Starting phenix.real_space_refine on Thu Sep 18 06:39:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2t_40987/09_2025/8t2t_40987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2t_40987/09_2025/8t2t_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t2t_40987/09_2025/8t2t_40987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2t_40987/09_2025/8t2t_40987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t2t_40987/09_2025/8t2t_40987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2t_40987/09_2025/8t2t_40987.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-2.0-5805/lib/python3.9/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: 3.90, per 1000 atoms: 0.26 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: 1.18 Conformation dependent library (CDL) restraints added in 353.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.49 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: 3.75 Time building geometry restraints manager: 1.68 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: 8873 35.49 - 70.98: 1308 70.98 - 106.48: 143 106.48 - 141.97: 4 141.97 - 177.46: 10 Dihedral angle restraints: 10338 sinusoidal: 9214 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 10335 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: 5.330 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.630 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0531 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 : 24.844 177.461 9614 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 aren 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 covalent geometry : bond 0.00588 (16327) covalent geometry : angle 0.97458 (24756) hydrogen bonds : bond 0.16869 ( 599) hydrogen bonds : angle 7.10956 ( 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 : 0.256 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: 0.6976 time to fit residues: 57.8582 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 : 0.263 ------------------------------------------------------------------------------- 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: 4.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 121 GLN D 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.147734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.134030 restraints weight = 54633.867| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 1.68 r_work: 0.4352 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2643 moved from start: 0.8822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 16327 Z= 0.500 Angle : 1.612 14.080 24756 Z= 0.779 Chirality : 0.077 0.578 3195 Planarity : 0.011 0.096 1089 Dihedral : 26.685 179.467 8809 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 43.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.56 % Favored : 93.18 % Rotamer: Outliers : 10.85 % Allowed : 25.81 % Favored : 63.34 % 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 aren not related in a simple way. whole: -2.69 (0.36), residues: 381 helix: -1.39 (0.28), residues: 239 sheet: 0.52 (1.63), residues: 14 loop : -2.61 (0.46), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG D 160 TYR 0.025 0.004 TYR D 420 PHE 0.025 0.006 PHE D 277 TRP 0.053 0.006 TRP D 328 HIS 0.010 0.003 HIS D 107 Details of bonding type rmsd covalent geometry : bond 0.00895 (16327) covalent geometry : angle 1.61233 (24756) hydrogen bonds : bond 0.24383 ( 599) hydrogen bonds : angle 5.15003 ( 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 81 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 44 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: -0.0115 (OUTLIER) cc_final: -0.0403 (tmt) REVERT: D 26 ASN cc_start: 0.6268 (m-40) cc_final: 0.6060 (t0) REVERT: D 27 LYS cc_start: 0.6225 (mttp) cc_final: 0.5715 (tttm) REVERT: D 106 PHE cc_start: 0.2825 (OUTLIER) cc_final: 0.2465 (m-80) REVERT: D 140 ILE cc_start: 0.2792 (OUTLIER) cc_final: 0.1552 (pp) REVERT: D 236 MET cc_start: 0.2728 (mtt) cc_final: 0.1560 (ptm) REVERT: D 354 MET cc_start: -0.0304 (ptt) cc_final: -0.0788 (ppp) REVERT: D 403 ILE cc_start: 0.4793 (OUTLIER) cc_final: 0.4230 (pt) REVERT: D 424 CYS cc_start: -0.0742 (OUTLIER) cc_final: -0.1041 (p) outliers start: 37 outliers final: 8 residues processed: 77 average time/residue: 0.4721 time to fit residues: 41.2734 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 166 ASP Chi-restraints excluded: chain D residue 263 LYS 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: 9.