Starting phenix.real_space_refine on Thu Aug 6 10:13:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t2t_40987/08_2026/8t2t_40987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2t_40987/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t2t_40987/08_2026/8t2t_40987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2t_40987/08_2026/8t2t_40987.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8t2t_40987/08_2026/8t2t_40987.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t2t_40987/08_2026/8t2t_40987.cif" model { file = "/net/cci-nas-00/data/ceres_data/8t2t_40987/08_2026/8t2t_40987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2t_40987/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: {'RNAv2': 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: {'RNAv2': 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: 2.48, per 1000 atoms: 0.17 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: 0.91 Conformation dependent library (CDL) restraints added in 258.7 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: 2.08 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: 3.43 Time building geometry restraints manager: 1.35 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 1.415 1.454 -0.039 2.00e-02 2.50e+03 3.74e+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=" C3' A B 67 " pdb=" O3' A B 67 " ideal model delta sigma weight residual 1.415 1.447 -0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 16322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 23052 2.39 - 4.79: 1507 4.79 - 7.18: 166 7.18 - 9.57: 27 9.57 - 11.96: 4 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 119.70 128.70 -9.00 1.20e+00 6.94e-01 5.63e+01 angle pdb=" C3' U B 89 " pdb=" O3' U B 89 " pdb=" P A B 90 " ideal model delta sigma weight residual 119.70 127.41 -7.71 1.20e+00 6.94e-01 4.13e+01 angle pdb=" C3' A B 67 " pdb=" O3' A B 67 " pdb=" P U B 68 " ideal model delta sigma weight residual 119.70 126.81 -7.11 1.20e+00 6.94e-01 3.51e+01 angle pdb=" C3' U B 302 " pdb=" O3' U B 302 " pdb=" P A B 303 " ideal model delta sigma weight residual 119.70 126.76 -7.06 1.20e+00 6.94e-01 3.46e+01 angle pdb=" C3' G B 52 " pdb=" O3' G B 52 " pdb=" P G B 53 " ideal model delta sigma weight residual 119.70 126.41 -6.71 1.20e+00 6.94e-01 3.13e+01 ... (remaining 24751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 8015 35.49 - 70.98: 1688 70.98 - 106.48: 148 106.48 - 141.97: 2 141.97 - 177.46: 9 Dihedral angle restraints: 9862 sinusoidal: 8738 harmonic: 1124 Sorted by residual: dihedral pdb=" C4' A B 426 " pdb=" C3' A B 426 " pdb=" C2' A B 426 " pdb=" C1' A B 426 " ideal model delta sinusoidal sigma weight residual 36.34 -41.51 77.86 1 3.10e+00 1.04e-01 7.89e+02 dihedral pdb=" C4' C B 440 " pdb=" C3' C B 440 " pdb=" C2' C B 440 " pdb=" C1' C B 440 " ideal model delta sinusoidal sigma weight residual 36.34 -40.19 76.53 1 3.10e+00 1.04e-01 7.66e+02 dihedral pdb=" C4' A B 438 " pdb=" C3' A B 438 " pdb=" C2' A B 438 " pdb=" C1' A B 438 " ideal model delta sinusoidal sigma weight residual 36.34 -39.05 75.39 1 3.10e+00 1.04e-01 7.47e+02 ... (remaining 9859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2354 0.081 - 0.162: 196 0.162 - 0.243: 480 0.243 - 0.325: 146 0.325 - 0.406: 19 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 4.12e+00 chirality pdb=" P G B 53 " pdb=" OP1 G B 53 " pdb=" OP2 G B 53 " pdb=" O5' G B 53 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C2' A B 426 " pdb=" C3' A B 426 " pdb=" O2' A B 426 " pdb=" C1' A B 426 " both_signs ideal model delta sigma weight residual False -2.79 -2.39 -0.40 2.00e-01 2.50e+01 3.92e+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: 5.