Starting phenix.real_space_refine on Thu Aug 6 10:39:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t2s_40986/08_2026/8t2s_40986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2s_40986/08_2026/8t2s_40986.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/8t2s_40986/08_2026/8t2s_40986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2s_40986/08_2026/8t2s_40986.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8t2s_40986/08_2026/8t2s_40986.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t2s_40986/08_2026/8t2s_40986.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t2s_40986/08_2026/8t2s_40986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2s_40986/08_2026/8t2s_40986.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= 0.032 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 Ca 11 9.91 5 P 551 5.49 5 S 21 5.16 5 C 7283 2.51 5 N 2764 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 14998 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3146 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 10, 'TRANS': 378} Chain breaks: 2 Chain: "B" Number of atoms: 11839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 11839 Classifications: {'RNAv2': 551} Modifications used: {'rna2p_pur': 46, 'rna2p_pyr': 17, 'rna3p_pur': 283, 'rna3p_pyr': 205} Link IDs: {'rna2p': 62, 'rna3p': 488} Chain breaks: 6 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CA': 11, 'NH4': 2} Classifications: {'undetermined': 13} Link IDs: {None: 12} Time building chain proxies: 2.87, per 1000 atoms: 0.19 Number of scatterers: 14998 At special positions: 0 Unit cell: (110.564, 136.728, 160.36, 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) Ca 11 19.99 S 21 16.00 P 551 15.00 O 4368 8.00 N 2764 7.00 C 7283 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 196.1 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 2 sheets defined 65.8% alpha, 6.2% beta 181 base pairs and 323 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'D' and resid 5 through 11 removed outlier: 3.886A pdb=" N GLN D 9 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 39 through 57 removed outlier: 5.712A pdb=" N GLU D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 Processing helix chain 'D' and resid 97 through 104 removed outlier: 4.251A pdb=" N ILE D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 133 removed outlier: 3.671A pdb=" N ALA D 122 " --> pdb=" O CYS D 118 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 removed outlier: 3.532A pdb=" N VAL D 149 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 160 Processing helix chain 'D' and resid 166 through 176 removed outlier: 4.359A pdb=" N ILE D 170 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 217 removed outlier: 3.863A pdb=" N GLU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU D 210 " --> pdb=" O MET D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 252 Processing helix chain 'D' and resid 291 through 306 removed outlier: 3.577A pdb=" N LYS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 330 removed outlier: 3.985A pdb=" N ASN D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 361 removed outlier: 3.663A pdb=" N LYS D 361 " --> pdb=" O TRP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 372 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 404 through 410 Processing helix chain 'D' and resid 415 through 424 Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 224 removed outlier: 4.133A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS D 228 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 271 through 272 178 hydrogen bonds defined for protein. 525 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 447 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 181 basepair parallelities 323 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1521 1.32 - 1.45: 7659 1.45 - 1.57: 6151 1.57 - 1.69: 1096 1.69 - 1.82: 35 Bond restraints: 16462 Sorted by residual: bond pdb=" C THR D 99 " pdb=" N PRO D 100 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.28e-02 6.10e+03 4.24e+00 bond pdb=" CG GLN D 63 " pdb=" CD GLN D 63 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 3.98e+00 bond pdb=" C3' G B 369 " pdb=" O3' G B 369 " ideal model delta sigma weight residual 1.415 1.453 -0.038 2.00e-02 2.50e+03 3.59e+00 bond pdb=" O3' A B 551 " pdb=" P U B 552 " ideal model delta sigma weight residual 1.607 1.629 -0.022 1.20e-02 6.94e+03 3.40e+00 bond pdb=" CB GLN D 63 " pdb=" CG GLN D 63 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.27e+00 ... (remaining 16457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 23805 2.76 - 5.51: 1068 5.51 - 8.27: 73 8.27 - 11.02: 14 11.02 - 13.78: 4 Bond