Chi-restraints excluded: chain O residue 272 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 241 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 35 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.0000 chunk 39 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 256 ASN A 260 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.150619 restraints weight = 7422.355| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.46 r_work: 0.3833 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5065 Z= 0.225 Angle : 0.634 8.807 6864 Z= 0.339 Chirality : 0.046 0.146 785 Planarity : 0.005 0.046 882 Dihedral : 7.592 76.107 702 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.01 % Favored : 91.82 % Rotamer: Outliers : 3.35 % Allowed : 15.17 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.34), residues: 599 helix: 0.38 (0.40), residues: 174 sheet: 0.20 (0.59), residues: 81 loop : -1.01 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.012 0.002 TYR D 43 PHE 0.039 0.002 PHE A 221 TRP 0.004 0.001 TRP A 236 HIS 0.007 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00530 ( 5061) covalent geometry : angle 0.62732 ( 6861) hydrogen bonds : bond 0.05899 ( 166) hydrogen bonds : angle 4.51449 ( 450) metal coordination : bond 0.00806 ( 4) metal coordination : angle 4.31013 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: D 175 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7940 (ptp90) REVERT: A 60 GLU cc_start: 0.6750 (mp0) cc_final: 0.6512 (mp0) REVERT: A 136 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8309 (mt) REVERT: A 216 ASN cc_start: 0.6483 (p0) cc_final: 0.6161 (p0) REVERT: A 310 ASN cc_start: 0.7594 (t0) cc_final: 0.7350 (t0) outliers start: 19 outliers final: 12 residues processed: 113 average time/residue: 0.5161 time to fit residues: 60.9706 Evaluate side-chains 116 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 216 ASN Chi-restraints excluded: chain O residue 272 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 0.0670 chunk 55 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 0.0010 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.170811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.150738 restraints weight = 7593.226| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.52 r_work: 0.3828 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5065 Z= 0.182 Angle : 0.619 10.788 6864 Z= 0.327 Chirality : 0.046 0.154 785 Planarity : 0.004 0.044 882 Dihedral : 7.333 70.716 700 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.18 % Favored : 92.65 % Rotamer: Outliers : 2.82 % Allowed : 17.11 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.34), residues: 599 helix: 0.40 (0.40), residues: 174 sheet: 0.11 (0.56), residues: 87 loop : -0.98 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.010 0.002 TYR D 43 PHE 0.039 0.002 PHE A 221 TRP 0.002 0.001 TRP A 236 HIS 0.006 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 5061) covalent geometry : angle 0.61333 ( 6861) hydrogen bonds : bond 0.05407 ( 166) hydrogen bonds : angle 4.43845 ( 450) metal coordination : bond 0.00727 ( 4) metal coordination : angle 4.01111 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.7745 (m110) cc_final: 0.7528 (m110) REVERT: A 8 ASN cc_start: 0.7588 (t0) cc_final: 0.7347 (t0) REVERT: A 133 PHE cc_start: 0.7110 (OUTLIER) cc_final: 0.6623 (p90) REVERT: A 310 ASN cc_start: 0.7626 (t0) cc_final: 0.7387 (t0) outliers start: 16 outliers final: 10 residues processed: 104 average time/residue: 0.4705 time to fit residues: 51.3487 Evaluate side-chains 110 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain O residue 272 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.0670 chunk 32 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.169990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.149719 restraints weight = 7681.334| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.55 r_work: 0.3814 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5065 Z= 0.223 Angle : 0.659 10.475 6864 Z= 0.350 Chirality : 0.047 0.180 785 Planarity : 0.005 0.049 882 Dihedral : 7.368 64.776 700 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.68 % Favored : 92.15 % Rotamer: Outliers : 4.94 % Allowed : 16.05 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.34), residues: 599 helix: 0.35 (0.40), residues: 174 sheet: 0.14 (0.59), residues: 81 loop : -1.12 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.013 0.002 TYR D 43 PHE 0.037 0.002 PHE A 221 TRP 0.004 0.001 TRP A 236 HIS 0.007 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 5061) covalent geometry : angle 0.65385 ( 6861) hydrogen bonds : bond 0.05947 ( 166) hydrogen bonds : angle 4.58673 ( 450) metal coordination : bond 0.00784 ( 4) metal coordination : angle 4.11011 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.7238 (tt0) cc_final: 0.6937 (tt0) REVERT: A 60 GLU cc_start: 0.6767 (mp0) cc_final: 0.6552 (mp0) REVERT: A 133 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6632 (p90) REVERT: A 310 ASN cc_start: 0.7638 (t0) cc_final: 0.7407 (t0) outliers start: 28 outliers final: 14 residues processed: 114 average time/residue: 0.4952 time to fit residues: 59.1311 Evaluate side-chains 112 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain O residue 272 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 253 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 40 optimal weight: 0.0980 chunk 25 optimal weight: 0.0980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.0060 overall best weight: 0.