Starting phenix.real_space_refine on Thu Jul 2 02:07:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jo4_36455/07_2026/8jo4_36455_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jo4_36455/07_2026/8jo4_36455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jo4_36455/07_2026/8jo4_36455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jo4_36455/07_2026/8jo4_36455.map" model { file = "/net/cci-nas-00/data/ceres_data/8jo4_36455/07_2026/8jo4_36455_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jo4_36455/07_2026/8jo4_36455_neut.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.078 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 6 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 3616 2.51 5 N 951 2.21 5 O 1117 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5719 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2846 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 11, 'TRANS': 338} Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2809 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 0.96, per 1000 atoms: 0.17 Number of scatterers: 5719 At special positions: 0 Unit cell: (64.17, 80.91, 113.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 27 16.00 P 6 15.00 Mg 1 11.99 O 1117 8.00 N 951 7.00 C 3616 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: 0.38 Conformation dependent library (CDL) restraints added in 217.6 milliseconds 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1348 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 59.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 41 through 55 removed outlier: 3.659A pdb=" N PHE A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 72 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 77 through 89 removed outlier: 3.693A pdb=" N SER A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 118 Processing helix chain 'A' and resid 121 through 134 removed outlier: 4.226A pdb=" N PHE A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 244 through 259 removed outlier: 3.795A pdb=" N SER A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 284 Processing helix chain 'A' and resid 288 through 297 removed outlier: 3.552A pdb=" N VAL A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.660A pdb=" N ALA A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 352 Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 99 through 103 Processing helix chain 'B' and resid 114 through 128 Processing helix chain 'B' and resid 139 through 147 removed outlier: 3.782A pdb=" N SER B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 198 Processing helix chain 'B' and resid 204 through 218 Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.548A pdb=" N CYS B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 263 through 264 No H-bonds generated for 'chain 'B' and resid 263 through 264' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 275 through 286 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 310 through 323 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.908A pdb=" N GLN B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.728A pdb=" N ARG B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 193 Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 34 removed outlier: 6.180A pdb=" N LEU B 10 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N THR B 108 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N CYS B 12 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA6, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.274A pdb=" N ASN B 299 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 243 317 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1854 1.34 - 1.46: 1040 1.46 - 1.57: 2881 1.57 - 1.69: 10 1.69 - 1.81: 47 Bond restraints: 5832 Sorted by residual: bond pdb=" N ILE A 316 " pdb=" CA ILE A 316 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.17e-02 7.31e+03 1.03e+01 bond pdb=" N ILE B 359 " pdb=" CA ILE B 359 " ideal model delta sigma weight residual 1.461 1.490 -0.030 1.08e-02 8.57e+03 7.65e+00 bond pdb=" N ASN A 164 " pdb=" CA ASN A 164 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.27e-02 6.20e+03 7.00e+00 bond pdb=" N SER A 22 " pdb=" CA SER A 22 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.20e-02 6.94e+03 4.92e+00 bond pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.33e-02 5.65e+03 4.87e+00 ... (remaining 5827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 7744 1.67 - 3.33: 128 3.33 - 5.00: 28 5.00 - 6.67: 2 6.67 - 8.34: 3 Bond angle restraints: 7905 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 131.70 8.17 1.00e+00 1.00e+00 6.67e+01 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 132.54 4.29 1.00e+00 1.00e+00 1.84e+01 angle pdb=" C SER B 273 " pdb=" CA SER B 273 " pdb=" CB SER B 273 " ideal model delta sigma weight residual 111.78 103.44 8.34 2.20e+00 2.07e-01 1.44e+01 angle pdb=" N THR B 360 " pdb=" CA THR B 360 " pdb=" C THR B 360 " ideal model delta sigma weight residual 110.55 105.47 5.08 1.35e+00 5.49e-01 1.41e+01 angle pdb=" N ILE B 359 " pdb=" CA ILE B 359 " pdb=" C ILE B 359 " ideal model delta sigma weight residual 108.12 103.61 4.51 