Starting phenix.real_space_refine on Thu Aug 6 00:51:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8znj_60273/08_2026/8znj_60273.cif Found real_map, /net/cci-nas-00/data/ceres_data/8znj_60273/08_2026/8znj_60273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8znj_60273/08_2026/8znj_60273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8znj_60273/08_2026/8znj_60273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8znj_60273/08_2026/8znj_60273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8znj_60273/08_2026/8znj_60273.map" } resolution = 3.0 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= -0.001 sd= 0.085 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: 7 Type Number sf(0) Gaussians P 43 5.49 5 Mg 1 5.21 5 S 14 5.16 5 C 4023 2.51 5 N 1112 2.21 5 O 1316 1.98 5 H 6190 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12699 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 7310 Classifications: {'peptide': 444} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 422} Chain breaks: 2 Chain: "B" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 4038 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 3, 'TRANS': 233} Chain: "D" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 663 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "E" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 687 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.61, per 1000 atoms: 0.21 Number of scatterers: 12699 At special positions: 0 Unit cell: (75.97, 77.04, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 14 16.00 P 43 15.00 Mg 1 11.99 O 1316 8.00 N 1112 7.00 C 4023 6.00 H 6190 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 85 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 326.9 milliseconds 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1306 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 35.2% alpha, 18.9% beta 20 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 28 through 33 Processing helix chain 'A' and resid 50 through 62 Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 107 through 117 removed outlier: 3.661A pdb=" N SER A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.125A pdb=" N GLU A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASP A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 167 through 171 Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 194 through 201 removed outlier: 4.192A pdb=" N ASP A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A 200 " --> pdb=" O TYR A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 402 through 416 removed outlier: 3.529A pdb=" N ALA A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 441 Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 454 through 459 Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.809A pdb=" N LYS B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 74 removed outlier: 3.510A pdb=" N TYR B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 114 removed outlier: 3.691A pdb=" N PHE B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 114 " --> pdb=" O TYR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 removed outlier: 4.015A pdb=" N ARG B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 213 removed outlier: 3.655A pdb=" N ILE B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.858A pdb=" N THR A 339 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU A 356 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N SER A 397 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 286 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE A 315 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE A 288 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ALA A 317 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS A 290 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET A 208 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE A 289 " --> pdb=" O MET A 208 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N MET A 210 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 213 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.248A pdb=" N ILE A 40 " --> pdb=" O ASN A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA5, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.738A pdb=" N LYS A 370 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 127 through 128 removed outlier: 4.125A pdb=" N VAL B 135 " --> pdb=" O PHE B 155 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B 151 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG B 141 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 149 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP B 143 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 47 removed outlier: 6.727A pdb=" N THR B 55 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N ILE B 18 " --> pdb=" O THR B 55 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6188 1.03 - 1.23: 27 1.23 - 1.42: 2858 