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.000 Find NCS groups from input model: 0.030 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:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.360 ------------------------------------------------------------------------------- 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 : 1.210 11.964 24756 Z= 0.509 Chirality : 0.112 0.406 3195 Planarity : 0.007 0.081 1089 Dihedral : 27.075 177.461 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 0.00629 / 0.32 (16327) covalent geometry : angle 1.21040 / 0.51 (24756) hydrogen bonds : bond 0.16869 / 8.71 ( 599) hydrogen bonds : angle 7.10956 / 2.64 ( 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 : 0.244 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: 0.5692 time to fit residues: 47.5519 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 : 0.184 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN D 107 HIS D 121 GLN D 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.146888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.132519 restraints weight = 53000.173| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 1.57 r_work: 0.4321 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2572 moved from start: 0.7945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.079 16327 Z= 0.487 Angle : 2.181 26.064 24756 Z= 0.848 Chirality : 0.141 1.715 3195 Planarity : 0.010 0.095 1089 Dihedral : 26.437 176.382 8333 Min Nonbonded Distance : 0.667 Molprobity Statistics. All-atom Clashscore : 40.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.99 % Favored : 94.75 % Rotamer: Outliers : 7.62 % Allowed : 26.98 % Favored : 65.40 % 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: -1.99 (0.38), residues: 381 helix: -0.88 (0.30), residues: 239 sheet: -0.14 (1.12), residues: 24 loop : -2.27 (0.49), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG D 160 TYR 0.026 0.004 TYR D 385 PHE 0.025 0.006 PHE D 145 TRP 0.042 0.005 TRP D 328 HIS 0.012 0.003 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00971 / 0.49 (16327) covalent geometry : angle 2.18059 / 0.85 (24756) hydrogen bonds : bond 0.21774 / 11.11 ( 599) hydrogen bonds : angle 4.84311 / 1.83 ( 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 69 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: -0.0540 (OUTLIER) cc_final: -0.0957 (tmt) REVERT: D 27 LYS cc_start: 0.6288 (mttp) cc_final: 0.5739 (tttm) REVERT: D 236 MET cc_start: 0.3601 (mtt) cc_final: 0.2375 (ptt) REVERT: D 285 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6264 (mm110) outliers start: 26 outliers final: 6 residues processed: 65 average time/residue: 0.4096 time to fit residues: 29.9985 Evaluate side-chains 39 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 174 TYR Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 310 TRP 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 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: 0.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** 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 = 0.4578 r_free = 0.4578 target = 0.145198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.130703 restraints weight = 52704.554| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 1.47 r_work: 0.4300 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2344 moved from start: 0.8639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16327 Z= 0.236 Angle : 1.336 17.985 24756 Z= 0.530 Chirality : 0.103 1.096 3195 Planarity : 0.007 0.086 1089 Dihedral : 25.761 176.276 8333 Min Nonbonded Distance : 0.977 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.72 % Favored : 95.01 % Rotamer: Outliers : 7.33 % Allowed : 29.33 % 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 are not related in a simple way. whole: -1.18 (0.39), residues: 381 helix: -0.06 (0.30), residues: 240 sheet: 0.44 (1.30), residues: 24 loop : -2.48 (0.49), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 88 TYR 0.011 0.002 TYR D 272 PHE 0.028 0.004 PHE D 411 TRP 0.034 0.002 TRP D 328 HIS 0.004 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.24 (16327) covalent geometry : angle 1.33648 / 0.53 (24756) hydrogen bonds : bond 0.10361 / 5.37 ( 599) hydrogen bonds : angle 3.75032 / 1.43 ( 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 62 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 37 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6696 (mttp) cc_final: 0.6125 (tttm) REVERT: D 89 PHE cc_start: 0.7821 (t80) cc_final: 0.7593 (t80) REVERT: D 102 TYR cc_start: 0.2537 (OUTLIER) cc_final: 0.1864 (t80) REVERT: D 236 MET cc_start: 0.3350 (mtt) cc_final: 0.2342 (ptm) REVERT: D 253 LEU cc_start: 0.2507 (OUTLIER) cc_final: 0.2171 (tt) REVERT: D 259 MET cc_start: 0.2905 (tpt) cc_final: 0.2585 (tpt) REVERT: D 347 ARG cc_start: 0.3088 (OUTLIER) cc_final: 0.1841 (mmt90) outliers start: 25 outliers final: 8 residues processed: 57 average time/residue: 0.3771 time to fit residues: 24.6212 Evaluate side-chains 41 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 395 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 8 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 0.0370 chunk 70 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 7 optimal weight: 5.