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.147026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.132578 restraints weight = 54736.667| |-----------------------------------------------------------------------------| r_work (start): 0.4418 rms_B_bonded: 1.46 r_work: 0.4337 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2787 moved from start: 1.0148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 16327 Z= 0.252 Angle : 0.979 9.772 24756 Z= 0.489 Chirality : 0.052 0.390 3195 Planarity : 0.008 0.082 1089 Dihedral : 26.218 178.704 8809 Min Nonbonded Distance : 0.937 Molprobity Statistics. All-atom Clashscore : 24.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 8.50 % Allowed : 28.74 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.39), residues: 381 helix: -0.80 (0.29), residues: 251 sheet: 0.45 (1.70), residues: 14 loop : -2.63 (0.50), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 58 TYR 0.020 0.003 TYR D 419 PHE 0.030 0.004 PHE D 275 TRP 0.044 0.004 TRP D 328 HIS 0.009 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00477 (16327) covalent geometry : angle 0.97867 (24756) hydrogen bonds : bond 0.12380 ( 599) hydrogen bonds : angle 4.08990 ( 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 74 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 45 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6352 (mttp) cc_final: 0.5996 (tttm) REVERT: D 37 TYR cc_start: 0.4010 (p90) cc_final: 0.3462 (p90) REVERT: D 102 TYR cc_start: 0.2901 (OUTLIER) cc_final: 0.2188 (t80) REVERT: D 236 MET cc_start: 0.4701 (mtt) cc_final: 0.1354 (ptt) REVERT: D 253 LEU cc_start: 0.3978 (OUTLIER) cc_final: 0.3469 (tt) REVERT: D 259 MET cc_start: 0.2640 (OUTLIER) cc_final: 0.2145 (tpt) REVERT: D 284 HIS cc_start: 0.5316 (t-90) cc_final: 0.5063 (t-90) REVERT: D 310 TRP cc_start: 0.0463 (OUTLIER) cc_final: 0.0111 (m-10) REVERT: D 347 ARG cc_start: 0.3137 (OUTLIER) cc_final: 0.1661 (tpt170) REVERT: D 354 MET cc_start: -0.0440 (ptt) cc_final: -0.0961 (ppp) outliers start: 29 outliers final: 9 residues processed: 68 average time/residue: 0.5485 time to fit residues: 41.5287 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU 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 202 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 259 MET 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 395 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.152581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.139664 restraints weight = 58723.748| |-----------------------------------------------------------------------------| r_work (start): 0.4524 rms_B_bonded: 1.52 r_work: 0.4444 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3595 moved from start: 1.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.196 16327 Z= 0.306 Angle : 1.123 13.436 24756 Z= 0.560 Chirality : 0.055 0.382 3195 Planarity : 0.009 0.111 1089 Dihedral : 26.359 177.702 8809 Min Nonbonded Distance : 0.894 Molprobity Statistics. All-atom Clashscore : 32.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 10.26 % Allowed : 30.50 % Favored : 59.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.39), residues: 381 helix: -0.57 (0.30), residues: 246 sheet: -0.76 (1.45), residues: 14 loop : -2.68 (0.50), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG D 266 TYR 0.043 0.005 TYR D 420 PHE 0.060 0.007 PHE D 89 TRP 0.045 0.004 TRP D 328 HIS 0.005 0.002 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00588 (16327) covalent geometry : angle 1.12332 (24756) hydrogen bonds : bond 0.16413 ( 599) hydrogen bonds : angle 4.40237 ( 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 85 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 50 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6797 (mttp) cc_final: 0.6275 (tttm) REVERT: D 102 TYR cc_start: 0.3112 (OUTLIER) cc_final: 0.2539 (t80) REVERT: D 130 MET cc_start: 0.5278 (ptt) cc_final: 0.4767 (ptt) REVERT: D 236 MET cc_start: 0.4289 (mtt) cc_final: 0.1717 (ptt) REVERT: D 259 MET cc_start: 0.2233 (tpt) cc_final: 0.1860 (tpt) REVERT: D 310 TRP cc_start: 0.0945 (OUTLIER) cc_final: -0.0334 (m-10) REVERT: D 347 ARG cc_start: 0.3198 (OUTLIER) cc_final: 0.1516 (tpt170) REVERT: D 354 MET cc_start: 0.0642 (OUTLIER) cc_final: -0.0110 (ttp) outliers start: 35 outliers final: 9 residues processed: 77 average time/residue: 0.5500 time to fit residues: 47.1763 Evaluate side-chains 53 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 153 LYS Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 248 PHE 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 354 MET 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: 5.9990 