angle restraints: 24964 Sorted by residual: angle pdb=" C3' G B 369 " pdb=" O3' G B 369 " pdb=" P A B 370 " ideal model delta sigma weight residual 119.70 127.87 -8.17 1.20e+00 6.94e-01 4.64e+01 angle pdb=" C3' A B 551 " pdb=" O3' A B 551 " pdb=" P U B 552 " ideal model delta sigma weight residual 119.70 127.62 -7.92 1.20e+00 6.94e-01 4.35e+01 angle pdb=" C3' A B 67 " pdb=" O3' A B 67 " pdb=" P U B 68 " ideal model delta sigma weight residual 119.70 127.32 -7.62 1.20e+00 6.94e-01 4.03e+01 angle pdb=" CA MET D 7 " pdb=" CB MET D 7 " pdb=" CG MET D 7 " ideal model delta sigma weight residual 114.10 124.56 -10.46 2.00e+00 2.50e-01 2.73e+01 angle pdb=" CA GLU D 235 " pdb=" CB GLU D 235 " pdb=" CG GLU D 235 " ideal model delta sigma weight residual 114.10 124.39 -10.29 2.00e+00 2.50e-01 2.65e+01 ... (remaining 24959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 8073 35.46 - 70.92: 1710 70.92 - 106.37: 149 106.37 - 141.83: 1 141.83 - 177.29: 5 Dihedral angle restraints: 9938 sinusoidal: 8808 harmonic: 1130 Sorted by residual: dihedral pdb=" C4' A B 147 " pdb=" C3' A B 147 " pdb=" C2' A B 147 " pdb=" C1' A B 147 " ideal model delta sinusoidal sigma weight residual 36.34 -39.43 75.77 1 3.10e+00 1.04e-01 7.53e+02 dihedral pdb=" C4' A B 426 " pdb=" C3' A B 426 " pdb=" C2' A B 426 " pdb=" C1' A B 426 " ideal model delta sinusoidal sigma weight residual 36.34 -39.11 75.45 1 3.10e+00 1.04e-01 7.48e+02 dihedral pdb=" C4' A B 370 " pdb=" C3' A B 370 " pdb=" C2' A B 370 " pdb=" C1' A B 370 " ideal model delta sinusoidal sigma weight residual 36.34 -39.05 75.39 1 3.10e+00 1.04e-01 7.47e+02 ... (remaining 9935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2468 0.105 - 0.211: 150 0.211 - 0.316: 586 0.316 - 0.421: 18 0.421 - 0.526: 1 Chirality restraints: 3223 Sorted by residual: chirality pdb=" P U B 552 " pdb=" OP1 U B 552 " pdb=" OP2 U B 552 " pdb=" O5' U B 552 " both_signs ideal model delta sigma weight residual True 2.17 -2.70 -0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" P U B 68 " pdb=" OP1 U B 68 " pdb=" OP2 U B 68 " pdb=" O5' U B 68 " both_signs ideal model delta sigma weight residual True 2.17 -2.59 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C2' A B 185 " pdb=" C3' A B 185 " pdb=" O2' A B 185 " pdb=" C1' A B 185 " both_signs ideal model delta sigma weight residual False -2.79 -2.42 -0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 3220 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 185 " -0.043 2.00e-02 2.50e+03 1.91e-02 1.01e+01 pdb=" N9 A B 185 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A B 185 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A B 185 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A B 185 " -0.003 2.00e-02 2.50e+03 pdb=" C6 A B 185 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A B 185 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A B 185 " -0.004 2.00e-02 2.50e+03 pdb=" C2 A B 185 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A B 185 " 0.013 2.00e-02 2.50e+03 pdb=" C4 A B 185 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 266 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO D 267 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 267 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 267 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U B 175 " 0.033 2.00e-02 2.50e+03 1.66e-02 6.18e+00 pdb=" N1 U B 175 " -0.033 2.00e-02 2.50e+03 pdb=" C2 U B 175 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U B 175 " -0.006 2.00e-02 2.50e+03 pdb=" N3 U B 175 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U B 175 " 0.007 2.00e-02 2.50e+03 pdb=" O4 U B 175 " 0.011 2.00e-02 2.50e+03 pdb=" C5 U B 175 " -0.007 2.00e-02 2.50e+03 pdb=" C6 U B 175 " -0.006 2.00e-02 2.50e+03 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2986 2.78 - 3.31: 12012 3.31 - 3.84: 33245 3.84 - 4.37: 38293 4.37 - 4.90: 49211 Nonbonded interactions: 135747 Sorted by model distance: nonbonded pdb=" OP2 A B 137 " pdb=" O2' A B 147 " model vdw 2.251 3.040 nonbonded pdb=" O2' G B 276 " pdb=" O4 U B 325 " model vdw 2.259 3.040 nonbonded pdb=" O2' G B 136 " pdb=" OP1 U B 148 " model vdw 2.277 3.040 nonbonded pdb=" OD1 ASN D 395 " pdb=" O2' A B -33 " model vdw 2.287 3.040 nonbonded pdb=" N2 G B 287 " pdb=" O2 C B 315 " model vdw 2.304 2.496 ... (remaining 135742 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=0.00 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: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.170 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:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 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 : 0.004 0.054 16463 Z= 0.215 Angle : 1.158 13.780 