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 15 ASN D 22 GLN D 43 HIS ** D 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.150358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.137039 restraints weight = 55585.375| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 1.44 r_work: 0.4393 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2656 moved from start: 1.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16327 Z= 0.219 Angle : 1.292 15.873 24756 Z= 0.512 Chirality : 0.094 0.717 3195 Planarity : 0.007 0.088 1089 Dihedral : 25.436 174.472 8333 Min Nonbonded Distance : 1.143 Molprobity Statistics. All-atom Clashscore : 20.47 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 : 0.00 % 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: -1.02 (0.40), residues: 381 helix: 0.19 (0.32), residues: 238 sheet: 0.29 (1.49), residues: 14 loop : -2.41 (0.48), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 301 TYR 0.012 0.002 TYR D 224 PHE 0.021 0.003 PHE D 248 TRP 0.036 0.003 TRP D 328 HIS 0.003 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (16327) covalent geometry : angle 1.29227 / 0.51 (24756) hydrogen bonds : bond 0.11084 / 5.77 ( 599) hydrogen bonds : angle 3.70168 / 1.40 ( 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 74 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 44 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 27 LYS cc_start: 0.6723 (mttp) cc_final: 0.6153 (tttm) REVERT: D 35 MET cc_start: 0.0453 (pmm) cc_final: -0.0244 (ptp) REVERT: D 101 ILE cc_start: 0.6883 (tp) cc_final: 0.6606 (tt) REVERT: D 130 MET cc_start: 0.4352 (ptt) cc_final: 0.4027 (ptt) REVERT: D 236 MET cc_start: 0.2925 (OUTLIER) cc_final: 0.2550 (ptm) REVERT: D 253 LEU cc_start: 0.3466 (OUTLIER) cc_final: 0.2708 (tp) REVERT: D 310 TRP cc_start: 0.0739 (OUTLIER) cc_final: 0.0395 (m-10) outliers start: 30 outliers final: 8 residues processed: 64 average time/residue: 0.3919 time to fit residues: 28.6235 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 : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 140 ILE 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 248 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 285 GLN Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 378 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 66 optimal weight: 0.0370 chunk 49 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.152415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.139534 restraints weight = 57455.491| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 1.46 r_work: 0.4432 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3179 moved from start: 1.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 16327 Z= 0.257 Angle : 1.348 17.590 24756 Z= 0.537 Chirality : 0.099 0.795 3195 Planarity : 0.007 0.081 1089 Dihedral : 25.564 176.495 8333 Min Nonbonded Distance : 1.062 Molprobity Statistics. All-atom Clashscore : 21.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.67 % Favored : 96.06 % Rotamer: Outliers : 6.74 % Allowed : 31.38 % Favored : 61.88 % 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: -1.18 (0.40), residues: 381 helix: 0.04 (0.31), residues: 239 sheet: -0.46 (1.46), residues: 14 loop : -2.36 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 240 TYR 0.029 0.003 TYR D 316 PHE 0.016 0.003 PHE D 275 TRP 0.030 0.003 TRP D 328 HIS 0.023 0.005 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.26 (16327) covalent geometry : angle 1.34821 / 0.54 (24756) hydrogen bonds : bond 0.11688 / 6.07 ( 599) hydrogen bonds : angle 3.91344 / 1.48 ( 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 64 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 41 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: D 27 LYS cc_start: 0.7107 (mttp) cc_final: 