Starting phenix.real_space_refine on Fri Jul 3 15:13:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t2t_40987/07_2026/8t2t_40987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2t_40987/07_2026/8t2t_40987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8t2t_40987/07_2026/8t2t_40987.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t2t_40987/07_2026/8t2t_40987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t2t_40987/07_2026/8t2t_40987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2t_40987/07_2026/8t2t_40987.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2t_40987/07_2026/8t2t_40987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2t_40987/07_2026/8t2t_40987.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= 0.000 sd= 0.016 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 P 546 5.49 5 Mg 10 5.21 5 S 21 5.16 5 C 7226 2.51 5 N 2738 2.21 5 O 4335 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14876 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 183 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 5} Chain: "B" Number of atoms: 11548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 11548 Classifications: {'RNA': 537} Modifications used: {'rna2p_pur': 37, 'rna2p_pyr': 11, 'rna3p_pur': 287, 'rna3p_pyr': 202} Link IDs: {'rna2p': 47, 'rna3p': 489} Chain breaks: 5 Chain: "D" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3133 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 10, 'TRANS': 376} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 9, 'NH4': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Time building chain proxies: 2.69, per 1000 atoms: 0.18 Number of scatterers: 14876 At special positions: 0 Unit cell: (103.168, 133.12, 161.408, 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) S 21 16.00 P 546 15.00 Mg 10 11.99 O 4335 8.00 N 2738 7.00 C 7226 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=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 276.4 milliseconds 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 724 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 70.5% alpha, 5.7% beta 172 base pairs and 301 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.661A pdb=" N GLN D 105 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 131 removed outlier: 3.754A pdb=" N ALA D 122 " --> pdb=" O CYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.607A pdb=" N ASP D 147 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR D 148 " --> pdb=" O PHE D 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 148' Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.672A pdb=" N LEU D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 177 removed outlier: 3.635A pdb=" N ILE D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 207 Processing helix chain 'D' and resid 207 through 218 Processing helix chain 'D' and resid 234 through 252 Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.803A pdb=" N LEU D 270 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 313 through 332 Processing helix chain 'D' and resid 337 through 361 removed outlier: 3.555A pdb=" N LYS D 361 " --> pdb=" O TRP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 373 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 389 through 396 removed outlier: 4.161A pdb=" N LYS D 396 " --> pdb=" O TYR D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 404 through 412 Processing helix chain 'D' and resid 415 through 424 removed outlier: 3.607A pdb=" N TYR D 419 " --> pdb=" O SER D 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 220 through 223 removed outlier: 4.030A pdb=" N ASN D 220 " --> pdb=" O MET D 231 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS D 228 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP D 265 " --> pdb=" O ILE D 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 275 through 279 183 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 416 hydrogen bonds 648 hydrogen bond angles 0 basepair planarities 172 basepair parallelities 301 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2323 1.33 - 1.46: 7393 1.46 - 1.58: 5495 1.58 - 1.70: 1081 1.70 - 1.83: 35 Bond restraints: 16327 Sorted by residual: bond pdb=" CG1 ILE D 325 " pdb=" CD1 ILE D 325 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.27e+00 bond pdb=" C3' A B 204 " pdb=" O3' A B 204 " ideal model delta sigma weight residual 1.427 1.454 -0.027 1.50e-02 4.44e+03 3.16e+00 bond pdb=" CG LEU D 16 " pdb=" CD2 LEU D 16 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.09e+00 bond pdb=" CB CYS D 341 " pdb=" SG CYS D 341 " ideal model delta sigma weight residual 1.808 1.753 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CA ASP D 265 " pdb=" CB ASP D 265 " ideal model delta sigma weight residual 1.532 1.558 -0.026 1.68e-02 3.54e+03 2.31e+00 ... (remaining 16322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 23986 2.39 - 4.79: 639 4.79 - 7.18: 103 7.18 - 9.57: 23 9.57 - 11.96: 5 Bond angle restraints: 24756 Sorted by residual: angle pdb=" C3' A B 204 " pdb=" O3' A B 204 " pdb=" P A B 205 " ideal model delta sigma weight residual 120.20 128.70 -8.50 1.50e+00 4.44e-01 3.21e+01 angle pdb=" O3' A B 204 " pdb=" C3' A B 204 " pdb=" C2' A B 204 " ideal model delta sigma weight residual 109.50 117.63 -8.13 1.50e+00 4.44e-01 2.94e+01 angle pdb=" O3' G B 123 " pdb=" C3' G B 123 " pdb=" C2' G B 123 " ideal model delta sigma weight residual 113.70 121.70 -8.00 1.50e+00 4.44e-01 2.84e+01 angle pdb=" C3' U B 89 " pdb=" O3' U B 89 " pdb=" P A B 90 " ideal model delta sigma weight residual 120.20 127.41 -7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" CA ILE D 325 " pdb=" CB ILE D 325 " pdb=" CG1 ILE D 325 " ideal model delta sigma weight residual 110.40 118.14 -7.74 1.70e+00 3.46e-01 2.07e+01 ... (remaining 24751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8576 35.49 - 70.98: 1129 70.98 - 106.48: 143 106.48 - 141.97: 4 141.97 - 177.46: 10 Dihedral angle restraints: 9862 sinusoidal: 8738 harmonic: 1124 Sorted by residual: dihedral pdb=" C4' C B 206 " pdb=" C3' C B 206 " pdb=" C2' C B 206 " pdb=" C1' C B 206 " ideal model delta sinusoidal sigma weight residual -35.00 29.06 -64.06 1 8.00e+00 1.56e-02 8.44e+01 dihedral pdb=" C5' C B 206 " pdb=" C4' C B 206 " pdb=" C3' C B 206 " pdb=" O3' C B 206 " ideal model delta sinusoidal sigma weight residual 147.00 84.54 62.46 1 8.00e+00 1.56e-02 8.06e+01 dihedral pdb=" O4' U B 2 " pdb=" C1' U B 2 " pdb=" N1 U B 2 " pdb=" C2 U B 2 " ideal model delta sinusoidal sigma weight residual 200.00 51.41 148.59 1 1.50e+01 4.44e-03 7.91e+01 ... (remaining 9859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2979 0.082 - 0.163: 192 0.163 - 0.245: 13 0.245 - 0.326: 3 0.326 - 0.408: 8 Chirality restraints: 3195 Sorted by residual: chirality pdb=" C1' A B 370 " pdb=" O4' A B 370 " pdb=" C2' A B 370 " pdb=" N9 A B 370 " both_signs ideal model delta sigma weight residual False 2.46 2.05 0.41 2.00e-01 2.50e+01 4.15e+00 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 -2.74 -2.38 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C3' G B 123 " pdb=" C4' G B 123 " pdb=" O3' G B 123 " pdb=" C2' G B 123 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 3192 not shown) Planarity restraints: 1089 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 289 " 0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO D 290 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 290 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 290 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 102 " -0.019 2.00e-02 2.50e+03 2.04e-02 8.35e+00 pdb=" CG TYR D 102 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 102 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR D 102 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR D 102 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR D 102 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR D 102 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 102 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 99 " -0.044 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO D 100 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.038 5.00e-02 4.00e+02 ... (remaining 1086 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 142 2.57 - 3.15: 10129 3.15 - 3.73: 