chunk 69 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN ** D 395 ASN ** 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 = 0.4683 r_free = 0.4683 target = 0.151058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.137586 restraints weight = 57950.765| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 1.61 r_work: 0.4417 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4540 moved from start: 1.8063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 16327 Z= 0.335 Angle : 1.249 15.306 24756 Z= 0.615 Chirality : 0.063 0.736 3195 Planarity : 0.009 0.101 1089 Dihedral : 27.035 176.475 8809 Min Nonbonded Distance : 0.963 Molprobity Statistics. All-atom Clashscore : 33.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 7.33 % Allowed : 35.19 % Favored : 57.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.38), residues: 381 helix: -0.83 (0.29), residues: 238 sheet: -1.11 (1.67), residues: 10 loop : -2.59 (0.51), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 217 TYR 0.055 0.004 TYR D 419 PHE 0.030 0.005 PHE D 89 TRP 0.042 0.006 TRP D 328 HIS 0.027 0.004 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00631 (16327) covalent geometry : angle 1.24949 (24756) hydrogen bonds : bond 0.17663 ( 599) hydrogen bonds : angle 4.70465 ( 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 77 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 PHE cc_start: 0.8340 (t80) cc_final: 0.8065 (t80) REVERT: D 90 ILE cc_start: 0.6756 (pt) cc_final: 0.6478 (pp) REVERT: D 236 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.2270 (ptt) REVERT: D 302 MET cc_start: 0.4871 (OUTLIER) cc_final: 0.4645 (tmm) REVERT: D 328 TRP cc_start: 0.5292 (t60) cc_final: 0.4864 (t-100) REVERT: D 354 MET cc_start: 0.0906 (ptt) cc_final: -0.0430 (ppp) outliers start: 25 outliers final: 11 residues processed: 69 average time/residue: 0.4761 time to fit residues: 37.2584 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 : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 370 LEU 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: 0.9980 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.152377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.138488 restraints weight = 60776.857| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 1.69 r_work: 0.4433 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4559 moved from start: 1.9192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16327 Z= 0.209 Angle : 0.916 16.693 24756 Z= 0.452 Chirality : 0.046 0.408 3195 Planarity : 0.007 0.101 1089 Dihedral : 26.337 176.729 8809 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.25 % Favored : 94.49 % Rotamer: Outliers : 5.87 % Allowed : 37.24 % 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 aren not related in a simple way. whole: -1.36 (0.40), residues: 381 helix: -0.14 (0.31), residues: 239 sheet: -0.93 (1.67), residues: 10 loop : -2.24 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 223 TYR 0.021 0.003 TYR D 385 PHE 0.028 0.004 PHE D 248 TRP 0.019 0.002 TRP D 328 HIS 0.006 0.002 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00400 (16327) covalent geometry : angle 0.91621 (24756) hydrogen bonds : bond 0.12318 ( 599) hydrogen bonds : angle 4.04506 ( 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: 20 poor density : 49 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 PHE cc_start: 0.8563 (t80) cc_final: 0.8121 (t80) REVERT: D 236 MET cc_start: 0.4410 (OUTLIER) cc_final: 0.2964 (ptt) REVERT: D 347 ARG cc_start: 0.4057 (OUTLIER) cc_final: 0.2732 (tpt170) REVERT: D 354 MET cc_start: 0.1468 (OUTLIER) cc_final: 0.0434 (ppp) outliers start: 20 outliers final: 8 residues processed: 63 average time/residue: 0.4976 time to fit residues: 35.3548 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 415 SER Chi-restraints excluded: chain D residue 418 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.145419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.130075 restraints weight = 55953.567| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 1.74 r_work: 0.4307 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 2.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.111 16327 Z= 0.379 Angle : 1.327 13.589 24756 Z= 0.648 Chirality : 0.064 0.503 3195 Planarity : 0.008 0.108 1089 Dihedral : 27.228 179.196 8809 Min Nonbonded Distance : 0.945 Molprobity Statistics. All-atom Clashscore : 37.