24964 Z= 0.483 Chirality : 0.116 0.526 3223 Planarity : 0.006 0.064 1096 Dihedral : 26.813 177.289 9210 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.04 % Allowed : 24.49 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.71 (0.36), residues: 383 helix: -1.32 (0.28), residues: 246 sheet: -1.07 (0.98), residues: 24 loop : -2.72 (0.45), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 347 TYR 0.019 0.002 TYR D 60 PHE 0.019 0.003 PHE D 89 TRP 0.016 0.002 TRP D 357 HIS 0.008 0.002 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 (16462) covalent geometry : angle 1.15810 / 0.48 (24964) hydrogen bonds : bond 0.10370 / 6.81 ( 625) hydrogen bonds : angle 4.99506 / 3.47 ( 1233) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.203 Fit side-chains REVERT: D 130 MET cc_start: 0.7843 (mtt) cc_final: 0.7623 (mtt) REVERT: D 236 MET cc_start: 0.7785 (ppp) cc_final: 0.7583 (ppp) REVERT: D 266 ARG cc_start: 0.8347 (mmt90) cc_final: 0.7959 (mmm-85) REVERT: D 406 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7592 (mppt) outliers start: 7 outliers final: 2 residues processed: 38 average time/residue: 0.6179 time to fit residues: 25.7654 Evaluate side-chains 29 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 166 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.177389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.105368 restraints weight = 18150.642| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 0.89 r_work: 0.2988 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 16463 Z= 0.420 Angle : 1.348 23.567 24964 Z= 0.545 Chirality : 0.107 1.249 3223 Planarity : 0.006 0.042 1096 Dihedral : 25.105 179.966 8406 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 6.41 % Allowed : 17.78 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.39), residues: 383 helix: -0.21 (0.32), residues: 247 sheet: -1.52 (0.93), residues: 24 loop : -2.66 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 240 TYR 0.028 0.002 TYR D 385 PHE 0.014 0.003 PHE D 146 TRP 0.011 0.002 TRP D 357 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.42 (16462) covalent geometry : angle 1.34756 / 0.55 (24964) hydrogen bonds : bond 0.07843 / 5.25 ( 625) hydrogen bonds : angle 3.52343 / 2.47 ( 1233) Misc. bond : bond 0.00114 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 30 time to evaluate : 0.250 Fit side-chains REVERT: D 59 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7354 (mtmp) REVERT: D 236 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7728 (ptm) REVERT: D 251 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: D 347 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7617 (mmm-85) REVERT: D 364 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7530 (mm-40) REVERT: D 406 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8155 (mppt) outliers start: 22 outliers final: 4 residues processed: 46 average time/residue: 0.6532 time to fit residues: 32.8569 Evaluate side-chains 36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 92 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 80 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.180718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110779 restraints weight = 18298.006| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 0.83 r_work: 0.3054 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16463 Z= 0.283 Angle : 1.139 14.838 24964 Z= 0.458 Chirality : 0.090 1.083 3223 Planarity : 0.005 0.037 1096 Dihedral : 25.027 178.326 8406 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.41 % Allowed : 18.95 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.42), residues: 383 helix: 0.40 (0.33), residues: 249 sheet: -1.68 (0.92), residues: 24 loop : -2.57 (0.49), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 240 TYR 0.023 0.002 TYR D 385 PHE 0.013 0.002 PHE D 89 TRP 0.009 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.28 (16462) covalent geometry : angle 1.13921 / 0.46 (24964) hydrogen bonds : bond 0.06721 / 4.43 ( 625) hydrogen bonds : angle 3.27697 / 2.30 ( 1233) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 33 time to evaluate : 0.206 Fit side-chains REVERT: D 59 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7288 (mtmp) REVERT: D 132 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7939 (m-30) REVERT: D 201 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7354 (tt) REVERT: D 247 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7191 (ttp80) REVERT: D 251 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: D 261 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7489 (mtpp) REVERT: D 280 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7537 (t0) REVERT: D 347 