31199 3.73 - 4.32: 40526 4.32 - 4.90: 52341 Nonbonded interactions: 134337 Sorted by model distance: nonbonded pdb=" OP1 C B 581 " pdb="MG MG B 701 " model vdw 1.982 2.170 nonbonded pdb=" O2' U B 638 " pdb="MG MG B 701 " model vdw 2.005 2.170 nonbonded pdb=" OP2 G B 136 " pdb="MG MG B 709 " model vdw 2.013 2.170 nonbonded pdb=" OP2 G B 578 " pdb="MG MG B 708 " model vdw 2.020 2.170 nonbonded pdb=" O3' U B 638 " pdb="MG MG B 701 " model vdw 2.036 2.170 ... (remaining 134332 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: 5.250 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: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0606 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 : 0.006 0.090 16327 Z= 0.315 Angle : 0.975 11.964 24756 Z= 0.481 Chirality : 0.047 0.408 3195 Planarity : 0.007 0.081 1089 Dihedral : 24.061 177.461 9138 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.46 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 24.93 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.39), residues: 381 helix: -0.91 (0.29), residues: 244 sheet: -0.56 (1.06), residues: 28 loop : -1.59 (0.54), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 25 TYR 0.045 0.004 TYR D 102 PHE 0.027 0.003 PHE D 89 TRP 0.012 0.003 TRP D 328 HIS 0.011 0.003 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.31 (16327) covalent geometry : angle 0.97458 / 0.48 (24756) hydrogen bonds : bond 0.16869 / 9.85 ( 599) hydrogen bonds : angle 7.10956 / 4.24 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6329 (mttp) cc_final: 0.5684 (mtpp) REVERT: D 37 TYR cc_start: 0.4045 (p90) cc_final: 0.3790 (p90) REVERT: D 241 VAL cc_start: 0.2833 (t) cc_final: 0.2266 (p) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.5898 time to fit residues: 49.2096 Evaluate side-chains 35 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 121 GLN D 364 GLN D 378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.148744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.135329 restraints weight = 55233.368| |-----------------------------------------------------------------------------| r_work (start): 0.4447 rms_B_bonded: 1.58 r_work: 0.4369 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2731 moved from start: 0.9058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 16327 Z= 0.451 Angle : 1.614 14.548 24756 Z= 0.780 Chirality : 0.076 0.600 3195 Planarity : 0.011 0.100 1089 Dihedral : 26.075 179.808 8333 Min Nonbonded Distance : 1.179 Molprobity Statistics. All-atom Clashscore : 46.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.09 % Favored : 92.65 % Rotamer: Outliers : 10.26 % Allowed : 26.69 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.37), residues: 381 helix: -1.34 (0.28), residues: 239 sheet: 0.65 (1.63), residues: 14 loop : -2.64 (0.46), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.003 ARG D 160 TYR 0.025 0.004 TYR D 350 PHE 0.026 0.005 PHE D 145 TRP 0.050 0.005 TRP D 328 HIS 0.010 0.003 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.45 (16327) covalent geometry : angle 1.61403 / 0.78 (24756) hydrogen bonds : bond 0.24890 / 15.08 ( 599) hydrogen bonds : angle 5.19124 / 2.90 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 42 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: -0.0195 (OUTLIER) cc_final: -0.0424 (tmt) REVERT: D 26 ASN cc_start: 0.6262 (m-40) cc_final: 0.6054 (t0) REVERT: D 27 LYS cc_start: 0.6214 (mttp) cc_final: 0.5721 (tttm) REVERT: D 106 PHE cc_start: 0.2950 (OUTLIER) cc_final: 0.2544 (m-80) REVERT: D 140 ILE cc_start: 0.2809 (OUTLIER) cc_final: 0.1518 (pp) REVERT: D 236 MET cc_start: 0.2832 (mtt) cc_final: 0.1442 (ptm) REVERT: D 354 MET cc_start: -0.0263 (ptt) cc_final: -0.0864 (ppp) REVERT: D 403 ILE cc_start: 0.4760 (OUTLIER) cc_final: 0.4183 (pt) REVERT: D 424 CYS cc_start: -0.0566 (OUTLIER) cc_final: -0.0898 (p) outliers start: 35 outliers final: 6 residues processed: 73 average time/residue: 0.3970 time to fit residues: 32.8853 Evaluate side-chains 45 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 395 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 403 ILE Chi-restraints excluded: chain D residue 424 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.147416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.133342 restraints weight = 55004.503| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 1.48 r_work: 0.4345 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2904 moved from start: 1.0343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 16327 Z= 0.254 Angle : 1.011 10.039 24756 Z= 0.502 Chirality : 0.053 0.400 3195 Planarity : 0.008 0.081 1089 Dihedral : 25.487 178.895 8333 Min Nonbonded Distance : 1.013 Molprobity Statistics. All-atom Clashscore : 25.