Starting phenix.real_space_refine on Thu Jul 24 02:13:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9im0_60678/07_2025/9im0_60678.cif Found real_map, /net/cci-nas-00/data/ceres_data/9im0_60678/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9im0_60678/07_2025/9im0_60678.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9im0_60678/07_2025/9im0_60678.map" model { file = "/net/cci-nas-00/data/ceres_data/9im0_60678/07_2025/9im0_60678.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9im0_60678/07_2025/9im0_60678.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.06, per 1000 atoms: 1.02 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: 1.17 Conformation dependent library (CDL) restraints added in 654.3 milliseconds 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: 0.51 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: 1.15 Time building geometry restraints manager: 1.39 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: 7.640 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.760 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.001 TRP A 236 HIS 0.005 0.001 HIS D 109 PHE 0.033 0.002 PHE A 221 TYR 0.007 0.001 TYR A 62 ARG 0.005 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.18085 ( 166) hydrogen bonds : angle 5.31608 ( 450) metal coordination : bond 0.00622 ( 4) metal coordination : angle 3.24157 ( 3) covalent geometry : bond 0.00246 ( 5061) covalent geometry : angle 0.57352 ( 6861) *********************** 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 : 0.578 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 102 average time/residue: 0.9449 time to fit residues: 101.4063 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 : 0.552 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4191 r_free = 0.4191 target = 0.172164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.151940 restraints weight = 7338.254| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.44 r_work: 0.3847 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5065 Z= 0.241 Angle : 0.655 8.289 6864 Z= 0.351 Chirality : 0.048 0.158 785 Planarity : 0.005 0.039 882 Dihedral : 8.429 89.243 704 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.32 % Rotamer: Outliers : 2.12 % Allowed : 10.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.34), residues: 599 helix: 0.42 (0.40), residues: 174 sheet: 0.17 (0.56), residues: 87 loop : -0.91 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 236 HIS 0.008 0.002 HIS A 290 PHE 0.031 0.003 PHE A 100 TYR 0.012 0.002 TYR A 306 ARG 0.003 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.06540 ( 166) hydrogen bonds : angle 4.68472 ( 450) metal coordination : bond 0.00914 ( 4) metal coordination : angle 4.13001 ( 3) covalent geometry : bond 0.00569 ( 5061) covalent geometry : angle 0.64993 ( 6861) *********************** 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 120 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.582 Fit side-chains REVERT: D 206 ASP cc_start: 0.7908 (m-30) cc_final: 0.7689 (m-30) REVERT: D 217 ASN cc_start: 0.7517 (t0) cc_final: 0.7283 (t0) REVERT: A 310 ASN cc_start: 0.7614 (t0) cc_final: 0.7301 (t0) outliers start: 12 outliers final: 8 residues processed: 112 average time/residue: 1.0548 time to fit residues: 124.4758 Evaluate side-chains 112 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 O residue 308 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.0870 chunk 24 optimal weight: 0.0040 chunk 32 optimal weight: 0.0870 chunk 15 optimal weight: 0.0970 chunk 20 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 8 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 overall best weight: 0.0724 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.176658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.156192 restraints weight = 7544.799| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.52 r_work: 0.3900 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1425 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= 0.106 Angle : 0.530 7.971 6864 Z= 0.285 Chirality : 0.043 0.134 785 Planarity : 0.004 0.041 882 Dihedral : 7.589 87.772 704 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.49 % Rotamer: Outliers : 1.76 % Allowed : 14.64 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.35), residues: 599 helix: 0.57 (0.41), residues: 180 sheet: 0.37 (0.56), residues: 91 loop : -0.63 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 236 HIS 0.004 0.001 HIS D 109 PHE 0.018 0.002 PHE D 35 TYR 0.007 0.001 TYR O 306 ARG 0.001 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 166) hydrogen bonds : angle 4.16254 ( 450) metal coordination : bond 0.00874 ( 4) metal coordination : angle 3.48236 ( 3) covalent geometry : bond 0.00225 ( 5061) covalent geometry : angle 0.52502 ( 6861) *********************** 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 103 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6104 (mmm) outliers start: 10 outliers final: 5 residues processed: 100 average time/residue: 1.3066 time to fit residues: 140.0125 Evaluate side-chains 96 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 PHE 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 150 MET 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 