Starting phenix.real_space_refine on Sun Nov 17 23:08:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/11_2024/8t2s_40986.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/11_2024/8t2s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/11_2024/8t2s_40986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/11_2024/8t2s_40986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/11_2024/8t2s_40986.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t2s_40986/11_2024/8t2s_40986.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 10.69, per 1000 atoms: 0.71 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: 3.54 Conformation dependent library (CDL) restraints added in 627.8 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: 8.07 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: 8.56 Time building geometry restraints manager: 4.19 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.110 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: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 43.530 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.340 ------------------------------------------------------------------------------- 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 16462 Z= 0.227 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.016 0.002 TRP D 357 HIS 0.008 0.002 HIS D 43 PHE 0.019 0.003 PHE D 89 TYR 0.019 0.002 TYR D 60 ARG 0.005 0.001 ARG D 347 *********************** 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 : 0.780 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: 1.5910 time to fit residues: 66.0812 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 : 0.853 ------------------------------------------------------------------------------- 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 78 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16462 Z= 0.372 Angle : 0.703 7.499 24964 Z= 0.360 Chirality : 0.040 0.288 3223 Planarity : 0.005 0.041 1096 Dihedral : 24.623 176.244 8878 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 6.41 % Allowed : 18.08 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.40), residues: 383 helix: -0.20 (0.32), residues: 249 sheet: -1.50 (0.93), residues: 24 loop : -2.63 (0.48), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 357 HIS 0.005 0.001 HIS D 109 PHE 0.013 0.003 PHE D 298 TYR 0.023 0.002 TYR D 385 ARG 0.003 0.001 ARG D 243 *********************** 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 : 0.653 Fit side-chains REVERT: D 59 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7310 (mtmp) REVERT: D 251 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: D 347 ARG cc_start: 0.7582 (mtt-85) cc_final: 0.6998 (mtp180) REVERT: D 364 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7178 (mm-40) REVERT: D 406 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7880 (mppt) outliers start: 22 outliers final: 5 residues processed: 47 average time/residue: 1.3683 time to fit residues: 70.9590 Evaluate side-chains 37 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 84 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 30.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16462 Z= 0.252 Angle : 0.632 7.505 24964 Z= 0.323 Chirality : 0.036 0.281 3223 Planarity : 0.004 0.040 1096 Dihedral : 24.579 174.992 8878 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 6.12 % Allowed : 18.95 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.42), residues: 383 helix: 0.49 (0.33), residues: 249 sheet: -1.64 (0.94), residues: 24 loop : -2.51 (0.49), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 357 HIS 0.002 0.001 HIS D 109 PHE 0.014 0.002 PHE D 89 TYR 0.018 0.002 TYR D 385 ARG 0.002 0.000 ARG D 240 *********************** 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 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 31 time to evaluate : 0.739 Fit side-chains REVERT: D 59 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7302 (mtmp) REVERT: D 247 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6999 (ttp80) REVERT: D 251 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: D 261 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7383 (mtpp) REVERT: D 266 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7353 (mmm160) REVERT: D 280 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7397 (t0) REVERT: D 347 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.6913 (mtp180) REVERT: D 364 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7152 (mm-40) REVERT: D 400 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8365 (t160) REVERT: D 406 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7866 (mppt) REVERT: D 415 SER cc_start: 0.8514 (OUTLIER) cc_final: 0.8292 (p) outliers start: 21 outliers final: 7 residues processed: 47 average time/residue: 1.8054 time to fit residues: 91.9305 Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 28 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 149 VAL 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 266 ARG 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 Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 16462 Z= 0.536 Angle : 0.796 8.122 24964 Z= 0.405 Chirality : 0.046 0.304 3223 Planarity : 0.006 0.035 1096 Dihedral : 24.588 175.255 8878 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 7.58 % Allowed : 20.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.41), residues: 383 helix: 0.31 (0.33), residues: 247 sheet: -1.89 (0.94), residues: 24 loop : -2.55 (0.48), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 357 HIS 0.006 0.002 HIS D 109 PHE 0.015 0.003 PHE D 146 TYR 0.024 0.002 TYR D 385 ARG 0.004 0.001 ARG D 240 *********************** 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 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 29 time to evaluate : 0.731 Fit side-chains REVERT: D 17 ASN cc_start: 0.6525 (OUTLIER) cc_final: 0.6306 (m-40) REVERT: D 59 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7364 (mtmp) REVERT: D 216 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8781 (tttp) REVERT: D 247 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6961 (ttp80) REVERT: D 251 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7308 (mt-10) REVERT: D 261 LYS cc_start: 0.7905 (mtmm) cc_final: 0.7329 (mtpp) REVERT: D 266 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7208 (mmm160) REVERT: D 280 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7465 (t0) REVERT: D 347 ARG cc_start: 0.7577 (mtt-85) cc_final: 0.6869 (mtp180) REVERT: D 364 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7260 (mm-40) REVERT: D 406 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7796 (mtpt) REVERT: D 415 SER cc_start: 0.8575 (OUTLIER) cc_final: 0.8354 (p) outliers start: 26 outliers final: 9 residues processed: 48 average time/residue: 1.6125 time to fit residues: 84.3464 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 28 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 17 ASN Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 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 Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 chunk 22 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16462 Z= 0.371 Angle : 0.689 7.371 24964 Z= 0.352 Chirality : 0.040 0.288 3223 Planarity : 0.005 0.038 1096 Dihedral : 24.530 175.382 8878 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 7.00 % Allowed : 23.