0.6614 (mtpp) REVERT: D 37 TYR cc_start: 0.3468 (p90) cc_final: 0.3227 (p90) REVERT: D 54 GLN cc_start: 0.3478 (OUTLIER) cc_final: 0.3179 (tp-100) REVERT: D 89 PHE cc_start: 0.7963 (t80) cc_final: 0.7692 (t80) REVERT: D 130 MET cc_start: 0.4900 (ptt) cc_final: 0.4664 (ptt) REVERT: D 236 MET cc_start: 0.3272 (mtt) cc_final: 0.2899 (ptm) REVERT: D 253 LEU cc_start: 0.3884 (OUTLIER) cc_final: 0.3077 (tp) REVERT: D 259 MET cc_start: 0.3125 (tpt) cc_final: 0.2789 (tpt) REVERT: D 310 TRP cc_start: 0.0571 (OUTLIER) cc_final: -0.0361 (m-10) REVERT: D 347 ARG cc_start: 0.3439 (OUTLIER) cc_final: 0.1842 (tpp-160) outliers start: 23 outliers final: 9 residues processed: 58 average time/residue: 0.3788 time to fit residues: 25.0612 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 : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 248 PHE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 347 ARG Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 chunk 29 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 43 HIS D 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.154520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.141617 restraints weight = 58577.241| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 1.46 r_work: 0.4464 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3238 moved from start: 1.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16327 Z= 0.190 Angle : 1.198 13.280 24756 Z= 0.474 Chirality : 0.088 0.643 3195 Planarity : 0.006 0.087 1089 Dihedral : 25.389 178.897 8333 Min Nonbonded Distance : 1.128 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 6.45 % Allowed : 34.31 % 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 are not related in a simple way. whole: -0.92 (0.41), residues: 381 helix: 0.26 (0.33), residues: 236 sheet: -1.30 (1.42), residues: 14 loop : -2.07 (0.49), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 381 TYR 0.030 0.002 TYR D 420 PHE 0.015 0.002 PHE D 89 TRP 0.026 0.003 TRP D 328 HIS 0.007 0.002 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (16327) covalent geometry : angle 1.19758 / 0.47 (24756) hydrogen bonds : bond 0.09581 / 4.94 ( 599) hydrogen bonds : angle 3.63560 / 1.36 ( 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 64 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: -0.0352 (OUTLIER) cc_final: -0.0730 (tmt) REVERT: D 27 LYS cc_start: 0.7243 (mttp) cc_final: 0.6708 (tttm) REVERT: D 89 PHE cc_start: 0.8021 (t80) cc_final: 0.7602 (t80) REVERT: D 236 MET cc_start: 0.3429 (mtt) cc_final: 0.3046 (ptm) REVERT: D 259 MET cc_start: 0.2811 (tpt) cc_final: 0.2526 (tpt) REVERT: D 270 LEU cc_start: 0.3578 (OUTLIER) cc_final: 0.2992 (tt) REVERT: D 310 TRP cc_start: 0.0677 (OUTLIER) cc_final: -0.0269 (m-10) REVERT: D 378 ASN cc_start: 0.1329 (OUTLIER) cc_final: 0.1053 (p0) REVERT: D 423 LYS cc_start: 0.6215 (mmmt) cc_final: 0.4161 (ptmt) outliers start: 22 outliers final: 5 residues processed: 56 average time/residue: 0.4539 time to fit residues: 28.6945 Evaluate side-chains 46 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 337 MET Chi-restraints excluded: chain D residue 378 ASN Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4698 r_free = 0.4698 target = 0.153207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.139730 restraints weight = 59391.558| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 1.56 r_work: 0.4443 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4675 moved from start: 1.9167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.144 16327 Z= 0.359 Angle : 1.783 24.562 24756 Z= 0.706 Chirality : 0.126 1.251 3195 Planarity : 0.009 0.089 1089 Dihedral : 26.119 179.399 8333 Min Nonbonded Distance : 1.143 Molprobity Statistics. All-atom Clashscore : 31.