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 8.80 % Allowed : 34.31 % 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 aren not related in a simple way. whole: -2.46 (0.39), residues: 381 helix: -0.99 (0.30), residues: 235 sheet: -1.38 (1.00), residues: 24 loop : -2.78 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG D 223 TYR 0.040 0.005 TYR D 272 PHE 0.038 0.006 PHE D 221 TRP 0.062 0.007 TRP D 328 HIS 0.007 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00737 (16327) covalent geometry : angle 1.32676 (24756) hydrogen bonds : bond 0.18143 ( 599) hydrogen bonds : angle 4.96788 ( 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 87 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: D 41 LYS cc_start: 0.3855 (OUTLIER) cc_final: 0.3043 (tmtm) REVERT: D 89 PHE cc_start: 0.8537 (t80) cc_final: 0.8160 (t80) REVERT: D 102 TYR cc_start: 0.4290 (OUTLIER) cc_final: 0.3948 (t80) REVERT: D 157 LEU cc_start: 0.7847 (mt) cc_final: 0.7630 (pp) REVERT: D 235 GLU cc_start: 0.6826 (tp30) cc_final: 0.6400 (tp30) REVERT: D 236 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.2930 (ptt) REVERT: D 354 MET cc_start: 0.2596 (OUTLIER) cc_final: 0.1342 (ppp) outliers start: 30 outliers final: 9 residues processed: 74 average time/residue: 0.5143 time to fit residues: 42.8204 Evaluate side-chains 49 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 GLN Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 85 VAL 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 232 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 354 MET 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: 4.9990 chunk 19 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 0.0770 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** 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 = 0.4543 r_free = 0.4543 target = 0.139637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.121624 restraints weight = 55638.641| |-----------------------------------------------------------------------------| r_work (start): 0.4287 rms_B_bonded: 1.93 r_work: 0.4192 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 2.6642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 16327 Z= 0.376 Angle : 1.259 15.620 24756 Z= 0.610 Chirality : 0.059 0.520 3195 Planarity : 0.008 0.101 1089 Dihedral : 27.009 167.898 8809 Min Nonbonded Distance : 0.904 Molprobity Statistics. All-atom Clashscore : 30.64 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.77 % Favored : 93.70 % Rotamer: Outliers : 6.45 % Allowed : 38.12 % Favored : 55.43 % 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 aren not related in a simple way. whole: -2.59 (0.40), residues: 381 helix: -1.17 (0.30), residues: 234 sheet: -1.12 (1.14), residues: 24 loop : -2.70 (0.54), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG D 282 TYR 0.030 0.005 TYR D 102 PHE 0.043 0.006 PHE D 298 TRP 0.020 0.004 TRP D 328 HIS 0.037 0.008 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00714 (16327) covalent geometry : angle 1.25861 (24756) hydrogen bonds : bond 0.16600 ( 599) hydrogen bonds : angle 4.74887 ( 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 74 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: D 89 PHE cc_start: 0.8558 (t80) cc_final: 0.8233 (t80) REVERT: D 236 MET cc_start: 0.4874 (OUTLIER) cc_final: 0.4115 (ptt) REVERT: D 245 ILE cc_start: 0.7234 (mm) cc_final: 0.7001 (mm) REVERT: D 388 LYS cc_start: 0.3887 (mptt) cc_final: 0.3204 (mmtt) REVERT: D 389 ARG cc_start: 0.5928 (mtp180) cc_final: 0.5635 (mtp180) outliers start: 22 outliers final: 4 residues processed: 67 average time/residue: 0.6454 time to fit residues: 47.4117 Evaluate side-chains 40 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 257 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.133421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.113563 restraints weight = 53573.017| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 1.87 r_work: 0.4053 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 2.8625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 16327 Z= 0.383 Angle : 1.221 12.734 24756 Z= 0.596 Chirality : 0.060 0.489 3195 Planarity : 0.008 0.121 1089 Dihedral : 26.956 172.419 8809 Min Nonbonded Distance : 0.852 Molprobity Statistics. All-atom Clashscore : 32.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 4.69 % Allowed : 42.23 % Favored : 53.