15 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 54 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 32 optimal weight: 0.2980 overall best weight: 0.1274 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.176439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.155676 restraints weight = 7615.964| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.58 r_work: 0.3889 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5065 Z= 0.113 Angle : 0.535 8.371 6864 Z= 0.283 Chirality : 0.044 0.142 785 Planarity : 0.004 0.042 882 Dihedral : 7.292 85.119 704 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.01 % Favored : 93.82 % Rotamer: Outliers : 1.76 % Allowed : 15.70 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.35), residues: 599 helix: 0.63 (0.41), residues: 179 sheet: 0.33 (0.57), residues: 91 loop : -0.65 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 236 HIS 0.004 0.001 HIS D 109 PHE 0.017 0.001 PHE D 35 TYR 0.007 0.001 TYR D 43 ARG 0.001 0.000 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 166) hydrogen bonds : angle 4.06916 ( 450) metal coordination : bond 0.00606 ( 4) metal coordination : angle 2.94168 ( 3) covalent geometry : bond 0.00255 ( 5061) covalent geometry : angle 0.53154 ( 6861) *********************** 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 102 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 206 ASP cc_start: 0.7820 (m-30) cc_final: 0.7575 (m-30) outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 0.9066 time to fit residues: 94.5073 Evaluate side-chains 93 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 PHE 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 148 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.0470 chunk 28 optimal weight: 0.5980 chunk 59 optimal weight: 0.0770 chunk 4 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 49 optimal weight: 0.0870 overall best weight: 0.2614 ------------------------------------------------------------------------------- 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 = 0.4211 r_free = 0.4211 target = 0.173735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.153130 restraints weight = 7539.888| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.52 r_work: 0.3861 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5065 Z= 0.155 Angle : 0.570 7.679 6864 Z= 0.304 Chirality : 0.044 0.149 785 Planarity : 0.004 0.041 882 Dihedral : 7.201 80.346 702 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.84 % Favored : 92.99 % Rotamer: Outliers : 1.76 % Allowed : 16.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.35), residues: 599 helix: 0.54 (0.41), residues: 179 sheet: 0.03 (0.56), residues: 87 loop : -0.69 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 236 HIS 0.004 0.001 HIS A 290 PHE 0.019 0.002 PHE D 35 TYR 0.010 0.001 TYR D 43 ARG 0.002 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 166) hydrogen bonds : angle 4.17554 ( 450) metal coordination : bond 0.00778 ( 4) metal coordination : angle 3.23100 ( 3) covalent geometry : bond 0.00357 ( 5061) covalent geometry : angle 0.56645 ( 6861) *********************** 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 100 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 260 ASN cc_start: 0.3782 (t0) cc_final: 0.3554 (t0) outliers start: 10 outliers final: 7 residues processed: 97 average time/residue: 1.9029 time to fit residues: 195.3149 Evaluate side-chains 98 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 PHE 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 136 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 241 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 0.2980 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 0.0050 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 217 ASN A 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.172593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152307 restraints weight = 7467.469| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.47 r_work: 0.3845 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5065 Z= 0.176 Angle : 0.594 8.647 6864 Z= 0.315 Chirality : 0.045 0.150 785 Planarity : 0.004 0.038 882 Dihedral : 7.150 73.887 702 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.32 % Rotamer: Outliers : 3.00 % Allowed : 16.75 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.35), residues: 599 helix: 0.62 (0.41), residues: 173 sheet: -0.17 (0.52), residues: 97 loop : -0.82 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 236 HIS 0.006 0.001 HIS A 290 PHE 0.042 0.002 PHE A 221 TYR 0.009 0.001 TYR D 43 ARG 0.002 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.05213 ( 166) hydrogen bonds : angle 4.28559 ( 450) metal coordination : bond 0.00827 ( 4) metal coordination : angle 3.90163 ( 3) covalent geometry : bond 0.00412 ( 5061) covalent geometry : angle 0.58895 ( 6861) *********************** 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 114 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: D 175 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7863 (ptp90) REVERT: A 54 GLU cc_start: 0.7192 (tt0) cc_final: 0.6985 (tt0) REVERT: A 60 GLU cc_start: 0.6741 (mp0) cc_final: 0.6539 (mp0) REVERT: A 133 