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7680 (mtp180) REVERT: D 364 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7498 (mm-40) REVERT: D 406 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8134 (mppt) outliers start: 22 outliers final: 6 residues processed: 47 average time/residue: 0.6438 time to fit residues: 33.0304 Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.182987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111860 restraints weight = 18385.505| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 0.86 r_work: 0.3081 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16463 Z= 0.212 Angle : 1.099 14.044 24964 Z= 0.441 Chirality : 0.087 0.957 3223 Planarity : 0.004 0.038 1096 Dihedral : 25.052 178.276 8406 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 7.00 % Allowed : 19.53 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.43), residues: 383 helix: 0.80 (0.34), residues: 249 sheet: -1.80 (0.94), residues: 24 loop : -2.39 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 240 TYR 0.023 0.001 TYR D 385 PHE 0.014 0.002 PHE D 89 TRP 0.008 0.001 TRP D 328 HIS 0.002 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (16462) covalent geometry : angle 1.09879 / 0.44 (24964) hydrogen bonds : bond 0.06594 / 4.36 ( 625) hydrogen bonds : angle 3.14274 / 2.21 ( 1233) Misc. bond : bond 0.00045 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 30 time to evaluate : 0.259 Fit side-chains REVERT: D 59 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7285 (mtmp) REVERT: D 132 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7940 (m-30) REVERT: D 247 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7153 (ttp80) REVERT: D 251 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: D 259 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7478 (tpp) REVERT: D 261 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7554 (mtpp) REVERT: D 280 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7565 (t0) REVERT: D 347 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7665 (mtp180) REVERT: D 364 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7501 (mm-40) REVERT: D 406 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8152 (mppt) outliers start: 24 outliers final: 8 residues processed: 48 average time/residue: 0.6114 time to fit residues: 32.1354 Evaluate side-chains 45 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 29 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.178983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.108319 restraints weight = 18212.979| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 0.83 r_work: 0.3022 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 16463 Z= 0.323 Angle : 1.175 14.691 24964 Z= 0.474 Chirality : 0.093 1.167 3223 Planarity : 0.005 0.035 1096 Dihedral : 25.014 177.022 8404 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 7.00 % Allowed : 20.99 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.43), residues: 383 helix: 0.78 (0.34), residues: 248 sheet: -1.93 (0.94), residues: 24 loop : -2.47 (0.52), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 240 TYR 0.027 0.002 TYR D 385 PHE 0.011 0.002 PHE D 89 TRP 0.009 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00665 / 0.32 (16462) covalent geometry : angle 1.17467 / 0.47 (24964) hydrogen bonds : bond 0.06926 / 4.62 ( 625) hydrogen bonds : angle 3.20747 / 2.26 ( 1233) Misc. bond : bond 0.00069 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 30 time to evaluate : 0.265 Fit side-chains REVERT: D 59 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7249 (mtmp) REVERT: D 247 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7160 (ttp80) REVERT: D 251 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: D 261 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7594 (mtpp) REVERT: D 280 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7519 (t0) REVERT: D 347 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7585 (mtp180) REVERT: D 364 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7544 (mm-40) REVERT: D 406 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8148 (tttt) outliers start: 24 outliers final: 7 residues processed: 43 average time/residue: 0.6861 time to fit residues: 32.2056 Evaluate side-chains 42 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 66 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 68 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 96 GLN D 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.189513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.120625 restraints weight = 18454.754| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 0.84 r_work: 0.3203 