1.42 - 1.62: 3815 1.62 - 1.81: 24 Bond restraints: 12912 Sorted by residual: bond pdb=" C3' DT E 3 " pdb=" C2' DT E 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DG E 17 " pdb=" C2' DG E 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.04e+00 bond pdb=" C3' DA E 11 " pdb=" C2' DA E 11 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.03e+00 bond pdb=" C3' DT E 21 " pdb=" C2' DT E 21 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.89e+00 bond pdb=" C3' DT E 10 " pdb=" C2' DT E 10 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.74e+00 ... (remaining 12907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 22323 1.31 - 2.63: 944 2.63 - 3.94: 109 3.94 - 5.26: 9 5.26 - 6.57: 4 Bond angle restraints: 23389 Sorted by residual: angle pdb=" N3 DT E 14 " pdb=" C4 DT E 14 " pdb=" O4 DT E 14 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT E 3 " pdb=" C4 DT E 3 " pdb=" O4 DT E 3 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT E 20 " pdb=" C4 DT E 20 " pdb=" O4 DT E 20 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT E 12 " pdb=" C4 DT E 12 " pdb=" O4 DT E 12 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT E 10 " pdb=" C4 DT E 10 " pdb=" O4 DT E 10 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 23384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 5453 25.94 - 51.88: 411 51.88 - 77.81: 86 77.81 - 103.75: 8 103.75 - 129.69: 2 Dihedral angle restraints: 5960 sinusoidal: 3574 harmonic: 2386 Sorted by residual: dihedral pdb=" CA ALA A 416 " pdb=" C ALA A 416 " pdb=" N ASP A 417 " pdb=" CA ASP A 417 " ideal model delta harmonic sigma weight residual 180.00 153.06 26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ARG A 216 " pdb=" C ARG A 216 " pdb=" N THR A 217 " pdb=" CA THR A 217 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 85 " pdb=" CB CYS B 85 " ideal model delta sinusoidal sigma weight residual 93.00 52.28 40.72 1 1.00e+01 1.00e-02 2.32e+01 ... (remaining 5957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 718 0.037 - 0.073: 186 0.073 - 0.110: 90 0.110 - 0.146: 48 0.146 - 0.183: 14 Chirality restraints: 1056 Sorted by residual: chirality pdb=" C3' DT E 12 " pdb=" C4' DT E 12 " pdb=" O3' DT E 12 " pdb=" C2' DT E 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" C3' DA E 16 " pdb=" C4' DA E 16 " pdb=" O3' DA E 16 " pdb=" C2' DA E 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" C3' DG E 8 " pdb=" C4' DG E 8 " pdb=" O3' DG E 8 " pdb=" C2' DG E 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 1053 not shown) Planarity restraints: 1699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 94 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 95 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 166 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C ARG A 166 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG A 166 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS A 167 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C D 7 " 0.021 2.00e-02 2.50e+03 9.86e-03 2.67e+00 pdb=" N1 C D 7 " -0.024 2.00e-02 2.50e+03 pdb=" C2 C D 7 " 0.001 2.00e-02 2.50e+03 pdb=" O2 C D 7 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C D 7 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C D 7 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C D 7 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C D 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C D 7 " -0.002 2.00e-02 2.50e+03 pdb=" H5 C D 7 " 0.004 2.00e-02 2.50e+03 pdb=" H6 C D 7 " -0.004 2.00e-02 2.50e+03 ... (remaining 1696 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 885 2.20 - 2.80: 26200 2.80 - 3.40: 34765 3.40 - 4.00: 48829 4.00 - 4.60: 73458 Nonbonded interactions: 184137 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 183 " pdb="MG MG A 501 " model vdw 1.601 1.700 nonbonded pdb="HH12 ARG A 216 " pdb=" H22 G D 11 " model vdw 1.804 2.100 nonbonded pdb=" OP2 U D 1 " pdb="MG MG A 501 " model vdw 1.861 2.050 nonbonded pdb=" H GLY B 44 " pdb="HD21 ASN B 103 " model vdw 1.864 2.100 nonbonded pdb=" O ASN A 165 " pdb="HD21 ASN A 165 " model vdw 1.869 2.450 ... (remaining 184132 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: 1.070 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: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.030 Find NCS groups from input model: 0.030 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:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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 : 0.003 0.035 6723 Z= 0.248 Angle : 0.645 6.572 9266 Z= 0.465 Chirality : 0.049 0.183 1056 Planarity : 0.005 0.056 1015 Dihedral : 19.149 129.689 2745 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 1.75 % Allowed : 24.64 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.32), residues: 673 helix: 0.78 (0.38), residues: 212 sheet: -1.63 (0.42), residues: 136 loop : -2.29 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 125 