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6668 (p90) REVERT: A 217 ASN cc_start: 0.7249 (p0) cc_final: 0.7008 (p0) REVERT: A 310 ASN cc_start: 0.7567 (t0) cc_final: 0.7304 (t0) outliers start: 17 outliers final: 12 residues processed: 105 average time/residue: 1.4931 time to fit residues: 166.0104 Evaluate side-chains 109 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 ARG 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 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 253 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 57 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.4182 r_free = 0.4182 target = 0.171318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.150968 restraints weight = 7464.650| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.50 r_work: 0.3833 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5065 Z= 0.201 Angle : 0.643 10.513 6864 Z= 0.339 Chirality : 0.046 0.174 785 Planarity : 0.004 0.037 882 Dihedral : 7.185 67.923 702 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.85 % Favored : 91.99 % Rotamer: Outliers : 3.17 % Allowed : 17.46 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.35), residues: 599 helix: 0.46 (0.41), residues: 173 sheet: -0.05 (0.57), residues: 87 loop : -0.94 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 236 HIS 0.007 0.001 HIS A 290 PHE 0.042 0.002 PHE A 221 TYR 0.012 0.002 TYR D 43 ARG 0.002 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.05609 ( 166) hydrogen bonds : angle 4.46292 ( 450) metal coordination : bond 0.00763 ( 4) metal coordination : angle 4.10942 ( 3) covalent geometry : bond 0.00475 ( 5061) covalent geometry : angle 0.63766 ( 6861) *********************** 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 109 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: D 175 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7873 (ptp90) REVERT: A 133 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6677 (p90) REVERT: A 216 ASN cc_start: 0.6425 (p0) cc_final: 0.6072 (p0) REVERT: A 217 ASN cc_start: 0.7337 (p0) cc_final: 0.7074 (p0) REVERT: A 260 ASN cc_start: 0.4202 (t0) cc_final: 0.3888 (t0) REVERT: A 310 ASN cc_start: 0.7621 (t0) cc_final: 0.7356 (t0) outliers start: 18 outliers final: 11 residues processed: 101 average time/residue: 1.0264 time to fit residues: 109.5682 Evaluate side-chains 103 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 PHE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 ARG Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain O residue 272 VAL Chi-restraints excluded: chain O residue 308 THR 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 253 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.4980 chunk 15 optimal weight: 0.0970 chunk 42 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.3980 chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.1980 overall best weight: 0.2576 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.172401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.152098 restraints weight = 7522.058| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.51 r_work: 0.3846 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5065 Z= 0.157 Angle : 0.630 11.534 6864 Z= 0.327 Chirality : 0.046 0.252 785 Planarity : 0.004 0.036 882 Dihedral : 6.909 61.909 700 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.18 % Favored : 92.65 % Rotamer: Outliers : 3.17 % Allowed : 17.64 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.35), residues: 599 helix: 0.46 (0.41), residues: 173 sheet: -0.18 (0.53), residues: 97 loop : -0.81 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 236 HIS 0.005 0.001 HIS A 290 PHE 0.041 0.002 PHE A 221 TYR 0.008 0.001 TYR D 43 ARG 0.002 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.05033 ( 166) hydrogen bonds : angle 4.39069 ( 450) metal coordination : bond 0.00735 ( 4) metal coordination : angle 3.79114 ( 3) covalent geometry : bond 0.00363 ( 5061) covalent geometry : angle 0.62472 ( 6861) *********************** 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 109 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: D 175 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7845 (ptp90) REVERT: A 60 GLU cc_start: 0.6743 (mp0) cc_final: 0.6540 (mp0) REVERT: A 133 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6650 (p90) REVERT: A 217 ASN cc_start: 0.7277 (p0) cc_final: 0.6997 (p0) REVERT: A 260 ASN cc_start: 0.4168 (t0) cc_final: 0.3919 (t0) REVERT: A 310 ASN cc_start: 0.7582 (t0) cc_final: 0.7322 (t0) outliers start: 18 outliers final: 13 residues processed: 99 average time/residue: 1.1683 time to fit residues: 123.0584 Evaluate side-chains 108 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 35 PHE 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 40 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 0.0050 chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.0020 chunk 57 optimal weight: 0.0870 overall best weight: 0.0978 ------------------------------------------------------------------------------- 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 = 0.4226 r_free = 0.4226 target = 0.175437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.155316 restraints weight = 7524.069| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.48 