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16463 Z= 0.162 Angle : 1.027 12.101 24964 Z= 0.408 Chirality : 0.079 0.567 3223 Planarity : 0.004 0.037 1096 Dihedral : 24.927 179.927 8404 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.50 % Allowed : 26.53 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.44), residues: 383 helix: 1.10 (0.35), residues: 249 sheet: -1.93 (0.96), residues: 24 loop : -2.28 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 240 TYR 0.014 0.001 TYR D 385 PHE 0.016 0.001 PHE D 89 TRP 0.008 0.001 TRP D 357 HIS 0.002 0.000 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (16462) covalent geometry : angle 1.02674 / 0.41 (24964) hydrogen bonds : bond 0.06524 / 4.36 ( 625) hydrogen bonds : angle 3.02899 / 2.11 ( 1233) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: D 201 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7169 (tp) REVERT: D 261 LYS cc_start: 0.8093 (mtmm) cc_final: 0.7619 (mtpp) REVERT: D 347 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7628 (mmm-85) REVERT: D 406 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7959 (ttpp) outliers start: 12 outliers final: 2 residues processed: 41 average time/residue: 0.5962 time to fit residues: 26.8597 Evaluate side-chains 32 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.181941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110481 restraints weight = 18175.789| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 0.83 r_work: 0.3060 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16463 Z= 0.307 Angle : 1.134 14.952 24964 Z= 0.456 Chirality : 0.089 1.110 3223 Planarity : 0.005 0.044 1096 Dihedral : 24.911 178.550 8403 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.08 % Allowed : 24.49 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.44), residues: 383 helix: 1.06 (0.34), residues: 248 sheet: -1.80 (0.95), residues: 24 loop : -2.38 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 240 TYR 0.029 0.002 TYR D 385 PHE 0.011 0.002 PHE D 89 TRP 0.009 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.31 (16462) covalent geometry : angle 1.13361 / 0.46 (24964) hydrogen bonds : bond 0.06774 / 4.54 ( 625) hydrogen bonds : angle 3.13363 / 2.19 ( 1233) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 29 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: D 59 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7247 (mtmp) REVERT: D 105 GLN cc_start: 0.8141 (mt0) cc_final: 0.7808 (mt0) REVERT: D 231 MET cc_start: 0.8652 (mpp) cc_final: 0.8431 (mtt) REVERT: D 247 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7357 (ttp80) REVERT: D 261 LYS cc_start: 0.8071 (mtmm) cc_final: 0.7544 (mtpp) REVERT: D 347 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7625 (mtp180) REVERT: D 364 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7619 (mm-40) REVERT: D 406 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7982 (ttpp) outliers start: 14 outliers final: 5 residues processed: 37 average time/residue: 0.6725 time to fit residues: 27.0004 Evaluate side-chains 36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 73 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.184152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.113145 restraints weight = 18268.370| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 0.84 r_work: 0.3097 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16463 Z= 0.205 Angle : 1.092 14.172 24964 Z= 0.438 Chirality : 0.084 0.963 3223 Planarity : 0.004 0.053 1096 Dihedral : 24.962 178.507 8403 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.37 % Allowed : 25.95 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.44), residues: 383 helix: 1.12 (0.34), residues: 248 sheet: -1.64 (0.98), residues: 24 loop : -2.36 (0.53), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 240 TYR 0.026 0.002 TYR D 385 PHE 0.011 0.002 PHE D 89 TRP 0.009 0.001 TRP D 357 HIS 0.007 0.002 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (16462) covalent geometry : angle 1.09243 / 0.44 (24964) hydrogen bonds : bond 0.06679 / 4.46 ( 625) hydrogen bonds : angle 3.09708 / 2.17 ( 1233) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: D 59 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7254 (mtmp) REVERT: D 247 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7338 (ttp80) REVERT: D 261 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7521 (mtpp) REVERT: D 347 ARG cc_start: 0.8143 (mtt-85) cc_final: 0.7667 (mmm-85) REVERT: D 364 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7586 (mm-40) REVERT: D 406 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7958 (ttpp) outliers start: 15 outliers final: 5 residues processed: 