Starting phenix.real_space_refine on Sat Aug 23 21:38:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2s_40986/08_2025/8t2s_40986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2s_40986/08_2025/8t2s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t2s_40986/08_2025/8t2s_40986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2s_40986/08_2025/8t2s_40986.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2s_40986/08_2025/8t2s_40986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2s_40986/08_2025/8t2s_40986.cif" } 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-2.0-5787/lib/python3.9/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: 4.03, per 1000 atoms: 0.27 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: 1.23 Conformation dependent library (CDL) restraints added in 318.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 2.97 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: 4.35 Time building geometry restraints manager: 1.72 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: 8923 35.46 - 70.92: 1328 70.92 - 106.37: 142 106.37 - 141.83: 7 141.83 - 177.29: 10 Dihedral angle restraints: 10410 sinusoidal: 9280 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 10407 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.330 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 24.681 177.289 9682 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 aren 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 covalent geometry : bond 0.00379 (16462) covalent geometry : angle 0.88888 (24964) hydrogen bonds : bond 0.10370 ( 625) hydrogen bonds : angle 4.99506 ( 1233) Misc. bond : bond 0.00023 ( 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 : 0.284 Fit side-chains REVERT: D 130 MET cc_start: 0.7844 (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: 0.7364 time to fit residues: 30.4986 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 : 0.298 ------------------------------------------------------------------------------- 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: 6.9990 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.174592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101504 restraints weight = 17980.841| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.06 r_work: 0.2929 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 16463 Z= 0.378 Angle : 0.743 7.965 24964 Z= 0.380 Chirality : 0.043 0.300 3223 Planarity : 0.006 0.042 1096 Dihedral : 24.636 176.100 8878 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.71 % Allowed : 18.37 % Favored : 74.93 % 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 aren not related in a simple way. whole: -1.62 (0.39), residues: 383 helix: -0.26 (0.31), residues: 247 sheet: -1.49 (0.93), residues: 24 loop : -2.68 (0.47), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 243 TYR 0.021 0.002 TYR D 385 PHE 0.014 0.003 PHE D 298 TRP 0.011 0.002 TRP D 357 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00732 (16462) covalent geometry : angle 0.74260 (24964) hydrogen bonds : bond 0.07218 ( 625) hydrogen bonds : angle 3.51922 ( 1233) Misc. bond : bond 0.00083 ( 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 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 30 time to evaluate : 0.275 Fit side-chains REVERT: D 59 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7342 (mtmp) REVERT: D 251 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: D 347 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7579 (mmm-85) REVERT: D 364 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7508 (mm-40) REVERT: D 406 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8225 (mppt) outliers start: 23 outliers final: 5 residues processed: 48 average time/residue: 0.7177 time to fit residues: 37.5665 Evaluate side-chains 37 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 262 SER 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: 0.9990 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: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.176147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103531 restraints weight = 18115.105| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 0.93 r_work: 0.2958 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16463 Z= 0.293 Angle : 0.676 7.594 24964 Z= 0.345 Chirality : 0.038 0.286 3223 Planarity : 0.005 0.037 1096 Dihedral : 24.544 175.824 8878 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.41 % Allowed : 19.53 % Favored : 74.05 % 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 aren not related in a simple way. whole: -1.01 (0.41), residues: 383 helix: 0.30 (0.33), residues: 249 sheet: -1.68 (0.94), residues: 24 loop : -2.59 (0.49), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 240 TYR 0.021 0.002 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 109 Details of bonding type rmsd covalent geometry : bond 0.00569 (16462) covalent geometry : angle 0.67635 (24964) hydrogen bonds : bond 0.06597 ( 625) hydrogen bonds : angle 3.31743 ( 1233) Misc. bond : bond 0.00083 ( 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 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 29 time to evaluate : 0.278 Fit side-chains REVERT: D 59 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7353 (mtmp) REVERT: D 132 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7883 (m-30) REVERT: D 247 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7105 (ttp80) REVERT: D 251 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7517 (mt-10) REVERT: D 261 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7478 (mtpp) REVERT: D 266 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8000 (mmm-85) REVERT: D 280 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7509 (t0) REVERT: D 347 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7463 (mtp180) REVERT: D 364 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7470 (mm-40) REVERT: D 406 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8118 (tttt) outliers start: 22 outliers final: 5 residues processed: 47 average time/residue: 0.7795 time to fit