Starting phenix.real_space_refine on Fri Jul 3 15:37:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t2s_40986/07_2026/8t2s_40986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2s_40986/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8t2s_40986/07_2026/8t2s_40986.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t2s_40986/07_2026/8t2s_40986.cif" model { file = "/net/cci-nas-00/data/ceres_data/8t2s_40986/07_2026/8t2s_40986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2s_40986/07_2026/8t2s_40986.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t2s_40986/07_2026/8t2s_40986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2s_40986/07_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-dev-6108/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: {'RNA': 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: 2.44, per 1000 atoms: 0.16 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: 0.79 Conformation dependent library (CDL) restraints added in 176.1 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: 1.69 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: 1.09 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=" 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 bond pdb=" C3' G B 369 " pdb=" O3' G B 369 " ideal model delta sigma weight residual 1.427 1.453 -0.026 1.50e-02 4.44e+03 2.98e+00 bond pdb=" CB ASP D 226 " pdb=" CG ASP D 226 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.93e+00 ... (remaining 16457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 24506 2.76 - 5.51: 379 5.51 - 8.27: 62 8.27 - 11.02: 13 11.02 - 13.78: 4 Bond angle restraints: 24964 Sorted by residual: 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 angle pdb=" C3' G B 369 " pdb=" O3' G B 369 " pdb=" P A B 370 " ideal model delta sigma weight residual 120.20 127.87 -7.67 1.50e+00 4.44e-01 2.62e+01 angle pdb=" C3' A B 551 " pdb=" O3' A B 551 " pdb=" P U B 552 " ideal model delta sigma weight residual 120.20 127.62 -7.42 1.50e+00 4.44e-01 2.44e+01 angle pdb=" C3' A B 67 " pdb=" O3' A B 67 " pdb=" P U B 68 " ideal model delta sigma weight residual 120.20 127.32 -7.12 1.50e+00 4.44e-01 2.25e+01 ... (remaining 24959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 8668 35.46 - 70.92: 1111 70.92 - 106.37: 142 106.37 - 141.83: 7 141.83 - 177.29: 10 Dihedral angle restraints: 9938 sinusoidal: 8808 harmonic: 1130 Sorted by residual: dihedral pdb=" O4' C B 581 " pdb=" C1' C B 581 " pdb=" N1 C B 581 " pdb=" C2 C B 581 " ideal model delta sinusoidal sigma weight residual -160.00 12.10 -172.10 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U B 172 " pdb=" C1' U B 172 " pdb=" N1 U B 172 " pdb=" C2 U B 172 " ideal model delta sinusoidal sigma weight residual 200.00 31.97 168.03 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' C B 439 " pdb=" C1' C B 439 " pdb=" N1 C B 439 " pdb=" C2 C B 439 " ideal model delta sinusoidal sigma weight residual 200.00 43.48 156.52 1 1.50e+01 4.44e-03 8.18e+01 ... (remaining 9935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2939 0.068 - 0.135: 241 0.135 - 0.203: 25 0.203 - 0.271: 10 0.271 - 0.338: 8 Chirality restraints: 3223 Sorted by residual: chirality pdb=" C3' C B 206 " pdb=" C4' C B 206 " pdb=" O3' C B 206 " pdb=" C2' C B 206 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C3' G B 369 " pdb=" C4' G B 369 " pdb=" O3' G B 369 " pdb=" C2' G B 369 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C3' C B 39 " pdb=" C4' C B 39 " pdb=" O3' C B 39 " pdb=" C2' C B 39 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.56e+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: 3.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.320 Find NCS groups from input model: 0.050 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:5.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- 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= 0.201 Angle : 0.889 13.780 24964 Z= 0.433 Chirality : 0.042 0.338 3223 Planarity : 0.006 0.064 1096 Dihedral : 23.781 177.289 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 0.00379 / 0.20 (16462) covalent geometry : angle 0.88888 / 0.43 (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 : 0.241 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: 0.5871 time to fit residues: 24.4564 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 : 0.309 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.175067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.103638 restraints weight = 17881.388| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.04 r_work: 0.2940 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 16463 Z= 0.374 Angle : 0.738 7.847 24964 Z= 0.378 Chirality : 0.042 0.294 3223 Planarity : 0.006 0.042 1096 Dihedral : 23.702 175.533 8406 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.41 % Allowed : 18.37 % Favored : 75.22 % 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: -1.58 (0.39), residues: 383 helix: -0.22 (0.31), residues: 247 sheet: -1.51 (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 243 TYR 0.024 0.002 TYR D 385 PHE 0.015 0.003 PHE D 146 TRP 0.010 0.002 TRP D 357 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.37 (16462) covalent geometry : angle 0.73809 / 0.38 (24964) hydrogen bonds : bond 0.07178 / 4.70 ( 625) hydrogen bonds : angle 3.50890 / 2.46 ( 1233) Misc. bond : bond 0.00102 / 0.05 ( 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 : 0.179 Fit side-chains REVERT: D 59 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7350 (mtmp) REVERT: D 251 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: D 347 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7582 (mmm-85) REVERT: D 364 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7484 (mm-40) REVERT: D 406 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8230 (mppt) outliers start: 22 outliers final: 4 residues processed: 46 average time/residue: 0.6276 time to fit residues: 31.7276 Evaluate side-chains 36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 89 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.174619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101763 restraints weight = 18099.294| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.00 r_work: 0.2937 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 16463 Z= 0.346 Angle : 0.711 7.670 24964 Z= 0.363 Chirality : 0.041 0.295 3223 Planarity : 0.005 0.037 1096 Dihedral : 23.665 175.800 8406 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 7.87 % Allowed : 18.66 % 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: -1.10 (0.41), residues: 383 helix: 0.24 (0.33), residues: 249 sheet: -1.77 (0.93), residues: 24 loop : -2.64 (0.48), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 240 TYR 0.022 0.002 TYR D 385 PHE 0.014 0.002 PHE D 146 TRP 0.011 0.002 TRP D 357 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.35 (16462) covalent geometry : angle 0.71098 / 0.36 (24964) hydrogen bonds : bond 0.06922 / 4.57 ( 625) hydrogen bonds : angle 3.35647 / 2.38 ( 1233) Misc. bond : bond 0.00103 / 0.05 ( 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 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 31 time to evaluate : 0.261 Fit side-chains REVERT: D 59 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7333 (mtmp) REVERT: D 132 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: D 247 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7125 (ttp80) REVERT: D 251 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: D 280 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7509 (t0) REVERT: D 347 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7472 (mtp180) REVERT: D 364 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7515 (mm-40) REVERT: D 400 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8697 (t160) REVERT: D 406 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8154 (mtpt) outliers start: 27 outliers final: 9 residues processed: 52 average time/residue: 0.6367 time to fit residues: 36.3294 Evaluate side-chains 46 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 29 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 101 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 166 ASP 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 262 SER Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 400 ASN 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: 2.9990 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.176277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103656 restraints weight = 18075.191| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 0.90 r_work: 0.2967 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16463 Z= 0.248 Angle : 0.654 7.511 24964 Z= 0.335 Chirality : 0.038 0.293 3223 Planarity : 0.005 0.037 1096 Dihedral : 23.681 175.252 8406 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.71 % Allowed : 20.99 % Favored : 72.30 % 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: -0.69 (0.42), residues: 383 helix: 0.62 (0.34), residues: 249 sheet: -1.93 (0.92), residues: 24 loop : -2.57 (0.49), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 240 TYR 0.020 0.002 TYR D 385 PHE 0.014 0.002 PHE D 89 TRP 0.010 0.002 TRP D 328 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.25 (16462) covalent geometry : angle 0.65406 / 0.34 (24964) hydrogen bonds : bond 0.06623 / 4.35 ( 625) hydrogen bonds : angle 3.22647 / 2.28 ( 1233) Misc. bond : bond 0.00079 / 0.04 ( 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: 23 poor density : 31 time to evaluate : 0.250 Fit side-chains REVERT: D 59 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7334 (mtmp) REVERT: D 132 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: D 247 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7099 (ttp80) REVERT: D 251 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7515 (mt-10) REVERT: D 261 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7514 (mtpp) REVERT: D 280 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7510 (t0) REVERT: D 347 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7501 (mtp180) REVERT: D 364 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7469 (mm-40) REVERT: D 388 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7402 (ptmm) REVERT: D 406 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8099 (tttt) outliers start: 