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.94 (0.39), residues: 381 helix: -1.56 (0.29), residues: 245 sheet: -0.14 (1.27), residues: 24 loop : -2.93 (0.53), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG D 349 TYR 0.036 0.006 TYR D 102 PHE 0.053 0.006 PHE D 298 TRP 0.031 0.006 TRP D 328 HIS 0.009 0.003 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00726 (16327) covalent geometry : angle 1.22069 (24756) hydrogen bonds : bond 0.16040 ( 599) hydrogen bonds : angle 4.82281 ( 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 64 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.249 Fit side-chains REVERT: D 35 MET cc_start: 0.0772 (OUTLIER) cc_final: 0.0006 (pp-130) REVERT: D 89 PHE cc_start: 0.8603 (t80) cc_final: 0.8314 (t80) REVERT: D 213 GLU cc_start: 0.8017 (tp30) cc_final: 0.7782 (tp30) REVERT: D 236 MET cc_start: 0.4892 (OUTLIER) cc_final: 0.3928 (ptt) REVERT: D 388 LYS cc_start: 0.5272 (mptt) cc_final: 0.4727 (mmtp) REVERT: D 389 ARG cc_start: 0.6163 (mtp180) cc_final: 0.5934 (mtp180) outliers start: 16 outliers final: 5 residues processed: 57 average time/residue: 0.4936 time to fit residues: 31.8847 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 : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 373 LEU 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: 6.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 0.0770 chunk 17 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 43 HIS ** D 366 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 = 0.4423 r_free = 0.4423 target = 0.130566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.110087 restraints weight = 51123.235| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.78 r_work: 0.3994 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 3.0088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 16327 Z= 0.337 Angle : 1.112 12.448 24756 Z= 0.538 Chirality : 0.054 0.453 3195 Planarity : 0.007 0.099 1089 Dihedral : 26.804 168.757 8809 Min Nonbonded Distance : 0.894 Molprobity Statistics. All-atom Clashscore : 27.31 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.30 % Favored : 93.18 % Rotamer: Outliers : 3.52 % Allowed : 44.87 % Favored : 51.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.40), residues: 381 helix: -1.00 (0.29), residues: 244 sheet: 0.17 (1.25), residues: 24 loop : -2.57 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG D 353 TYR 0.045 0.005 TYR D 350 PHE 0.018 0.004 PHE D 106 TRP 0.026 0.005 TRP D 357 HIS 0.009 0.003 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00633 (16327) covalent geometry : angle 1.11156 (24756) hydrogen bonds : bond 0.13713 ( 599) hydrogen bonds : angle 4.59136 ( 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 56 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: 0.1374 (tmt) cc_final: 0.0839 (ttt) REVERT: D 35 MET cc_start: 0.0646 (OUTLIER) cc_final: -0.0120 (pp-130) REVERT: D 42 GLU cc_start: 0.6854 (mm-30) cc_final: 0.6430 (mp0) REVERT: D 89 PHE cc_start: 0.8416 (t80) cc_final: 0.8152 (t80) REVERT: D 236 MET cc_start: 0.5012 (OUTLIER) cc_final: 0.4122 (ptt) REVERT: D 345 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7365 (t70) REVERT: D 381 ARG cc_start: 0.6556 (ttp80) cc_final: 0.5952 (ptt180) REVERT: D 382 ARG cc_start: 0.6646 (ttt180) cc_final: 0.6388 (ppt-90) outliers start: 12 outliers final: 3 residues processed: 51 average time/residue: 0.5991 time to fit residues: 33.7470 Evaluate side-chains 44 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 345 ASP 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: 4.9990 chunk 5 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS D 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.128982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.108456 restraints weight = 51235.974| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.78 r_work: 0.3972 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 3.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16327 Z= 0.283 Angle : 0.981 11.847 24756 Z= 0.480 Chirality : 0.049 0.450 3195 Planarity : 0.007 0.111 1089 Dihedral : 26.549 166.710 8809 Min Nonbonded Distance : 0.968 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.11 % Allowed : 45.75 % Favored : 50.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.41), residues: 381 helix: -0.59 (0.31), residues: 237 sheet: 0.33 (1.27), residues: 24 loop : -2.52 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 389 TYR 0.028 0.004 TYR D 316 PHE 0.016 0.003 PHE D 89 TRP 0.017 0.004 TRP D 360 HIS 0.005 0.002 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00533 (16327) covalent geometry : angle 0.98147 (24756) hydrogen bonds : bond 0.12159 ( 599) hydrogen bonds : angle 4.45991 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5059.29 seconds wall clock time: 87 minutes 23.18 seconds (5243.18 seconds total)