37 average time/residue: 0.7473 time to fit residues: 30.0292 Evaluate side-chains 36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.1002 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.184382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.113428 restraints weight = 18311.086| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 0.84 r_work: 0.3097 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16463 Z= 0.222 Angle : 1.092 14.184 24964 Z= 0.438 Chirality : 0.085 0.954 3223 Planarity : 0.005 0.051 1096 Dihedral : 24.940 178.629 8403 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.50 % Allowed : 27.11 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.44), residues: 383 helix: 1.12 (0.34), residues: 248 sheet: -1.87 (0.95), residues: 24 loop : -2.34 (0.54), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 240 TYR 0.025 0.001 TYR D 385 PHE 0.012 0.002 PHE D 89 TRP 0.008 0.001 TRP D 328 HIS 0.002 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 (16462) covalent geometry : angle 1.09176 / 0.44 (24964) hydrogen bonds : bond 0.06623 / 4.42 ( 625) hydrogen bonds : angle 3.11359 / 2.17 ( 1233) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: D 39 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6711 (pp20) REVERT: D 59 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7247 (mtmp) REVERT: D 247 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7341 (ttp80) REVERT: D 261 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7520 (mtpp) REVERT: D 347 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7610 (mtp180) REVERT: D 406 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7971 (ttpp) outliers start: 12 outliers final: 4 residues processed: 34 average time/residue: 0.7717 time to fit residues: 28.2213 Evaluate side-chains 34 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 406 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.4123 r_free = 0.4123 target = 0.184102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114945 restraints weight = 18216.162| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 0.79 r_work: 0.3111 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16463 Z= 0.232 Angle : 1.088 14.211 24964 Z= 0.436 Chirality : 0.084 0.938 3223 Planarity : 0.005 0.053 1096 Dihedral : 24.919 178.697 8403 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.33 % Allowed : 28.57 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.44), residues: 383 helix: 1.16 (0.34), residues: 248 sheet: -1.74 (0.97), residues: 24 loop : -2.36 (0.53), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 243 TYR 0.024 0.001 TYR D 385 PHE 0.012 0.002 PHE D 89 TRP 0.009 0.002 TRP D 357 HIS 0.004 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (16462) covalent geometry : angle 1.08773 / 0.44 (24964) hydrogen bonds : bond 0.06594 / 4.41 ( 625) hydrogen bonds : angle 3.13247 / 2.18 ( 1233) Misc. bond : bond 0.00052 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: D 59 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7248 (mtmp) REVERT: D 247 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7323 (ttp80) REVERT: D 261 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7555 (mtpp) REVERT: D 347 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7615 (mtp180) REVERT: D 406 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8003 (ttpp) outliers start: 8 outliers final: 5 residues processed: 33 average time/residue: 0.7444 time to fit residues: 26.6278 Evaluate side-chains 34 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 255 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.181451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109904 restraints weight = 18220.839| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 0.83 r_work: 0.3050 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16463 Z= 0.309 Angle : 1.146 15.021 24964 Z= 0.460 Chirality : 0.090 1.138 3223 Planarity : 0.005 0.052 1096 Dihedral : 24.958 177.683 8403 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.62 % Allowed : 28.28 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.44), residues: 383 helix: 1.02 (0.34), residues: 248 sheet: -1.56 (1.04), residues: 24 loop : -2.42 (0.53), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 240 TYR 0.028 0.002 TYR D 385 PHE 0.011 0.002 PHE D 89 TRP 0.010 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.31 (16462) covalent geometry : angle 1.14553 / 0.46 (24964) hydrogen bonds : bond 0.06854 / 4.58 ( 625) hydrogen bonds : angle 3.20356 / 2.24 ( 1233) Misc. bond : bond 0.00081 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4563.98 seconds wall clock time: 78 minutes 29.24 seconds (4709.24 seconds total)