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 5.87 % Allowed : 35.19 % Favored : 58.94 % 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: -2.15 (0.39), residues: 381 helix: -0.81 (0.30), residues: 239 sheet: -1.66 (1.75), residues: 10 loop : -2.41 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARG D 381 TYR 0.021 0.003 TYR D 419 PHE 0.036 0.004 PHE D 298 TRP 0.046 0.005 TRP D 328 HIS 0.012 0.004 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.36 (16327) covalent geometry : angle 1.78291 / 0.71 (24756) hydrogen bonds : bond 0.17230 / 8.93 ( 599) hydrogen bonds : angle 4.72630 / 1.78 ( 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 74 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: -0.0622 (OUTLIER) cc_final: -0.0905 (ttt) REVERT: D 10 ILE cc_start: 0.6190 (OUTLIER) cc_final: 0.5807 (pp) REVERT: D 89 PHE cc_start: 0.8578 (t80) cc_final: 0.7981 (t80) REVERT: D 236 MET cc_start: 0.3097 (OUTLIER) cc_final: 0.2697 (ptt) REVERT: D 310 TRP cc_start: 0.1109 (OUTLIER) cc_final: -0.0888 (m-10) outliers start: 20 outliers final: 2 residues processed: 66 average time/residue: 0.4636 time to fit residues: 34.3069 Evaluate side-chains 46 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 174 TYR Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 310 TRP Chi-restraints excluded: chain D residue 415 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 5 ASN ** 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 = 0.4685 r_free = 0.4685 target = 0.152245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.138418 restraints weight = 64265.337| |-----------------------------------------------------------------------------| r_work (start): 0.4499 rms_B_bonded: 1.57 r_work: 0.4417 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 moved from start: 2.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 16327 Z= 0.333 Angle : 1.648 21.706 24756 Z= 0.653 Chirality : 0.112 1.051 3195 Planarity : 0.014 0.340 1089 Dihedral : 26.182 177.742 8333 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 6.45 % Allowed : 36.36 % Favored : 57.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.38), residues: 381 helix: -1.03 (0.29), residues: 233 sheet: -2.14 (0.91), residues: 24 loop : -2.33 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.003 ARG D 381 TYR 0.042 0.005 TYR D 385 PHE 0.074 0.006 PHE D 248 TRP 0.045 0.005 TRP D 328 HIS 0.005 0.002 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.33 (16327) covalent geometry : angle 1.64802 / 0.65 (24756) hydrogen bonds : bond 0.13896 / 7.18 ( 599) hydrogen bonds : angle 4.41593 / 1.66 ( 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 79 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 10 ILE cc_start: 0.6348 (OUTLIER) cc_final: 0.6025 (pp) REVERT: D 89 PHE cc_start: 0.8540 (t80) cc_final: 0.8312 (t80) REVERT: D 302 MET cc_start: 0.4822 (pp-130) cc_final: 0.4557 (pp-130) REVERT: D 373 LEU cc_start: 0.5454 (OUTLIER) cc_final: 0.5236 (tm) REVERT: D 401 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8563 (m) outliers start: 22 outliers final: 5 residues processed: 72 average time/residue: 0.4541 time to fit residues: 36.6046 Evaluate side-chains 48 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 325 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 63 optimal weight: 0.2980 chunk 57 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 131 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 = 0.4582 r_free = 0.4582 target = 0.143425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.126768 restraints weight = 58238.413| |-----------------------------------------------------------------------------| r_work (start): 0.4351 rms_B_bonded: 1.68 r_work: 0.4253 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 2.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 16327 Z= 0.396 Angle : 1.768 20.160 24756 Z= 0.704 Chirality : 0.123 1.213 3195 Planarity : 0.013 0.268 1089 Dihedral : 26.301 176.711 8333 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 32.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.69 % Allowed : 39.88 % Favored : 55.43 % 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: -2.26 (0.39), residues: 381 helix: -0.85 (0.30), residues: 236 sheet: -1.71 (1.40), residues: 14 loop : -2.54 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG D 381 TYR 0.048 0.005 TYR D 278 PHE 0.054 0.007 PHE D 248 TRP 0.039 0.006 TRP D 328 HIS 0.002 0.001 HIS D 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.40 (16327) covalent geometry : angle 1.76808 / 0.70 (24756) hydrogen bonds : bond 0.16519 / 8.71 ( 599) hydrogen bonds : angle 4.69554 / 1.74 ( 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 67 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.262 