1.34e+00 5.57e-01 1.13e+01 ... (remaining 7900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 3312 17.66 - 35.32: 198 35.32 - 52.98: 61 52.98 - 70.64: 16 70.64 - 88.30: 4 Dihedral angle restraints: 3591 sinusoidal: 1502 harmonic: 2089 Sorted by residual: dihedral pdb=" C SER B 273 " pdb=" N SER B 273 " pdb=" CA SER B 273 " pdb=" CB SER B 273 " ideal model delta harmonic sigma weight residual -122.60 -113.53 -9.07 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N VAL A 239 " pdb=" CA VAL A 239 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA HIS B 163 " pdb=" C HIS B 163 " pdb=" N ASN B 164 " pdb=" CA ASN B 164 " ideal model delta harmonic sigma weight residual 180.00 163.36 16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 739 0.056 - 0.112: 126 0.112 - 0.168: 15 0.168 - 0.224: 3 0.224 - 0.280: 2 Chirality restraints: 885 Sorted by residual: chirality pdb=" CA ILE B 359 " pdb=" N ILE B 359 " pdb=" C ILE B 359 " pdb=" CB ILE B 359 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA MET A 162 " pdb=" N MET A 162 " pdb=" C MET A 162 " pdb=" CB MET A 162 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA SER B 273 " pdb=" N SER B 273 " pdb=" C SER B 273 " pdb=" CB SER B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 882 not shown) Planarity restraints: 1004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 211 " -0.044 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO A 212 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 165 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 166 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 161 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C VAL A 161 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL A 161 " 0.008 2.00e-02 2.50e+03 pdb=" N MET A 162 " 0.007 2.00e-02 2.50e+03 ... (remaining 1001 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 589 2.74 - 3.28: 5909 3.28 - 3.82: 10157 3.82 - 4.36: 12580 4.36 - 4.90: 21365 Nonbonded interactions: 50600 Sorted by model distance: nonbonded pdb=" NE2 HIS B 90 " pdb=" OE2 GLU B 95 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU A 343 " pdb=" OG SER B 352 " model vdw 2.216 3.040 nonbonded pdb=" OG SER A 175 " pdb=" OD2 ASP A 298 " model vdw 2.228 3.040 nonbonded pdb=" O GLY B 158 " pdb=" OG1 THR B 305 " model vdw 2.242 3.040 nonbonded pdb=" OD1 ASP A 23 " pdb=" OG SER A 100 " model vdw 2.243 3.040 ... (remaining 50595 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=1.00 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 5.100 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5832 Z= 0.213 Angle : 0.588 8.337 7905 Z= 0.350 Chirality : 0.046 0.280 885 Planarity : 0.004 0.067 1004 Dihedral : 13.286 88.300 2243 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.99 % Favored : 97.87 % Rotamer: Outliers : 3.21 % Allowed : 4.01 % Favored : 92.78 % 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: 1.06 (0.32), residues: 703 helix: 1.15 (0.27), residues: 377 sheet: -0.26 (0.58), residues: 71 loop : 0.54 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 198 TYR 0.011 0.001 TYR A 42 PHE 0.012 0.001 PHE A 125 TRP 0.011 0.002 TRP A 277 HIS 0.005 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 ( 5832) covalent geometry : angle 0.58827 / 0.35 ( 7905) hydrogen bonds : bond 0.12606 / 7.86 ( 315) hydrogen bonds : angle 5.43081 / 3.73 ( 873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7429 (tt) REVERT: A 129 ASN cc_start: 0.6919 (t0) cc_final: 0.6595 (t0) REVERT: A 162 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6515 (mtp) REVERT: B 35 SER cc_start: 0.8186 (p) cc_final: 0.7902 (t) REVERT: B 298 ASN cc_start: 0.7643 (m-40) cc_final: 0.7382 (m-40) REVERT: B 336 GLU cc_start: 0.6742 (pm20) cc_final: 0.6373 (pm20) outliers start: 20 outliers final: 7 residues processed: 142 average time/residue: 0.0593 time to fit residues: 11.1291 Evaluate side-chains 97 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 346 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN B 299 ASN B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.155616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.132952 restraints weight = 6409.739| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.67 r_work: 0.3481 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5832 Z= 0.132 Angle : 0.493 4.778 7905 Z= 0.263 Chirality : 0.042 0.154 885 Planarity : 0.004 0.061 1004 Dihedral : 10.140 84.255 856 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.14 % Favored : 98.72 % Rotamer: Outliers : 2.73 % Allowed : 10.11 % Favored : 87.16 % 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: 1.41 (0.32), residues: 703 helix: 1.36 (0.26), residues: 383 sheet: 0.47 (0.58), residues: 71 loop : 0.62 (0.42), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 307 TYR 0.037 0.001 TYR A 52 PHE 0.013 0.001 PHE A 125 TRP 0.008 0.002 TRP A 277 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 5832) covalent geometry : angle 0.49286 / 0.26 ( 7905) hydrogen bonds : bond 0.03903 / 2.60 ( 315) hydrogen bonds : angle 4.38447 / 3.06 ( 873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7055 (t0) cc_final: 