TYR 0.010 0.001 TYR B 175 PHE 0.022 0.001 PHE A 109 TRP 0.009 0.001 TRP A 274 HIS 0.002 0.001 HIS A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.25 ( 6722) covalent geometry : angle 0.64466 / 0.47 ( 9264) SS BOND : bond 0.00082 / 0.04 ( 1) SS BOND : angle 0.81177 / 0.48 ( 2) hydrogen bonds : bond 0.11039 / 6.82 ( 272) hydrogen bonds : angle 6.41859 / 4.19 ( 713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7937 (p) REVERT: A 210 MET cc_start: 0.8380 (ttm) cc_final: 0.8067 (ttp) REVERT: B 130 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7559 (mp0) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.8327 time to fit residues: 81.9370 Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.184416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.157274 restraints weight = 20958.014| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.90 r_work: 0.3845 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.0457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6723 Z= 0.168 Angle : 0.585 7.596 9266 Z= 0.336 Chirality : 0.045 0.251 1056 Planarity : 0.004 0.048 1015 Dihedral : 17.801 133.212 1321 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.70 % Allowed : 24.64 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.33), residues: 673 helix: 0.76 (0.37), residues: 218 sheet: -1.59 (0.42), residues: 135 loop : -2.17 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.013 0.001 TYR B 175 PHE 0.017 0.001 PHE A 109 TRP 0.006 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 6722) covalent geometry : angle 0.58533 / 0.34 ( 9264) SS BOND : bond 0.00042 / 0.02 ( 1) SS BOND : angle 0.47760 / 0.28 ( 2) hydrogen bonds : bond 0.04924 / 3.20 ( 272) hydrogen bonds : angle 5.20183 / 3.45 ( 713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8018 (mt) REVERT: B 130 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7561 (mp0) outliers start: 17 outliers final: 8 residues processed: 102 average time/residue: 0.7795 time to fit residues: 85.4441 Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.184614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.157148 restraints weight = 20929.249| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.93 r_work: 0.3845 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.0554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6723 Z= 0.158 Angle : 0.572 7.484 9266 Z= 0.330 Chirality : 0.045 0.247 1056 Planarity : 0.004 0.045 1015 Dihedral : 17.731 132.826 1312 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 2.23 % Allowed : 24.32 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.32), residues: 673 helix: 0.73 (0.37), residues: 218 sheet: -1.60 (0.40), residues: 148 loop : -2.23 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.018 0.001 TYR B 175 PHE 0.008 0.001 PHE A 17 TRP 0.008 0.001 TRP A 274 HIS 0.002 0.000 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 6722) covalent geometry : angle 0.57154 / 0.33 ( 9264) SS BOND : bond 0.00010 / 0.00 ( 1) SS BOND : angle 0.44081 / 0.26 ( 2) hydrogen bonds : bond 0.04505 / 2.93 ( 272) hydrogen bonds : angle 4.99649 / 3.31 ( 713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8411 (ttm) cc_final: 0.8079 (ttp) REVERT: A 391 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8016 (mt) outliers start: 14 outliers final: 11 residues processed: 99 average time/residue: 0.9550 time to fit residues: 101.1023 Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.186124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.158714 restraints weight = 20687.945| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.91 r_work: 0.3863 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6723 Z= 0.128 Angle : 0.556 7.100 9266 Z= 0.319 Chirality : 0.044 0.245 1056 Planarity : 0.004 0.044 1015 Dihedral : 17.680 133.378 1309 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 2.54 % Allowed : 24.17 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.33), residues: 673 helix: 0.86 (0.37), residues: 218 sheet: -1.54 (0.40), residues: 148 loop : -2.22 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 125 TYR 0.009 0.001 TYR A 396 PHE 0.019 0.001 PHE A 109 TRP 0.008 0.001 TRP A 274 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 6722) covalent geometry : angle 0.55596 / 0.32 ( 9264) SS BOND : bond 0.00033 / 0.02 ( 1) SS BOND : angle 0.42978 / 0.25 ( 2) hydrogen bonds : bond 0.04097 / 2.67 ( 272) hydrogen bonds : angle 4.80286 / 3.19 ( 713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8002 (mt) REVERT: B 130 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7740 (mp0) outliers start: 16 outliers final: 10 residues processed: 99 average time/residue: 0.8177 time to fit residues: 86.3778 Evaluate side-chains 93 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.181404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.153013 restraints weight = 20861.905| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.00 