Fit side-chains REVERT: D 7 MET cc_start: -0.0196 (tmt) cc_final: -0.0448 (ttt) REVERT: D 10 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6125 (pp) REVERT: D 89 PHE cc_start: 0.8673 (t80) cc_final: 0.8156 (t80) REVERT: D 213 GLU cc_start: 0.7372 (tt0) cc_final: 0.6951 (tp30) REVERT: D 247 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6993 (ptp90) REVERT: D 289 LYS cc_start: 0.8432 (pttt) cc_final: 0.8216 (pttt) REVERT: D 354 MET cc_start: 0.4929 (tmm) cc_final: 0.3894 (tmt) REVERT: D 368 LYS cc_start: 0.7506 (mmpt) cc_final: 0.6987 (mtpt) REVERT: D 390 ILE cc_start: 0.6934 (mt) cc_final: 0.6415 (mt) outliers start: 16 outliers final: 5 residues processed: 64 average time/residue: 0.4911 time to fit residues: 35.0988 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 37 TYR 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 247 ARG Chi-restraints excluded: chain D residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 21 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 366 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 = 0.4506 r_free = 0.4506 target = 0.137034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.119011 restraints weight = 55156.546| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 1.65 r_work: 0.4132 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 2.8868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 16327 Z= 0.406 Angle : 1.739 21.317 24756 Z= 0.691 Chirality : 0.117 1.088 3195 Planarity : 0.010 0.198 1089 Dihedral : 26.456 177.426 8333 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 2.93 % Allowed : 43.40 % Favored : 53.67 % 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: -2.56 (0.40), residues: 381 helix: -1.26 (0.29), residues: 235 sheet: -1.74 (1.06), residues: 24 loop : -2.27 (0.60), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG D 282 TYR 0.063 0.005 TYR D 392 PHE 0.071 0.006 PHE D 106 TRP 0.050 0.008 TRP D 328 HIS 0.011 0.003 HIS D 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00821 / 0.41 (16327) covalent geometry : angle 1.73907 / 0.69 (24756) hydrogen bonds : bond 0.15239 / 7.75 ( 599) hydrogen bonds : angle 4.71691 / 1.75 ( 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 61 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 7 MET cc_start: 0.0678 (tmt) cc_final: 0.0201 (ttt) REVERT: D 10 ILE cc_start: 0.6448 (OUTLIER) cc_final: 0.6141 (pp) REVERT: D 89 PHE cc_start: 0.8638 (t80) cc_final: 0.8328 (t80) REVERT: D 214 MET cc_start: 0.7916 (mmp) cc_final: 0.7707 (mmt) REVERT: D 354 MET cc_start: 0.5438 (tmm) cc_final: 0.5185 (mtt) REVERT: D 388 LYS cc_start: 0.5368 (mptt) cc_final: 0.5163 (tptt) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 0.5798 time to fit residues: 37.0255 Evaluate side-chains 47 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 325 ILE 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: 9.9990 chunk 59 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 GLN ** 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 = 0.4506 r_free = 0.4506 target = 0.136765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.118579 restraints weight = 54300.336| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.57 r_work: 0.4142 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 2.9529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16327 Z= 0.296 Angle : 1.479 19.533 24756 Z= 0.586 Chirality : 0.103 0.913 3195 Planarity : 0.008 0.121 1089 Dihedral : 26.122 177.940 8333 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.64 % Allowed : 46.33 % Favored : 51.03 % 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: -1.54 (0.42), residues: 381 helix: -0.37 (0.32), residues: 238 sheet: -1.08 (1.46), residues: 14 loop : -2.11 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 243 TYR 0.046 0.005 TYR D 392 PHE 0.019 0.003 PHE D 411 TRP 0.041 0.006 TRP D 328 HIS 0.004 0.002 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00607 / 0.30 (16327) covalent geometry : angle 1.47873 / 0.59 (24756) hydrogen bonds : bond 0.12515 / 6.46 ( 599) hydrogen bonds : angle 4.19814 / 1.55 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3897.31 seconds wall clock time: 67 minutes 26.01 seconds (4046.01 seconds total)