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.42), residues: 383 helix: 0.50 (0.33), residues: 249 sheet: -1.98 (0.93), residues: 24 loop : -2.61 (0.48), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 PHE 0.012 0.002 PHE D 89 TYR 0.023 0.002 TYR D 385 ARG 0.003 0.000 ARG D 351 *********************** 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 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 29 time to evaluate : 0.745 Fit side-chains REVERT: D 59 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7364 (mtmp) REVERT: D 247 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6996 (ttp80) REVERT: D 251 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: D 253 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7986 (mp) REVERT: D 261 LYS cc_start: 0.7845 (mtmm) cc_final: 0.7274 (mtpp) REVERT: D 280 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7452 (t0) REVERT: D 347 ARG cc_start: 0.7607 (mtt-85) cc_final: 0.6922 (mtp180) REVERT: D 364 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7193 (mm-40) REVERT: D 388 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7081 (ptmm) REVERT: D 406 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7454 (ttpp) outliers start: 24 outliers final: 8 residues processed: 46 average time/residue: 1.5950 time to fit residues: 79.7131 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 : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 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 253 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.5980 chunk 80 optimal weight: 30.0000 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16462 Z= 0.224 Angle : 0.638 12.871 24964 Z= 0.326 Chirality : 0.036 0.294 3223 Planarity : 0.004 0.038 1096 Dihedral : 24.585 175.133 8878 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 7.29 % Allowed : 22.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.43), residues: 383 helix: 0.76 (0.34), residues: 249 sheet: -1.97 (0.94), residues: 24 loop : -2.47 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 328 HIS 0.003 0.001 HIS D 109 PHE 0.012 0.002 PHE D 89 TYR 0.020 0.002 TYR D 385 ARG 0.002 0.000 ARG D 117 *********************** 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 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 29 time to evaluate : 0.774 Fit side-chains REVERT: D 59 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7284 (mtmp) REVERT: D 247 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7013 (ttp80) REVERT: D 251 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: D 253 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7925 (mp) REVERT: D 259 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7288 (tpp) REVERT: D 261 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7316 (mtpp) REVERT: D 266 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.8070 (mmm-85) REVERT: D 280 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7412 (t0) REVERT: D 347 ARG cc_start: 0.7586 (mtt-85) cc_final: 0.6899 (mtp180) REVERT: D 364 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7135 (mm-40) REVERT: D 388 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.6930 (ptmm) REVERT: D 406 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7465 (ttpp) outliers start: 25 outliers final: 7 residues processed: 46 average time/residue: 1.7665 time to fit residues: 88.1987 Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR 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 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 388 LYS 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 86 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 16462 Z= 0.419 Angle : 0.727 10.196 24964 Z= 0.370 Chirality : 0.042 0.300 3223 Planarity : 0.005 0.037 1096 Dihedral : 24.530 175.247 8876 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 7.00 % Allowed : 23.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.42), residues: 383 helix: 0.64 (0.33), residues: 249 sheet: -1.97 (0.95), residues: 24 loop : -2.59 (0.49), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 PHE 0.013 0.002 PHE D 146 TYR 0.023 0.002 TYR D 385 ARG 0.002 0.000 ARG D 308 *********************** 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 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 28 time to evaluate : 0.748 Fit side-chains REVERT: D 59 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7342 (mtmp) REVERT: D 247 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6985 (ttp80) REVERT: D 251 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: D 253 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7891 (mp) REVERT: D 261 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7319 (mtpp) REVERT: D 280 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7487 (t0) REVERT: D 347 ARG cc_start: 0.7554 (mtt-85) cc_final: 0.6913 (mtp180) REVERT: D 364 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7243 (mm-40) REVERT: D 388 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7100 (ptmm) REVERT: D 406 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7441 (ttpp) outliers start: 24 outliers final: 9 residues processed: 45 average time/residue: 1.7788 time to fit residues: 87.1000 Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR 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 261 LYS Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 313 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16462 Z= 0.281 Angle : 0.662 9.466 24964 Z= 0.338 Chirality : 0.038 0.296 3223 Planarity : 0.005 0.040 1096 Dihedral : 24.562 174.800 8876 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.71 % Allowed : 24.49 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.43), residues: 383 helix: 0.73 (0.33), residues: 249 sheet: -1.85 (0.98), residues: 24 loop : -2.48 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 357 HIS 0.003 0.001 HIS D 109 PHE 0.019 0.002 PHE D 89 TYR 0.020 0.002 