23 outliers final: 7 residues processed: 45 average time/residue: 0.6464 time to fit residues: 31.7750 Evaluate side-chains 42 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 27 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 166 ASP 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 388 LYS 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: 0.7980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 0.4980 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.174640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101820 restraints weight = 18125.535| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 0.95 r_work: 0.2941 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16463 Z= 0.332 Angle : 0.701 7.443 24964 Z= 0.357 Chirality : 0.040 0.290 3223 Planarity : 0.005 0.036 1096 Dihedral : 23.640 175.439 8406 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 6.12 % Allowed : 22.16 % Favored : 71.72 % 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: -0.67 (0.42), residues: 383 helix: 0.65 (0.34), residues: 249 sheet: -2.06 (0.92), residues: 24 loop : -2.56 (0.50), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 240 TYR 0.023 0.002 TYR D 385 PHE 0.012 0.002 PHE D 146 TRP 0.011 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.33 (16462) covalent geometry : angle 0.70075 / 0.36 (24964) hydrogen bonds : bond 0.06776 / 4.45 ( 625) hydrogen bonds : angle 3.25174 / 2.30 ( 1233) Misc. bond : bond 0.00092 / 0.05 ( 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 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 30 time to evaluate : 0.249 Fit side-chains REVERT: D 59 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7348 (mtmp) REVERT: D 132 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: D 247 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7057 (ttp80) REVERT: D 251 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: D 261 LYS cc_start: 0.8053 (mtmt) cc_final: 0.7574 (mtpp) REVERT: D 280 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7502 (t0) REVERT: D 347 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7507 (mtp180) REVERT: D 364 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.7505 (mm-40) REVERT: D 388 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7427 (ptmm) REVERT: D 406 LYS cc_start: 0.8492 (mtmm) cc_final: 0.7934 (ttpp) outliers start: 21 outliers final: 9 residues processed: 44 average time/residue: 0.7242 time to fit residues: 34.6736 Evaluate side-chains 43 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 27 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 161 THR Chi-restraints excluded: chain D residue 166 ASP 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 388 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 66 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 68 optimal weight: 30.0000 chunk 58 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.182752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110927 restraints weight = 18168.179| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 0.87 r_work: 0.3071 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 16463 Z= 0.130 Angle : 0.596 10.257 24964 Z= 0.301 Chirality : 0.032 0.252 3223 Planarity : 0.004 0.036 1096 Dihedral : 23.631 176.396 8406 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.08 % Allowed : 25.07 % Favored : 70.85 % 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: -0.12 (0.44), residues: 383 helix: 1.02 (0.34), residues: 251 sheet: -1.92 (0.97), residues: 24 loop : -2.25 (0.53), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 407 TYR 0.010 0.001 TYR D 385 PHE 0.016 0.002 PHE D 89 TRP 0.007 0.001 TRP D 357 HIS 0.001 0.001 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (16462) covalent geometry : angle 0.59558 / 0.30 (24964) hydrogen bonds : bond 0.05925 / 3.88 ( 625) hydrogen bonds : angle 3.06582 / 2.13 ( 1233) Misc. bond : bond 0.00015 / 0.01 ( 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 42 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 28 time to evaluate : 0.158 Fit side-chains REVERT: D 35 MET cc_start: 0.3954 (OUTLIER) cc_final: 0.3188 (tmt) REVERT: D 59 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7150 (mtmp) REVERT: D 259 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7422 (tpp) REVERT: D 261 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7582 (mtpp) REVERT: D 280 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7502 (t0) REVERT: D 347 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7536 (mtp180) REVERT: D 406 LYS cc_start: 0.8477 (mtmm) cc_final: 0.7957 (ttpp) outliers start: 14 outliers final: 4 residues processed: 37 average time/residue: 0.6849 time to fit residues: 27.6839 Evaluate side-chains 36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET 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 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 280 ASP 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: 4.9990 chunk 47 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 67 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.174219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.099905 