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 8.80 % Allowed : 29.03 % Favored : 62.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.39), residues: 381 helix: -0.70 (0.30), residues: 245 sheet: -0.42 (1.16), residues: 29 loop : -2.60 (0.52), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 266 TYR 0.017 0.003 TYR D 419 PHE 0.019 0.004 PHE D 286 TRP 0.041 0.005 TRP D 328 HIS 0.012 0.002 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.25 (16327) covalent geometry : angle 1.01059 / 0.50 (24756) hydrogen bonds : bond 0.12871 / 7.75 ( 599) hydrogen bonds : angle 4.21740 / 2.32 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 40 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: 0.0425 (OUTLIER) cc_final: 0.0138 (tmt) REVERT: D 27 LYS cc_start: 0.6294 (mttp) cc_final: 0.5938 (tttm) REVERT: D 37 TYR cc_start: 0.4147 (p90) cc_final: 0.3642 (p90) REVERT: D 102 TYR cc_start: 0.2755 (OUTLIER) cc_final: 0.2063 (t80) REVERT: D 236 MET cc_start: 0.4789 (mtt) cc_final: 0.1020 (ptt) REVERT: D 253 LEU cc_start: 0.4055 (OUTLIER) cc_final: 0.3646 (tt) REVERT: D 310 TRP cc_start: 0.0429 (OUTLIER) cc_final: 0.0084 (m-10) REVERT: D 347 ARG cc_start: 0.3237 (OUTLIER) cc_final: 0.1736 (tpt170) REVERT: D 354 MET cc_start: -0.0760 (ptt) cc_final: -0.1193 (ppp) outliers start: 30 outliers final: 10 residues processed: 66 average time/residue: 0.4687 time to fit residues: 34.8063 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 395 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.150918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.137958 restraints weight = 55645.912| |-----------------------------------------------------------------------------| r_work (start): 0.4495 rms_B_bonded: 1.48 r_work: 0.4413 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3329 moved from start: 1.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 16327 Z= 0.262 Angle : 0.959 17.600 24756 Z= 0.480 Chirality : 0.049 0.372 3195 Planarity : 0.008 0.089 1089 Dihedral : 25.277 178.737 8333 Min Nonbonded Distance : 1.080 Molprobity Statistics. All-atom Clashscore : 25.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 8.80 % Allowed : 30.50 % Favored : 60.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.40), residues: 381 helix: -0.23 (0.31), residues: 245 sheet: -1.05 (1.31), residues: 14 loop : -2.75 (0.47), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 88 TYR 0.032 0.004 TYR D 420 PHE 0.064 0.006 PHE D 89 TRP 0.037 0.004 TRP D 328 HIS 0.007 0.002 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.26 (16327) covalent geometry : angle 0.95918 / 0.48 (24756) hydrogen bonds : bond 0.12414 / 7.46 ( 599) hydrogen bonds : angle 4.19202 / 2.30 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6720 (mttp) cc_final: 0.6200 (tttm) REVERT: D 89 PHE cc_start: 0.8121 (t80) cc_final: 0.7827 (t80) REVERT: D 101 ILE cc_start: 0.7029 (tp) cc_final: 0.6809 (tt) REVERT: D 130 MET cc_start: 0.4625 (OUTLIER) cc_final: 0.4180 (ptt) REVERT: D 236 MET cc_start: 0.3766 (mtt) cc_final: 0.0909 (ptt) REVERT: D 310 TRP cc_start: 0.0680 (OUTLIER) cc_final: -0.0194 (m-10) REVERT: D 347 ARG cc_start: 0.3232 (OUTLIER) cc_final: 0.2041 (tpp-160) REVERT: D 354 MET cc_start: -0.0165 (ptt) cc_final: -0.0681 (ppp) outliers start: 30 outliers final: 11 residues processed: 73 average time/residue: 0.4380 time to fit residues: 36.0893 Evaluate side-chains 54 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.152193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.138589 restraints weight = 58499.449| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 1.63 r_work: 0.4427 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4126 moved from start: 1.6427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 16327 Z= 0.267 Angle : 1.054 13.584 24756 Z= 0.527 Chirality : 0.054 0.407 3195 Planarity : 0.008 0.093 1089 Dihedral : 25.826 176.700 8333 Min Nonbonded Distance : 1.223 Molprobity Statistics. All-atom Clashscore : 28.