r_work: 0.3815 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6723 Z= 0.228 Angle : 0.620 8.557 9266 Z= 0.351 Chirality : 0.046 0.244 1056 Planarity : 0.005 0.043 1015 Dihedral : 17.741 132.267 1309 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 3.02 % Allowed : 24.80 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.32), residues: 673 helix: 0.58 (0.36), residues: 218 sheet: -1.68 (0.40), residues: 148 loop : -2.30 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 125 TYR 0.012 0.002 TYR B 175 PHE 0.013 0.002 PHE B 8 TRP 0.009 0.001 TRP A 274 HIS 0.002 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.23 ( 6722) covalent geometry : angle 0.61956 / 0.35 ( 9264) SS BOND : bond 0.00098 / 0.05 ( 1) SS BOND : angle 0.42218 / 0.25 ( 2) hydrogen bonds : bond 0.04454 / 2.90 ( 272) hydrogen bonds : angle 4.87801 / 3.23 ( 713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7910 (p) REVERT: B 130 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7651 (mp0) outliers start: 19 outliers final: 15 residues processed: 98 average time/residue: 0.9165 time to fit residues: 96.3981 Evaluate side-chains 97 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 39 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.184343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.156944 restraints weight = 20291.457| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.92 r_work: 0.3858 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3713 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6723 Z= 0.161 Angle : 0.583 7.577 9266 Z= 0.332 Chirality : 0.045 0.242 1056 Planarity : 0.004 0.041 1015 Dihedral : 17.739 133.656 1309 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 3.02 % Allowed : 25.12 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.32), residues: 673 helix: 0.65 (0.37), residues: 218 sheet: -1.65 (0.40), residues: 148 loop : -2.29 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 125 TYR 0.009 0.001 TYR A 396 PHE 0.020 0.002 PHE A 109 TRP 0.008 0.001 TRP A 274 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 6722) covalent geometry : angle 0.58333 / 0.33 ( 9264) SS BOND : bond 0.00001 / 0.00 ( 1) SS BOND : angle 0.45518 / 0.27 ( 2) hydrogen bonds : bond 0.04084 / 2.67 ( 272) hydrogen bonds : angle 4.77406 / 3.16 ( 713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8374 (ttm) cc_final: 0.8057 (ttp) REVERT: B 130 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7541 (mp0) outliers start: 19 outliers final: 14 residues processed: 96 average time/residue: 0.9628 time to fit residues: 98.8003 Evaluate side-chains 93 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.182135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.154828 restraints weight = 20403.977| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.91 r_work: 0.3840 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6723 Z= 0.207 Angle : 0.613 8.250 9266 Z= 0.346 Chirality : 0.045 0.243 1056 Planarity : 0.005 0.041 1015 Dihedral : 17.766 132.980 1309 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 3.02 % Allowed : 25.44 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.32), residues: 673 helix: 0.56 (0.36), residues: 218 sheet: -1.73 (0.38), residues: 158 loop : -2.35 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 125 TYR 0.011 0.001 TYR A 433 PHE 0.012 0.002 PHE B 8 TRP 0.008 0.001 TRP A 274 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 ( 6722) covalent geometry : angle 0.61265 / 0.35 ( 9264) SS BOND : bond 0.00044 / 0.02 ( 1) SS BOND : angle 0.48985 / 0.29 ( 2) hydrogen bonds : bond 0.04204 / 2.75 ( 272) hydrogen bonds : angle 4.80365 / 3.18 ( 713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.8018 (p) REVERT: A 210 MET cc_start: 0.8402 (ttm) cc_final: 0.8088 (ttp) REVERT: B 130 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7521 (mp0) outliers start: 19 outliers final: 16 residues processed: 97 average time/residue: 0.8260 time to fit residues: 86.0982 Evaluate side-chains 98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 28 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 0.0970 chunk 67 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.184411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.157998 restraints weight = 20173.451| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.85 r_work: 0.3868 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6723 Z= 0.161 Angle : 0.593 7.505 9266 Z= 0.335 Chirality : 0.045 0.241 1056 Planarity : 0.005 0.041 1015 Dihedral : 17.764 133.737 1309 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 2.54 % Allowed : 26.07 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.32), residues: 673 helix: 0.63 (0.36), residues: 219 sheet: -1.70 (0.39), residues: 158 loop : -2.27 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 125 TYR 0.009 0.001 TYR A 433 PHE 0.022 0.002 PHE A 109 TRP 0.008 0.001 TRP A 274 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 