restraints weight = 17863.838| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.16 r_work: 0.2914 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 16463 Z= 0.436 Angle : 0.768 8.649 24964 Z= 0.389 Chirality : 0.044 0.299 3223 Planarity : 0.005 0.037 1096 Dihedral : 23.628 175.186 8403 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.08 % Allowed : 26.24 % 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: -0.57 (0.43), residues: 383 helix: 0.72 (0.33), residues: 249 sheet: -1.87 (1.03), residues: 24 loop : -2.54 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 326 TYR 0.025 0.002 TYR D 385 PHE 0.014 0.002 PHE D 146 TRP 0.012 0.003 TRP D 357 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00846 / 0.44 (16462) covalent geometry : angle 0.76843 / 0.39 (24964) hydrogen bonds : bond 0.07254 / 4.80 ( 625) hydrogen bonds : angle 3.31302 / 2.34 ( 1233) Misc. bond : bond 0.00109 / 0.06 ( 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 41 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 27 time to evaluate : 0.253 Fit side-chains REVERT: D 35 MET cc_start: 0.4121 (OUTLIER) cc_final: 0.3554 (tmt) REVERT: D 39 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: D 59 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7332 (mtmp) REVERT: D 201 LEU cc_start: 0.7802 (tp) cc_final: 0.7561 (tt) REVERT: D 247 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7135 (ttp80) REVERT: D 251 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: D 253 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8037 (mp) REVERT: D 261 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7606 (mtpp) REVERT: D 280 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7627 (t0) REVERT: D 347 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7564 (mtp180) REVERT: D 364 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7734 (mm-40) REVERT: D 406 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8015 (ttpp) outliers start: 14 outliers final: 3 residues processed: 37 average time/residue: 0.7386 time to fit residues: 29.6889 Evaluate side-chains 38 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 26 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET 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 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 262 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 73 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 30.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.181674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.111376 restraints weight = 18086.364| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 0.83 r_work: 0.3049 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16463 Z= 0.152 Angle : 0.590 9.191 24964 Z= 0.300 Chirality : 0.033 0.253 3223 Planarity : 0.004 0.039 1096 Dihedral : 23.587 176.065 8403 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.21 % Allowed : 26.53 % Favored : 70.26 % 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: 249 sheet: -1.96 (1.01), residues: 24 loop : -2.34 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 266 TYR 0.014 0.001 TYR D 385 PHE 0.022 0.002 PHE D 89 TRP 0.008 0.001 TRP D 357 HIS 0.002 0.000 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (16462) covalent geometry : angle 0.59048 / 0.30 (24964) hydrogen bonds : bond 0.05875 / 3.85 ( 625) hydrogen bonds : angle 3.07122 / 2.13 ( 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 38 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.236 Fit side-chains REVERT: D 35 MET cc_start: 0.4146 (OUTLIER) cc_final: 0.3627 (tmt) REVERT: D 39 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: D 59 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7259 (mtmp) REVERT: D 247 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7273 (ttp80) REVERT: D 259 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7414 (tpp) REVERT: D 261 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7584 (mtpp) REVERT: D 280 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7529 (t0) REVERT: D 347 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7599 (mtp180) REVERT: D 406 LYS cc_start: 0.8465 (mtmm) cc_final: 0.7921 (ttpp) outliers start: 11 outliers final: 2 residues processed: 33 average time/residue: 0.7542 time to fit residues: 27.0341 Evaluate side-chains 33 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET 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 247 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 280 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 81 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 8 optimal weight: 0.0870 chunk 80 optimal weight: 30.0000 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 overall best weight: 1.3360 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.179489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108479 restraints weight = 18037.477| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 0.84 r_work: 0.3014 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16463 Z= 0.202 Angle : 0.608 9.953 24964 Z= 0.309 Chirality : 0.034 0.265 3223 Planarity : 0.004 0.039 1096 Dihedral : 23.539 173.646 