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.25 % Favored : 94.49 % Rotamer: Outliers : 6.45 % Allowed : 33.43 % Favored : 60.12 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.40), residues: 381 helix: -0.33 (0.31), residues: 242 sheet: -1.79 (0.98), residues: 24 loop : -2.72 (0.52), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 266 TYR 0.044 0.004 TYR D 419 PHE 0.036 0.004 PHE D 275 TRP 0.038 0.005 TRP D 328 HIS 0.015 0.003 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.27 (16327) covalent geometry : angle 1.05396 / 0.53 (24756) hydrogen bonds : bond 0.14865 / 8.97 ( 599) hydrogen bonds : angle 4.53276 / 2.50 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.7182 (mttp) cc_final: 0.6647 (mtpp) REVERT: D 102 TYR cc_start: 0.3518 (OUTLIER) cc_final: 0.3230 (t80) REVERT: D 236 MET cc_start: 0.4260 (mtt) cc_final: 0.1437 (ptt) REVERT: D 302 MET cc_start: 0.4584 (OUTLIER) cc_final: 0.3874 (tmm) REVERT: D 310 TRP cc_start: 0.0834 (OUTLIER) cc_final: -0.0785 (m-10) REVERT: D 316 TYR cc_start: 0.6456 (t80) cc_final: 0.5719 (t80) REVERT: D 354 MET cc_start: 0.0690 (OUTLIER) cc_final: -0.0140 (ppp) outliers start: 22 outliers final: 9 residues processed: 67 average time/residue: 0.4674 time to fit residues: 35.3192 Evaluate side-chains 55 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 0.0970 chunk 29 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 overall best weight: 2.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.151334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.137456 restraints weight = 59477.008| |-----------------------------------------------------------------------------| r_work (start): 0.4499 rms_B_bonded: 1.76 r_work: 0.4415 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4957 moved from start: 2.0220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 16327 Z= 0.316 Angle : 1.151 13.726 24756 Z= 0.565 Chirality : 0.056 0.478 3195 Planarity : 0.008 0.102 1089 Dihedral : 26.022 178.333 8333 Min Nonbonded Distance : 1.227 Molprobity Statistics. All-atom Clashscore : 28.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.99 % Allowed : 38.12 % Favored : 56.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.41), residues: 381 helix: -0.36 (0.32), residues: 238 sheet: -1.14 (1.13), residues: 22 loop : -2.51 (0.53), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG D 223 TYR 0.022 0.004 TYR D 111 PHE 0.033 0.005 PHE D 277 TRP 0.024 0.004 TRP D 328 HIS 0.014 0.004 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.32 (16327) covalent geometry : angle 1.15078 / 0.56 (24756) hydrogen bonds : bond 0.16284 / 9.78 ( 599) hydrogen bonds : angle 4.53618 / 2.73 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 10 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.6021 (pp) REVERT: D 89 PHE cc_start: 0.8606 (t80) cc_final: 0.8253 (t80) REVERT: D 94 ILE cc_start: 0.8737 (tt) cc_final: 0.8463 (tp) REVERT: D 236 MET cc_start: 0.3376 (mtt) cc_final: 0.2089 (ptt) REVERT: D 354 MET cc_start: 0.1797 (OUTLIER) cc_final: 0.1138 (tmm) outliers start: 17 outliers final: 5 residues processed: 62 average time/residue: 0.4136 time to fit residues: 29.1713 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 342 LYS Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 413 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.143894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.127394 restraints weight = 56431.758| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 1.81 r_work: 0.4267 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6110 moved from start: 2.