r_work: 0.3885 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5065 Z= 0.112 Angle : 0.564 10.132 6864 Z= 0.299 Chirality : 0.043 0.140 785 Planarity : 0.004 0.037 882 Dihedral : 6.521 59.613 700 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.34 % Favored : 93.49 % Rotamer: Outliers : 1.59 % Allowed : 18.87 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.36), residues: 599 helix: 0.71 (0.42), residues: 173 sheet: 0.17 (0.57), residues: 91 loop : -0.71 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 236 HIS 0.004 0.001 HIS D 109 PHE 0.036 0.002 PHE A 221 TYR 0.008 0.001 TYR A 211 ARG 0.002 0.000 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 166) hydrogen bonds : angle 4.11774 ( 450) metal coordination : bond 0.00690 ( 4) metal coordination : angle 3.27458 ( 3) covalent geometry : bond 0.00246 ( 5061) covalent geometry : angle 0.55993 ( 6861) *********************** 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 102 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.599 Fit side-chains revert: symmetry clash REVERT: D 94 SER cc_start: 0.7430 (m) cc_final: 0.7111 (p) REVERT: A 54 GLU cc_start: 0.7041 (tt0) cc_final: 0.6819 (tt0) REVERT: A 133 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6622 (p90) outliers start: 9 outliers final: 8 residues processed: 98 average time/residue: 1.7613 time to fit residues: 184.3029 Evaluate side-chains 103 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 35 PHE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 0.0170 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 58 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 12 optimal weight: 0.0770 chunk 39 optimal weight: 0.5980 overall best weight: 0.1576 ------------------------------------------------------------------------------- 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 = 0.4221 r_free = 0.4221 target = 0.174960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154616 restraints weight = 7545.282| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.49 r_work: 0.3878 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2276 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= 0.127 Angle : 0.587 9.501 6864 Z= 0.309 Chirality : 0.044 0.144 785 Planarity : 0.004 0.036 882 Dihedral : 6.461 58.765 700 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.18 % Favored : 93.66 % Rotamer: Outliers : 1.41 % Allowed : 19.22 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.36), residues: 599 helix: 0.74 (0.42), residues: 173 sheet: 0.16 (0.57), residues: 91 loop : -0.69 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 236 HIS 0.004 0.001 HIS D 109 PHE 0.039 0.002 PHE A 221 TYR 0.007 0.001 TYR D 43 ARG 0.002 0.000 ARG D 186 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 166) hydrogen bonds : angle 4.15351 ( 450) metal coordination : bond 0.00646 ( 4) metal coordination : angle 3.07780 ( 3) covalent geometry : bond 0.00288 ( 5061) covalent geometry : angle 0.58344 ( 6861) ********************** 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 103 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.983 Fit side-chains REVERT: A 54 GLU cc_start: 0.7051 (tt0) cc_final: 0.6839 (tt0) REVERT: A 133 PHE cc_start: 0.7093 (OUTLIER) cc_final: 0.6634 (p90) REVERT: A 260 ASN cc_start: 0.4009 (t0) cc_final: 0.3750 (t0) outliers start: 8 outliers final: 7 residues processed: 100 average time/residue: 1.1244 time to fit residues: 118.7566 Evaluate side-chains 104 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 35 PHE 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 133 PHE 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 21 optimal weight: 0.0370 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.0030 chunk 42 optimal weight: 0.0980 chunk 33 optimal weight: 0.0040 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 overall best weight: 0.0680 ------------------------------------------------------------------------------- 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 = 0.4243 r_free = 0.4243 target = 0.176874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.156441 restraints weight = 7641.737| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.50 r_work: 0.3898 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5065 Z= 0.114 Angle : 0.569 9.671 6864 Z= 0.301 Chirality : 0.044 0.185 785 Planarity : 0.004 0.037 882 Dihedral : 6.339 57.714 700 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.34 % Favored : 93.49 % Rotamer: Outliers : 1.59 % Allowed : 19.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.36), residues: 599 helix: 0.77 (0.41), residues: 173 sheet: 0.15 (0.57), residues: 91 loop : -0.65 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 236 HIS 0.004 0.001 HIS D 109 PHE 0.039 0.002 PHE A 221 TYR 0.006 0.001 TYR O 306 ARG 0.002 0.000 ARG A 57 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 166) hydrogen bonds : angle 4.09168 ( 450) metal coordination : bond 0.00638 ( 4) metal coordination : angle 2.98584 ( 3) covalent geometry : bond 0.00247 ( 5061) covalent geometry : angle 0.56614 ( 6861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7234.78 seconds wall clock time: 133 minutes 32.08 seconds (8012.08 seconds total)