0.6660 (t0) REVERT: B 95 GLU cc_start: 0.6557 (tp30) cc_final: 0.5592 (tp30) REVERT: B 298 ASN cc_start: 0.7380 (m-40) cc_final: 0.7175 (m-40) REVERT: B 336 GLU cc_start: 0.6846 (pm20) cc_final: 0.6490 (pm20) outliers start: 17 outliers final: 8 residues processed: 112 average time/residue: 0.0600 time to fit residues: 8.9637 Evaluate side-chains 90 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 331 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 0.0270 chunk 31 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN B 75 HIS B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135326 restraints weight = 6383.161| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.69 r_work: 0.3512 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5832 Z= 0.116 Angle : 0.481 6.704 7905 Z= 0.253 Chirality : 0.042 0.154 885 Planarity : 0.004 0.060 1004 Dihedral : 8.857 81.510 843 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.14 % Favored : 98.72 % Rotamer: Outliers : 1.61 % Allowed : 10.91 % Favored : 87.48 % 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 are not related in a simple way. whole: 1.74 (0.32), residues: 703 helix: 1.61 (0.26), residues: 382 sheet: 0.80 (0.60), residues: 71 loop : 0.72 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 212 TYR 0.046 0.001 TYR A 52 PHE 0.014 0.001 PHE B 257 TRP 0.008 0.001 TRP B 358 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 5832) covalent geometry : angle 0.48089 / 0.25 ( 7905) hydrogen bonds : bond 0.03547 / 2.35 ( 315) hydrogen bonds : angle 4.16127 / 2.89 ( 873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7154 (t0) cc_final: 0.6762 (t0) REVERT: A 340 MET cc_start: 0.8139 (tmm) cc_final: 0.7874 (ttp) REVERT: B 95 GLU cc_start: 0.6444 (tp30) cc_final: 0.5526 (tp30) REVERT: B 298 ASN cc_start: 0.7342 (m-40) cc_final: 0.7022 (m-40) REVERT: B 336 GLU cc_start: 0.6925 (pm20) cc_final: 0.6558 (pm20) outliers start: 10 outliers final: 4 residues processed: 101 average time/residue: 0.0631 time to fit residues: 8.3436 Evaluate side-chains 85 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 87 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.154724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130992 restraints weight = 6482.306| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.81 r_work: 0.3452 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5832 Z= 0.174 Angle : 0.511 6.949 7905 Z= 0.271 Chirality : 0.043 0.141 885 Planarity : 0.004 0.060 1004 Dihedral : 8.883 86.949 843 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.13 % Favored : 97.72 % Rotamer: Outliers : 2.57 % Allowed : 11.56 % Favored : 85.87 % 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: 1.70 (0.32), residues: 703 helix: 1.58 (0.26), residues: 381 sheet: 0.75 (0.60), residues: 71 loop : 0.74 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 154 TYR 0.038 0.002 TYR A 52 PHE 0.014 0.002 PHE A 24 TRP 0.009 0.002 TRP A 277 HIS 0.004 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 5832) covalent geometry : angle 0.51134 / 0.27 ( 7905) hydrogen bonds : bond 0.03824 / 2.49 ( 315) hydrogen bonds : angle 4.19379 / 2.91 ( 873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 129 ASN cc_start: 0.7183 (t0) cc_final: 0.6781 (t0) REVERT: A 134 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7515 (mt-10) REVERT: A 186 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6566 (mt-10) REVERT: A 295 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.6999 (mp) REVERT: A 340 MET cc_start: 0.8206 (tmm) cc_final: 0.7908 (ttp) REVERT: B 95 GLU cc_start: 0.6670 (tp30) cc_final: 0.5664 (tp30) REVERT: B 243 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: B 298 ASN cc_start: 0.7558 (m-40) cc_final: 0.7212 (m-40) REVERT: B 336 GLU cc_start: 0.7124 (pm20) cc_final: 0.6765 (pm20) outliers start: 16 outliers final: 10 residues processed: 101 average time/residue: 0.0604 time to fit residues: 8.2090 Evaluate side-chains 95 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 20 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 0.0010 chunk 10 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN B 103 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.134572 restraints weight = 6542.493| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.83 r_work: 0.3492 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5832 Z= 0.115 Angle : 0.467 6.391 7905 Z= 0.249 Chirality : 0.041 0.131 885 Planarity : 0.004 0.059 1004 Dihedral : 8.539 82.329 843 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.42 % Favored : 98.44 % Rotamer: Outliers : 2.57 % Allowed : 12.20 % Favored : 85.23 % 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: 1.90 (0.32), residues: 703 helix: 1.72 (0.26), residues: 382 sheet: 0.90 (0.60), residues: 71 loop : 0.84 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 117 TYR 0.041 0.001 TYR A 52 PHE 0.018 0.001 PHE A 24 TRP 0.007 0.001 TRP A 277 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 5832) covalent geometry : angle 0.46722 / 0.25 ( 7905) hydrogen bonds : bond 0.03379 / 2.23 ( 315) hydrogen bonds : angle 4.07045 / 2.82 ( 