6722) covalent geometry : angle 0.59254 / 0.33 ( 9264) SS BOND : bond 0.00021 / 0.01 ( 1) SS BOND : angle 0.52947 / 0.31 ( 2) hydrogen bonds : bond 0.03974 / 2.61 ( 272) hydrogen bonds : angle 4.74512 / 3.14 ( 713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.8009 (p) REVERT: A 210 MET cc_start: 0.8335 (ttm) cc_final: 0.8018 (ttp) REVERT: B 130 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7519 (mp0) outliers start: 16 outliers final: 14 residues processed: 95 average time/residue: 0.8530 time to fit residues: 87.3302 Evaluate side-chains 95 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.183739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156802 restraints weight = 20432.831| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.89 r_work: 0.3845 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6723 Z= 0.183 Angle : 0.613 7.809 9266 Z= 0.344 Chirality : 0.045 0.242 1056 Planarity : 0.005 0.044 1015 Dihedral : 17.772 133.419 1309 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 2.86 % Allowed : 26.07 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.32), residues: 673 helix: 0.59 (0.36), residues: 219 sheet: -1.69 (0.39), residues: 158 loop : -2.29 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 125 TYR 0.010 0.001 TYR A 433 PHE 0.012 0.002 PHE A 137 TRP 0.008 0.001 TRP A 274 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 6722) covalent geometry : angle 0.61327 / 0.34 ( 9264) SS BOND : bond 0.00028 / 0.01 ( 1) SS BOND : angle 0.52334 / 0.31 ( 2) hydrogen bonds : bond 0.04010 / 2.63 ( 272) hydrogen bonds : angle 4.75576 / 3.15 ( 713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8002 (p) REVERT: A 210 MET cc_start: 0.8363 (ttm) cc_final: 0.8054 (ttp) REVERT: B 130 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7510 (mp0) outliers start: 18 outliers final: 12 residues processed: 93 average time/residue: 0.8504 time to fit residues: 85.0783 Evaluate side-chains 91 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 69 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.187037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.159648 restraints weight = 20287.035| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.93 r_work: 0.3877 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3728 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6723 Z= 0.121 Angle : 0.587 7.528 9266 Z= 0.330 Chirality : 0.044 0.239 1056 Planarity : 0.004 0.049 1015 Dihedral : 17.741 134.322 1307 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 2.38 % Allowed : 26.55 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.33), residues: 673 helix: 0.80 (0.37), residues: 219 sheet: -1.62 (0.39), residues: 158 loop : -2.24 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 125 TYR 0.011 0.001 TYR A 54 PHE 0.028 0.001 PHE A 109 TRP 0.009 0.001 TRP A 418 HIS 0.003 0.001 HIS A 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 6722) covalent geometry : angle 0.58686 / 0.33 ( 9264) SS BOND : bond 0.00061 / 0.03 ( 1) SS BOND : angle 0.62459 / 0.37 ( 2) hydrogen bonds : bond 0.03682 / 2.43 ( 272) hydrogen bonds : angle 4.62982 / 3.06 ( 713) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1346 Ramachandran restraints generated. 673 Oldfield, 0 Emsley, 673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 MET cc_start: 0.8335 (ttm) cc_final: 0.8011 (ttp) REVERT: B 130 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7489 (mp0) outliers start: 15 outliers final: 12 residues processed: 89 average time/residue: 0.9238 time to fit residues: 88.2427 Evaluate side-chains 88 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 0.0060 chunk 3 optimal weight: 0.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 442 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.183724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156579 restraints weight = 20332.230| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.91 r_work: 0.3859 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6723 Z= 0.174 Angle : 0.610 7.512 9266 Z= 0.342 Chirality : 0.045 0.242 1056 Planarity : 0.005 0.046 1015 Dihedral : 17.735 133.040 1307 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 2.23 % Allowed : 26.55 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.33), residues: 673 helix: 0.72 (0.37), residues: 219 sheet: -1.61 (0.39), residues: 158 loop : -2.25 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 125 TYR 0.010 0.001 TYR A 54 PHE 0.016 0.001 PHE A 137 TRP 0.009 0.001 TRP A 274 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 ( 6722) covalent geometry : angle 0.60972 / 0.34 ( 9264) SS BOND : bond 0.00050 / 0.02 ( 1) SS BOND : angle 0.54672 / 0.32 ( 2) hydrogen bonds : bond 0.03871 / 2.55 ( 272) hydrogen bonds : angle 4.66516 / 3.09 ( 713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4249.15 seconds wall clock time: 72 minutes 41.29 seconds (4361.29 seconds total)