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 256 ASN A 260 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.173518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.153180 restraints weight = 7566.565| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.52 r_work: 0.3861 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5065 Z= 0.125 Angle : 0.590 8.898 6864 Z= 0.315 Chirality : 0.045 0.240 785 Planarity : 0.004 0.036 882 Dihedral : 6.911 62.508 700 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.34 % Favored : 93.49 % Rotamer: Outliers : 2.65 % Allowed : 18.69 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.35), residues: 599 helix: 0.51 (0.41), residues: 173 sheet: 0.09 (0.57), residues: 87 loop : -0.88 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 175 TYR 0.007 0.001 TYR O 306 PHE 0.040 0.002 PHE A 221 TRP 0.001 0.000 TRP A 236 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5061) covalent geometry : angle 0.58565 ( 6861) hydrogen bonds : bond 0.04409 ( 166) hydrogen bonds : angle 4.30943 ( 450) metal coordination : bond 0.00759 ( 4) metal coordination : angle 3.49377 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: D 94 SER cc_start: 0.7389 (m) cc_final: 0.7140 (p) REVERT: A 8 ASN cc_start: 0.7554 (t0) cc_final: 0.7322 (t0) REVERT: A 133 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6594 (p90) REVERT: A 310 ASN cc_start: 0.7523 (t0) cc_final: 0.7303 (t0) outliers start: 15 outliers final: 10 residues processed: 98 average time/residue: 0.4824 time to fit residues: 49.5457 Evaluate side-chains 100 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain O residue 253 ILE Chi-restraints excluded: chain O residue 272 VAL Chi-restraints excluded: chain A residue 117 ARG Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 241 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 0.0970 chunk 27 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 ASN A 203 ASN A 256 ASN A 260 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.169782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149574 restraints weight = 7593.841| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.52 r_work: 0.3814 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5065 Z= 0.242 Angle : 0.666 11.643 6864 Z= 0.355 Chirality : 0.047 0.163 785 Planarity : 0.005 0.049 882 Dihedral : 7.248 61.712 700 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.01 % Favored : 91.82 % Rotamer: Outliers : 3.70 % Allowed : 17.99 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.35), residues: 599 helix: 0.44 (0.41), residues: 173 sheet: 0.04 (0.55), residues: 91 loop : -1.10 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 57 TYR 0.012 0.002 TYR D 43 PHE 0.042 0.003 PHE A 221 TRP 0.006 0.002 TRP A 236 HIS 0.007 0.001 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 5061) covalent geometry : angle 0.66054 ( 6861) hydrogen bonds : bond 0.06041 ( 166) hydrogen bonds : angle 4.67792 ( 450) metal coordination : bond 0.00863 ( 4) metal coordination : angle 4.27198 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: D 94 SER cc_start: 0.7392 (m) cc_final: 0.7183 (p) REVERT: A 54 GLU cc_start: 0.7213 (tt0) cc_final: 0.6928 (tt0) REVERT: A 60 GLU cc_start: 0.6740 (mp0) cc_final: 0.6526 (mp0) REVERT: A 133 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6640 (p90) REVERT: A 260 ASN cc_start: 0.4412 (t0) cc_final: 0.4120 (t0) REVERT: A 310 ASN cc_start: 0.7600 (t0) cc_final: 0.7383 (t0) outliers start: 21 outliers final: 15 residues processed: 108 average time/residue: 0.5020 time to fit residues: 56.7075 Evaluate side-chains 115 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain O residue 253 ILE Chi-restraints excluded: chain O residue 272 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 274 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 37 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.168558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.148399 restraints weight = 7452.935| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.48 r_work: 0.3804 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 5065 Z= 0.277 Angle : 0.717 12.217 6864 Z= 0.379 Chirality : 0.049 0.171 785 Planarity : 0.005 0.056 882 Dihedral : 7.445 62.400 700 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.51 % Favored : 91.32 % Rotamer: Outliers : 3.70 % Allowed : 17.81 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.34), residues: 599 helix: 0.13 (0.41), residues: 174 sheet: -0.08 (0.54), residues: 91 loop : -1.30 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 57 TYR 0.013 0.002 TYR D 43 PHE 0.043 0.003 PHE A 221 TRP 0.005 0.002 TRP A 236 HIS 0.009 0.002 HIS A 290 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 5061) covalent geometry : angle 0.71028 ( 6861) hydrogen bonds : bond 0.06383 ( 166) hydrogen bonds : angle 4.83072 ( 450) metal coordination : bond 0.00858 ( 4) metal coordination : angle 4.73434 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: D 94 SER cc_start: 0.7414 (m) cc_final: 0.7180 (p) REVERT: A 54 GLU cc_start: 0.7201 (tt0) cc_final: 0.6910 (tt0) REVERT: A 60 GLU cc_start: 0.6787 (mp0) cc_final: 0.6587 (mp0) REVERT: A 133 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6637 (p90) REVERT: A 214 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.6205 (ttm) REVERT: A 217 ASN cc_start: 0.7088 (p0) cc_final: 0.6884 (p0) REVERT: A 260 ASN cc_start: 0.4687 (t0) cc_final: 0.4460 (t0) REVERT: A 310 ASN cc_start: 0.7607 (t0) cc_final: 0.7381 (t0) outliers start: 21 outliers final: 15 residues processed: 112 average time/residue: 0.4904 time to fit residues: 57.5695 Evaluate side-chains 122 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain O residue 255 ILE Chi-restraints excluded: chain O residue 272 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 15 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 16 optimal weight: 0.0670 chunk 13 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.171644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.151162 restraints weight = 7574.999| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.54 r_work: 0.3835 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5065 Z= 0.159 Angle : 0.654 11.923 6864 Z= 0.340 Chirality : 0.045 0.185 785 Planarity : 0.004 0.046 882 Dihedral : 7.086 61.982 700 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.35 % Favored : 92.49 % Rotamer: Outliers : 3.17 % Allowed : 18.87 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.35), residues: 599 helix: 0.42 (0.42), residues: 173 sheet: -0.04 (0.56), residues: 87 loop : -1.18 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.009 0.001 TYR D 43 PHE 0.045 0.002 PHE A 221 TRP 0.002 0.001 TRP A 236 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5061) covalent geometry : angle 0.64893 ( 6861) hydrogen bonds : bond 0.05015 ( 166) hydrogen bonds : angle 4.58776 ( 450) metal coordination : bond 0.00745 ( 4) metal coordination : angle 3.82736 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1198 Ramachandran restraints generated. 599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: D 94 SER cc_start: 0.7363 (m) cc_final: 0.7158 (p) REVERT: A 54 GLU cc_start: 0.7223 (tt0) cc_final: 0.6923 (tt0) REVERT: A 133 PHE cc_start: 0.7099 (OUTLIER) cc_final: 0.6595 (p90) REVERT: A 260 ASN cc_start: 0.4346 (t0) cc_final: 0.4086 (t0) outliers start: 18 outliers final: 12 residues processed: 104 average time/residue: 0.5220 time to fit residues: 56.7637 Evaluate side-chains 111 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain O residue 272 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 133 PHE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 241 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 0.0040 chunk 51 optimal weight: 0.0870 chunk 32 optimal weight: 0.0070 chunk 17 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 43 optimal weight: 0.2980 chunk 1 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 overall best weight: 0.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN A 217 ASN A 256 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.174957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154681 restraints weight = 7762.488| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.56 r_work: 0.3875 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5065 Z= 0.118 Angle : 0.598 10.547 6864 Z= 0.315 Chirality : 0.044 0.221 785 Planarity : 0.004 0.036 882 Dihedral : 6.653 59.900 700 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.51 % Favored : 93.32 % Rotamer: Outliers : 1.76 % Allowed : 21.16 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.35), residues: 599 helix: 0.41 (0.42), residues: 173 sheet: 0.08 (0.53), residues: 101 loop : -1.04 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 181 TYR 0.007 0.001 TYR O 306 PHE 0.037 0.002 PHE A 221 TRP 0.003 0.001 TRP A 236 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5061) covalent geometry : angle 0.59413 ( 6861) hydrogen bonds : bond 0.04175 ( 166) hydrogen bonds : angle 4.39120 ( 450) metal coordination : bond 0.00669 ( 4) metal coordination : angle 3.23259 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.13 seconds wall clock time: 36 minutes 44.52 seconds (2204.52 seconds total)