residues: 39.8086 Evaluate side-chains 41 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 266 ARG 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: 1.9990 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN D 400 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.179839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107565 restraints weight = 18152.325| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 0.86 r_work: 0.3023 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16463 Z= 0.166 Angle : 0.600 7.495 24964 Z= 0.307 Chirality : 0.034 0.265 3223 Planarity : 0.004 0.036 1096 Dihedral : 24.519 174.843 8878 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.54 % Allowed : 20.99 % 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 aren not related in a simple way. whole: -0.34 (0.43), residues: 383 helix: 0.87 (0.34), residues: 249 sheet: -1.80 (0.93), residues: 24 loop : -2.39 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 240 TYR 0.016 0.001 TYR D 385 PHE 0.015 0.001 PHE D 89 TRP 0.008 0.001 TRP D 357 HIS 0.002 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00315 (16462) covalent geometry : angle 0.60040 (24964) hydrogen bonds : bond 0.06038 ( 625) hydrogen bonds : angle 3.10434 ( 1233) Misc. bond : bond 0.00052 ( 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 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 30 time to evaluate : 0.285 Fit side-chains REVERT: D 7 MET cc_start: 0.7381 (mmm) cc_final: 0.7152 (tpt) REVERT: D 59 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7267 (mtmp) REVERT: D 201 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7352 (tt) REVERT: D 247 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7126 (ttp80) REVERT: D 251 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: D 261 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7507 (mtpp) REVERT: D 266 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8047 (mmm-85) REVERT: D 280 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7464 (t0) REVERT: D 347 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7480 (mtp180) REVERT: D 364 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7465 (mm-40) REVERT: D 406 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7840 (ttpp) outliers start: 19 outliers final: 6 residues processed: 44 average time/residue: 0.8031 time to fit residues: 38.3166 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 : 0.319 ------------------------------------------------------------------------------- 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 149 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 201 LEU 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 266 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 28 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 24 optimal weight: 0.0060 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.175642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.102829 restraints weight = 18148.589| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 0.95 r_work: 0.2950 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16463 Z= 0.319 Angle : 0.681 7.442 24964 Z= 0.348 Chirality : 0.039 0.288 3223 Planarity : 0.005 0.037 1096 Dihedral : 24.490 174.765 8876 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 7.29 % Allowed : 19.53 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.43), residues: 383 helix: 0.83 (0.34), residues: 249 sheet: -1.88 (0.92), residues: 24 loop : -2.47 (0.51), 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 0.010 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00617 (16462) covalent geometry : angle 0.68145 (24964) hydrogen bonds : bond 0.06647 ( 625) hydrogen bonds : angle 3.18434 ( 1233) Misc. bond : bond 0.00074 ( 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 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 30 time to evaluate : 0.260 Fit side-chains REVERT: D 59 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7257 (mtmp) REVERT: D 132 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: D 247 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7118 (ttp80) REVERT: D 251 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7450 (mt-10) REVERT: D 259 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7561 (tpp) REVERT: D 261 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7435 (mtpp) REVERT: D 266 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7256 (mmm160) REVERT: D 280 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7514 (t0) REVERT: D 347 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7502 (mtp180) REVERT: D 364 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7511 (mm-40) REVERT: D 406 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8110 (tttt) outliers start: 25 outliers final: 6 residues processed: 44 average time/residue: 0.7903 time to fit residues: 37.5066 Evaluate side-chains 42 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 26 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 132 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR 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 261 LYS Chi-restraints excluded: chain D residue 266 ARG 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=3.00 ------------------------------------------------------------------------------- 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: 0.0970 chunk 66 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 68 optimal weight: 30.0000 chunk 58 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.182807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110804 restraints weight = 18152.568| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 0.87 r_work: 0.3063 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16463 Z= 0.129 Angle : 0.578 9.372 24964 Z= 0.293 Chirality : 0.032 0.237 3223 Planarity : 0.004 0.036 1096 Dihedral : 24.451 176.470 8876 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.92 % Allowed : 26.53 % Favored : 70.55 % 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 aren not related in a simple way. whole: 0.06 (0.45), residues: 383 helix: 1.22 (0.35), residues: 249 sheet: -1.84 (0.95), residues: 24 loop : -2.28 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 117 TYR 0.013 0.001 TYR D 385 PHE 0.015 0.001 PHE D 89 TRP 0.007 0.001 TRP D 357 HIS 0.002 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00239 (16462) covalent geometry : angle 0.57786 (24964) hydrogen bonds : bond 0.05767 ( 625) hydrogen bonds : angle 2.99846 ( 1233) Misc. bond : bond 0.00044 ( 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 39 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.300 Fit side-chains REVERT: D 251 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: D 259 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7383 (tpp) REVERT: D 261 LYS cc_start: 0.8014 (mtmm) cc_final: 0.7480 (mtpp) REVERT: D 266 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8057 (mmm-85) REVERT: D 347 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7534 (mtp180) REVERT: D 406 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7880 (ttpp) outliers start: 10 outliers final: 2 residues processed: 35 average time/residue: 0.8323 time to fit residues: 31.5581 Evaluate side-chains 33 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 259 MET Chi-restraints excluded: chain D residue 266 ARG 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: 0.9990 chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 67 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.176372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.102964 restraints weight = 17931.198| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 0.98 r_work: 0.2955 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16463 Z= 0.320 Angle : 0.684 8.631 24964 Z= 0.348 Chirality : 0.039 0.286 3223 Planarity : 0.005 0.043 1096 Dihedral : 24.444 173.818 8875 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.79 % Allowed : 25.07 % Favored : 71.14 % 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 aren not related in a simple way. whole: -0.23 (0.44), residues: 383 helix: 0.95 (0.34), residues: 249 sheet: -1.68 (0.98), residues: 24 loop : -2.35 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 326 TYR 0.023 0.002 TYR D 385 PHE 0.011 0.002 PHE D 146 TRP 0.009 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00620 (16462) covalent geometry : angle 0.68361 (24964) hydrogen bonds : bond 0.06594 ( 625) hydrogen bonds : angle 3.20765 ( 1233) Misc. bond : bond 0.00077 ( 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 40 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 27 time to evaluate : 0.260 Fit side-chains REVERT: D 59 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7260 (mtmp) REVERT: D 105 GLN cc_start: 0.8211 (mt0) cc_final: 0.7795 (mt0) REVERT: D 247 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7106 (ttp80) REVERT: D 251 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: D 259 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7470 (tpp) REVERT: D 261 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7502 (mtpp) REVERT: D 266 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7256 (mmm160) REVERT: D 347 ARG cc_start: 0.8159 (mtt-85) cc_final: 0.7563 (mtp180) REVERT: D 364 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7698 (mm-40) REVERT: D 406 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8130 (tttt) outliers start: 13 outliers final: 4 residues processed: 35 average time/residue: 0.9236 time to fit residues: 34.6807 Evaluate side-chains 36 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 25 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 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 266 ARG 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=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: 2.9990 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 30.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.180019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109056 restraints weight = 17994.254| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 0.81 r_work: 0.3022 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16463 Z= 0.148 Angle : 0.618 11.454 24964 Z= 0.313 Chirality : 0.033 0.285 3223 Planarity : 0.004 0.052 1096 Dihedral : 24.521 173.132 8875 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.19 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 : 0.27 % 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 aren not related in a simple way. whole: -0.09 (0.44), residues: 383 helix: 1.05 (0.34), residues: 249 sheet: -1.58 (1.00), residues: 24 loop : -2.28 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 351 TYR 0.019 0.002 TYR D 385 PHE 0.021 0.002 PHE D 89 TRP 0.009 0.002 TRP D 328 HIS 0.003 0.001 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00284 (16462) covalent geometry : angle 0.61808 (24964) hydrogen bonds : bond 0.06229 ( 625) hydrogen bonds : angle 3.12156 ( 1233) Misc. bond : bond 0.00024 ( 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 39 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.251 Fit side-chains REVERT: D 59 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7228 (mtmp) REVERT: D 132 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: D 247 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7139 (ttp80) REVERT: D 251 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: D 259 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.7411 (tpp) REVERT: D 261 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7476 (mtpp) REVERT: D 266 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7207 (mmm160) REVERT: D 406 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7863 (ttpp) outliers start: 11 outliers final: 3 residues processed: 35 average time/residue: 0.8188 time to fit residues: 30.8491 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 : 0.164 ------------------------------------------------------------------------------- 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 132 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 259 MET Chi-restraints excluded: chain D residue 266 ARG 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: 0.8980 chunk 14 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 8 optimal weight: 0.0270 chunk 80 optimal weight: 30.0000 chunk 73 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 overall best weight: 2.