8403 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.92 % Allowed : 27.11 % 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: 0.00 (0.44), residues: 383 helix: 1.18 (0.34), residues: 249 sheet: -1.80 (1.01), residues: 24 loop : -2.34 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 172 TYR 0.020 0.001 TYR D 385 PHE 0.018 0.002 PHE D 89 TRP 0.008 0.002 TRP D 357 HIS 0.002 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.20 (16462) covalent geometry : angle 0.60798 / 0.31 (24964) hydrogen bonds : bond 0.05984 / 3.92 ( 625) hydrogen bonds : angle 3.07464 / 2.14 ( 1233) Misc. bond : bond 0.00055 / 0.03 ( 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 35 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.260 Fit side-chains REVERT: D 35 MET cc_start: 0.4200 (OUTLIER) cc_final: 0.3628 (tmt) REVERT: D 59 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7152 (mtmp) REVERT: D 261 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7559 (mtpp) REVERT: D 280 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7576 (t0) REVERT: D 347 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7485 (mtp180) REVERT: D 406 LYS cc_start: 0.8477 (mtmm) cc_final: 0.7948 (ttpp) outliers start: 10 outliers final: 3 residues processed: 31 average time/residue: 0.8392 time to fit residues: 28.1852 Evaluate side-chains 31 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET 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 255 LEU Chi-restraints excluded: chain D residue 280 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 68 optimal weight: 30.0000 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.0170 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.5022 ------------------------------------------------------------------------------- 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 = 0.4062 r_free = 0.4062 target = 0.179013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.107938 restraints weight = 18022.341| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 0.84 r_work: 0.3005 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16463 Z= 0.219 Angle : 0.618 10.676 24964 Z= 0.314 Chirality : 0.035 0.266 3223 Planarity : 0.004 0.040 1096 Dihedral : 23.537 173.392 8403 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.92 % Allowed : 27.41 % 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: -0.01 (0.44), residues: 383 helix: 1.16 (0.34), residues: 249 sheet: -1.91 (0.96), residues: 24 loop : -2.31 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 266 TYR 0.020 0.001 TYR D 385 PHE 0.018 0.002 PHE D 89 TRP 0.008 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.22 (16462) covalent geometry : angle 0.61818 / 0.31 (24964) hydrogen bonds : bond 0.06034 / 3.95 ( 625) hydrogen bonds : angle 3.08595 / 2.15 ( 1233) Misc. bond : bond 0.00064 / 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 36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.256 Fit side-chains REVERT: D 35 MET cc_start: 0.4153 (OUTLIER) cc_final: 0.3592 (tmt) REVERT: D 59 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7190 (mtmp) REVERT: D 105 GLN cc_start: 0.8123 (mt0) cc_final: 0.7727 (mt0) REVERT: D 247 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7263 (ttp80) REVERT: D 261 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7562 (mtpp) REVERT: D 280 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7556 (t0) REVERT: D 347 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7490 (mtp180) REVERT: D 406 LYS cc_start: 0.8459 (mtmm) cc_final: 0.7939 (ttpp) outliers start: 10 outliers final: 3 residues processed: 32 average time/residue: 0.8537 time to fit residues: 29.4860 Evaluate side-chains 32 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET 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 247 ARG Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 280 ASP 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: 3.9990 chunk 38 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 0.0370 overall best weight: 1.9662 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.177399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.104193 restraints weight = 18012.144| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 0.93 r_work: 0.2968 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16463 Z= 0.273 Angle : 0.658 10.896 24964 Z= 0.333 Chirality : 0.037 0.280 3223 Planarity : 0.005 0.039 1096 Dihedral : 23.557 173.391 8403 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.92 % Allowed : 27.11 % 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: -0.12 (0.44), residues: 383 helix: 1.08 (0.34), residues: 249 sheet: -1.99 (0.95), residues: 24 loop : -2.31 (0.55), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 243 TYR 0.023 0.002 TYR D 385 PHE 0.016 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 0.00529 / 0.27 (16462) covalent geometry : angle 0.65786 / 0.33 (24964) hydrogen bonds : bond 0.06383 / 4.17 ( 625) hydrogen bonds : angle 3.14096 / 2.19 ( 1233) Misc. bond : bond 0.00087 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4800.11 seconds wall clock time: 82 minutes 39.94 seconds (4959.94 seconds total)