TYR D 385 ARG 0.004 0.000 ARG D 266 *********************** 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 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 26 time to evaluate : 0.733 Fit side-chains REVERT: D 35 MET cc_start: 0.4031 (OUTLIER) cc_final: 0.3150 (tmt) REVERT: D 59 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7380 (mtmp) REVERT: D 247 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6972 (ttp80) REVERT: D 251 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: D 253 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7977 (mp) REVERT: D 261 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7327 (mtpp) REVERT: D 280 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7504 (t0) REVERT: D 347 ARG cc_start: 0.7606 (mtt-85) cc_final: 0.6933 (mtp180) REVERT: D 364 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7168 (mm-40) REVERT: D 388 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7015 (ptmm) REVERT: D 406 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7457 (ttpp) outliers start: 23 outliers final: 9 residues processed: 41 average time/residue: 1.6416 time to fit residues: 73.3549 Evaluate side-chains 45 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 26 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain D residue 101 ILE 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 253 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 313 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16462 Z= 0.337 Angle : 0.680 9.983 24964 Z= 0.347 Chirality : 0.039 0.290 3223 Planarity : 0.005 0.040 1096 Dihedral : 24.504 175.088 8876 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 6.41 % Allowed : 24.78 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.43), residues: 383 helix: 0.80 (0.34), residues: 249 sheet: -1.64 (1.05), residues: 24 loop : -2.48 (0.51), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 PHE 0.017 0.002 PHE D 89 TYR 0.022 0.002 TYR D 385 ARG 0.002 0.000 ARG D 266 *********************** 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 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 27 time to evaluate : 0.670 Fit side-chains REVERT: D 35 MET cc_start: 0.4062 (OUTLIER) cc_final: 0.3362 (tmt) REVERT: D 39 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: D 59 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7399 (mtmp) REVERT: D 247 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.6969 (ttp80) REVERT: D 251 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7368 (mt-10) REVERT: D 253 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7925 (mp) REVERT: D 259 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7290 (tpp) REVERT: D 261 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7320 (mtpp) REVERT: D 280 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7498 (t0) REVERT: D 347 ARG cc_start: 0.7574 (mtt-85) cc_final: 0.6918 (mtp180) REVERT: D 364 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7198 (mm-40) REVERT: D 388 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7042 (ptmm) REVERT: D 406 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7442 (ttpp) outliers start: 22 outliers final: 8 residues processed: 41 average time/residue: 1.6355 time to fit residues: 73.1475 Evaluate side-chains 46 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 26 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain D residue 101 ILE 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 253 LEU 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 280 ASP Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 313 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 16462 Z= 0.427 Angle : 0.735 10.468 24964 Z= 0.373 Chirality : 0.042 0.301 3223 Planarity : 0.005 0.040 1096 Dihedral : 24.541 174.791 8876 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 6.12 % Allowed : 25.36 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.42), residues: 383 helix: 0.66 (0.33), residues: 249 sheet: -1.83 (1.04), residues: 24 loop : -2.59 (0.50), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 357 HIS 0.004 0.001 HIS D 109 PHE 0.016 0.002 PHE D 89 TYR 0.023 0.002 TYR D 385 ARG 0.002 0.000 ARG D 243 ********************** 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 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 26 time to evaluate : 0.922 Fit side-chains REVERT: D 35 MET cc_start: 0.4025 (OUTLIER) cc_final: 0.3396 (tmt) REVERT: D 39 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: D 59 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7355 (mtmp) REVERT: D 247 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6936 (ttp80) REVERT: D 251 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: D 253 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7945 (mp) REVERT: D 261 LYS cc_start: 0.7876 (mtmm) cc_final: 0.7318 (mtpp) REVERT: D 280 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7475 (t0) REVERT: D 347 ARG cc_start: 0.7564 (mtt-85) cc_final: 0.6931 (mtp180) REVERT: D 364 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7208 (mm-40) REVERT: D 388 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7098 (ptmm) REVERT: D 406 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7427 (ttpp) outliers start: 21 outliers final: 8 residues processed: 40 average time/residue: 1.5886 time to fit residues: 69.4835 Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 26 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 86 THR Chi-restraints excluded: chain D residue 101 ILE 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 253 LEU 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 313 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.4980 chunk 68 optimal weight: 30.0000 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.181987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110189 restraints weight = 18129.583| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 0.86 r_work: 0.3049 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16462 Z= 0.156 Angle : 0.599 10.669 24964 Z= 0.303 Chirality : 0.032 0.239 3223 Planarity : 0.004 0.043 1096 Dihedral : 24.444 177.419 8876 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.21 % Allowed : 27.70 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.44), residues: 383 helix: 1.10 (0.34), residues: 249 sheet: -1.85 (1.03), residues: 24 loop : -2.34 (0.54), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 357 HIS 0.002 0.001 HIS D 291 PHE 0.020 0.002 PHE D 89 TYR 0.014 0.001 TYR D 385 ARG 0.003 0.000 ARG D 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3009.46 seconds wall clock time: 68 minutes 46.70 seconds (4126.70 seconds total)