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.146 16327 Z= 0.426 Angle : 1.497 17.834 24756 Z= 0.720 Chirality : 0.069 0.479 3195 Planarity : 0.010 0.101 1089 Dihedral : 27.080 178.888 8333 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 41.44 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.40 % Favored : 91.08 % Rotamer: Outliers : 9.09 % Allowed : 34.31 % Favored : 56.60 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.40), residues: 381 helix: -1.30 (0.30), residues: 233 sheet: -1.24 (1.06), residues: 24 loop : -3.05 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG D 223 TYR 0.038 0.005 TYR D 419 PHE 0.038 0.007 PHE D 298 TRP 0.065 0.007 TRP D 328 HIS 0.014 0.004 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00812 / 0.43 (16327) covalent geometry : angle 1.49697 / 0.72 (24756) hydrogen bonds : bond 0.20311 / 12.25 ( 599) hydrogen bonds : angle 5.24485 / 2.94 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: D 7 MET cc_start: -0.0370 (OUTLIER) cc_final: -0.0618 (ttt) REVERT: D 10 ILE cc_start: 0.6178 (OUTLIER) cc_final: 0.5843 (pp) REVERT: D 157 LEU cc_start: 0.7877 (mt) cc_final: 0.7665 (pp) REVERT: D 235 GLU cc_start: 0.7144 (tp30) cc_final: 0.6731 (tp30) REVERT: D 236 MET cc_start: 0.4548 (mtt) cc_final: 0.2999 (ptt) REVERT: D 354 MET cc_start: 0.3120 (OUTLIER) cc_final: 0.2089 (tmt) outliers start: 31 outliers final: 9 residues processed: 81 average time/residue: 0.4807 time to fit residues: 43.8344 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.144144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.127301 restraints weight = 54687.325| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 1.81 r_work: 0.4267 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 2.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16327 Z= 0.253 Angle : 0.990 16.909 24756 Z= 0.485 Chirality : 0.049 0.429 3195 Planarity : 0.007 0.106 1089 Dihedral : 26.070 168.267 8333 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.69 % Allowed : 42.52 % Favored : 52.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.39), residues: 381 helix: -0.72 (0.30), residues: 238 sheet: -2.49 (1.54), residues: 10 loop : -2.45 (0.53), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG D 88 TYR 0.026 0.004 TYR D 385 PHE 0.048 0.003 PHE D 298 TRP 0.058 0.005 TRP D 328 HIS 0.011 0.002 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.25 (16327) covalent geometry : angle 0.99028 / 0.49 (24756) hydrogen bonds : bond 0.12862 / 7.55 ( 599) hydrogen bonds : angle 4.44945 / 2.50 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 35 MET cc_start: -0.0533 (OUTLIER) cc_final: -0.0995 (pmt) REVERT: D 89 PHE cc_start: 0.8338 (t80) cc_final: 0.8052 (t80) REVERT: D 160 ARG cc_start: 0.4480 (tmm-80) cc_final: 0.4041 (ptm-80) REVERT: D 213 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6311 (tp30) REVERT: D 235 GLU cc_start: 0.7027 (tp30) cc_final: 0.6518 (tp30) REVERT: D 236 MET cc_start: 0.4159 (mtt) cc_final: 0.3511 (ptt) REVERT: D 245 ILE cc_start: 0.6812 (mm) cc_final: 0.6583 (mm) REVERT: D 354 MET cc_start: 0.4443 (ptt) cc_final: 0.3999 (mtt) outliers start: 16 outliers final: 6 residues processed: 57 average time/residue: 0.4044 time to fit residues: 26.4488 Evaluate side-chains 41 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.132802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.112929 restraints weight = 52941.726| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.89 r_work: 0.4037 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 2.8639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 16327 Z= 0.444 Angle : 1.356 13.379 24756 Z= 0.657 Chirality : 0.066 0.457 3195 Planarity : 0.009 0.109 1089 Dihedral : 26.622 172.361 8333 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 35.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.14 % Favored : 91.60 % Rotamer: Outliers : 6.45 % Allowed : 43.11 % Favored : 50.