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.176221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102783 restraints weight = 18072.640| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 0.97 r_work: 0.2951 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2608 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= 0.316 Angle : 0.683 9.782 24964 Z= 0.348 Chirality : 0.039 0.287 3223 Planarity : 0.005 0.051 1096 Dihedral : 24.422 173.937 8875 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.37 % Allowed : 26.24 % 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 aren not related in a simple way. whole: -0.24 (0.43), residues: 383 helix: 0.94 (0.34), residues: 249 sheet: -1.53 (1.01), residues: 24 loop : -2.36 (0.53), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 347 TYR 0.023 0.002 TYR D 385 PHE 0.016 0.002 PHE D 89 TRP 0.010 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00611 (16462) covalent geometry : angle 0.68314 (24964) hydrogen bonds : bond 0.06670 ( 625) hydrogen bonds : angle 3.21576 ( 1233) Misc. bond : bond 0.00089 ( 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 41 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 26 time to evaluate : 0.279 Fit side-chains REVERT: D 59 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7289 (mtmp) REVERT: D 247 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7133 (ttp80) REVERT: D 251 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: D 259 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7442 (tpp) REVERT: D 261 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7415 (mtpp) REVERT: D 266 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7271 (mmm160) REVERT: D 347 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7540 (mtp180) REVERT: D 364 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7667 (mm-40) REVERT: D 406 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8139 (tttt) outliers start: 15 outliers final: 5 residues processed: 35 average time/residue: 0.8467 time to fit residues: 31.9250 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 : 0.193 ------------------------------------------------------------------------------- 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 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 266 ARG 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=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: 2.9990 chunk 68 optimal weight: 30.0000 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.177255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104025 restraints weight = 18050.236| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 0.90 r_work: 0.2964 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16463 Z= 0.240 Angle : 0.652 10.598 24964 Z= 0.333 Chirality : 0.036 0.288 3223 Planarity : 0.005 0.052 1096 Dihedral : 24.452 173.761 8875 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.79 % Allowed : 26.53 % 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 aren not related in a simple way. whole: -0.22 (0.43), residues: 383 helix: 0.96 (0.34), residues: 249 sheet: -1.51 (1.01), residues: 24 loop : -2.40 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 347 TYR 0.023 0.002 TYR D 385 PHE 0.016 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 covalent geometry : bond 0.00464 (16462) covalent geometry : angle 0.65190 (24964) hydrogen bonds : bond 0.06538 ( 625) hydrogen bonds : angle 3.19075 ( 1233) Misc. bond : bond 0.00064 ( 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 39 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 26 time to evaluate : 0.227 Fit side-chains REVERT: D 59 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7253 (mtmp) REVERT: D 247 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7113 (ttp80) REVERT: D 251 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: D 253 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.7946 (mp) REVERT: D 261 LYS cc_start: 0.7993 (mtmm) cc_final: 0.7443 (mtpp) REVERT: D 266 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7256 (mmm160) REVERT: D 347 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7542 (mtp180) REVERT: D 364 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7627 (mm-40) REVERT: D 406 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8120 (tttt) outliers start: 13 outliers final: 4 residues processed: 34 average time/residue: 0.8903 time to fit residues: 32.4229 Evaluate side-chains 37 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 266 ARG 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=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: 4.9990 chunk 29 optimal weight: 0.6980 chunk 78 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.176678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103339 restraints weight = 18026.944| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 0.95 r_work: 0.2956 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16463 Z= 0.291 Angle : 0.670 10.676 24964 Z= 0.341 Chirality : 0.038 0.285 3223 Planarity : 0.005 0.052 1096 Dihedral : 24.409 173.958 8875 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % 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 aren not related in a simple way. whole: -0.26 (0.44), residues: 383 helix: 0.94 (0.34), residues: 249 sheet: -1.58 (1.01), residues: 24 loop : -2.43 (0.52), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 347 TYR 0.023 0.002 TYR D 385 PHE 0.015 0.002 PHE D 89 TRP 0.011 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00563 (16462) covalent geometry : angle 0.67036 (24964) hydrogen bonds : bond 0.06520 ( 625) hydrogen bonds : angle 3.20166 ( 1233) Misc. bond : bond 0.00085 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5091.80 seconds wall clock time: 87 minutes 38.62 seconds (5258.62 seconds total)