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.41), residues: 381 helix: -1.06 (0.31), residues: 235 sheet: 0.06 (1.53), residues: 14 loop : -2.57 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG D 282 TYR 0.032 0.004 TYR D 392 PHE 0.020 0.004 PHE D 286 TRP 0.075 0.006 TRP D 328 HIS 0.007 0.002 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00843 / 0.44 (16327) covalent geometry : angle 1.35592 / 0.66 (24756) hydrogen bonds : bond 0.18206 / 11.02 ( 599) hydrogen bonds : angle 5.02300 / 2.88 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 41 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: D 89 PHE cc_start: 0.8321 (t80) cc_final: 0.8023 (t80) REVERT: D 236 MET cc_start: 0.5051 (mtt) cc_final: 0.3816 (ppp) REVERT: D 259 MET cc_start: 0.4204 (tpt) cc_final: 0.3874 (tpp) REVERT: D 280 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6549 (t0) REVERT: D 388 LYS cc_start: 0.5508 (mptt) cc_final: 0.5088 (mmtp) outliers start: 22 outliers final: 10 residues processed: 57 average time/residue: 0.4391 time to fit residues: 28.4032 Evaluate side-chains 45 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 34 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 280 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.135616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.116102 restraints weight = 51975.600| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 1.68 r_work: 0.4092 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 2.9003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 16327 Z= 0.237 Angle : 0.934 12.824 24756 Z= 0.457 Chirality : 0.047 0.494 3195 Planarity : 0.006 0.096 1089 Dihedral : 25.841 170.185 8333 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.25 % Favored : 94.49 % Rotamer: Outliers : 3.52 % Allowed : 48.09 % Favored : 48.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.41), residues: 381 helix: -0.68 (0.32), residues: 236 sheet: -0.06 (1.12), residues: 24 loop : -2.74 (0.54), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 347 TYR 0.033 0.003 TYR D 392 PHE 0.020 0.002 PHE D 277 TRP 0.065 0.006 TRP D 328 HIS 0.006 0.002 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.24 (16327) covalent geometry : angle 0.93370 / 0.46 (24756) hydrogen bonds : bond 0.11667 / 6.89 ( 599) hydrogen bonds : angle 4.20123 / 2.42 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 762 Ramachandran restraints generated. 381 Oldfield, 0 Emsley, 381 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 ILE cc_start: 0.7064 (tt) cc_final: 0.6837 (mt) REVERT: D 89 PHE cc_start: 0.8444 (t80) cc_final: 0.8180 (t80) REVERT: D 236 MET cc_start: 0.4377 (mtt) cc_final: 0.3743 (ppp) REVERT: D 388 LYS cc_start: 0.5754 (mptt) cc_final: 0.5543 (tptt) outliers start: 12 outliers final: 6 residues processed: 53 average time/residue: 0.4894 time to fit residues: 28.9521 Evaluate side-chains 39 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 257 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 53 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 5 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 17 ASN ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.127690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.107216 restraints weight = 51083.678| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.70 r_work: 0.3942 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 3.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 16327 Z= 0.362 Angle : 1.160 12.420 24756 Z= 0.563 Chirality : 0.055 0.442 3195 Planarity : 0.008 0.108 1089 Dihedral : 26.276 178.569 8333 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 31.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.87 % Favored : 91.86 % Rotamer: Outliers : 3.81 % Allowed : 46.63 % Favored : 49.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.40), residues: 381 helix: -1.08 (0.32), residues: 238 sheet: -0.30 (1.03), residues: 24 loop : -2.94 (0.53), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.002 ARG D 347 TYR 0.041 0.004 TYR D 392 PHE 0.040 0.004 PHE D 298 TRP 0.136 0.011 TRP D 328 HIS 0.004 0.002 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.36 (16327) covalent geometry : angle 1.16021 / 0.56 (24756) hydrogen bonds : bond 0.14348 / 8.49 ( 599) hydrogen bonds : angle 4.60812 / 2.61 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4154.84 seconds wall clock time: 72 minutes 0.39 seconds (4320.39 seconds total)