873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7458 (tp30) cc_final: 0.6820 (mt-10) REVERT: A 129 ASN cc_start: 0.7128 (t0) cc_final: 0.6738 (t0) REVERT: A 134 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7460 (mt-10) REVERT: A 186 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6588 (mt-10) REVERT: A 295 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.6937 (mp) REVERT: B 95 GLU cc_start: 0.6547 (tp30) cc_final: 0.5585 (tp30) REVERT: B 243 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6715 (mm-30) REVERT: B 298 ASN cc_start: 0.7391 (m-40) cc_final: 0.7066 (m-40) REVERT: B 336 GLU cc_start: 0.7071 (pm20) cc_final: 0.6735 (pm20) outliers start: 16 outliers final: 10 residues processed: 106 average time/residue: 0.0567 time to fit residues: 7.9858 Evaluate side-chains 93 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.0020 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.134241 restraints weight = 6434.997| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.81 r_work: 0.3490 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5832 Z= 0.123 Angle : 0.470 5.891 7905 Z= 0.250 Chirality : 0.041 0.126 885 Planarity : 0.004 0.059 1004 Dihedral : 8.287 81.919 841 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.71 % Favored : 98.15 % Rotamer: Outliers : 2.57 % Allowed : 12.36 % Favored : 85.07 % 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: 1.95 (0.32), residues: 703 helix: 1.76 (0.26), residues: 382 sheet: 0.99 (0.60), residues: 71 loop : 0.82 (0.42), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 154 TYR 0.031 0.001 TYR A 52 PHE 0.016 0.001 PHE A 24 TRP 0.008 0.001 TRP A 277 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 5832) covalent geometry : angle 0.47032 / 0.25 ( 7905) hydrogen bonds : bond 0.03415 / 2.24 ( 315) hydrogen bonds : angle 4.01635 / 2.78 ( 873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7405 (tp30) cc_final: 0.6801 (mt-10) REVERT: A 129 ASN cc_start: 0.7144 (t0) cc_final: 0.6755 (t0) REVERT: A 186 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6616 (mt-10) REVERT: A 295 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.6952 (mp) REVERT: B 95 GLU cc_start: 0.6534 (tp30) cc_final: 0.5569 (tp30) REVERT: B 243 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: B 336 GLU cc_start: 0.7087 (pm20) cc_final: 0.6710 (pm20) outliers start: 16 outliers final: 11 residues processed: 98 average time/residue: 0.0515 time to fit residues: 6.9303 Evaluate side-chains 96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 0.0570 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.156370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132771 restraints weight = 6538.673| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.78 r_work: 0.3481 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5832 Z= 0.138 Angle : 0.481 5.668 7905 Z= 0.257 Chirality : 0.042 0.128 885 Planarity : 0.004 0.060 1004 Dihedral : 8.286 81.869 841 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.85 % Favored : 98.01 % Rotamer: Outliers : 2.57 % Allowed : 12.36 % Favored : 85.07 % 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: 1.89 (0.32), residues: 703 helix: 1.69 (0.26), residues: 382 sheet: 1.11 (0.63), residues: 69 loop : 0.79 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.022 0.001 TYR A 52 PHE 0.016 0.002 PHE B 257 TRP 0.008 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 5832) covalent geometry : angle 0.48141 / 0.26 ( 7905) hydrogen bonds : bond 0.03476 / 2.28 ( 315) hydrogen bonds : angle 4.04121 / 2.79 ( 873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7414 (tp30) cc_final: 0.6849 (mt-10) REVERT: A 52 TYR cc_start: 0.7379 (m-80) cc_final: 0.7159 (m-80) REVERT: A 129 ASN cc_start: 0.7147 (t0) cc_final: 0.6743 (t0) REVERT: A 186 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: B 243 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6722 (mm-30) REVERT: B 336 GLU cc_start: 0.7087 (pm20) cc_final: 0.6725 (pm20) outliers start: 16 outliers final: 11 residues processed: 99 average time/residue: 0.0565 time to fit residues: 7.5080 Evaluate side-chains 96 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.0060 chunk 17 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3865 r_free = 0.3865 target = 0.156639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.133091 restraints weight = 6506.490| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.78 r_work: 0.3479 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5832 Z= 0.136 Angle : 0.487 5.602 7905 Z= 0.260 Chirality : 0.042 0.127 885 Planarity : 0.004 0.059 1004 Dihedral : 8.211 81.668 841 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.25 % Allowed : 13.16 % Favored : 84.59 % 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: 1.90 (0.32), residues: 703 helix: 1.69 (0.26), residues: 382 sheet: 1.11 (0.64), residues: 69 loop : 0.81 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 154 TYR 0.014 0.001 TYR A 52 PHE 0.021 0.001 PHE A 24 TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 5832) covalent geometry : angle 0.48698 / 0.26 ( 7905) hydrogen bonds : bond 0.03457 / 2.27 ( 315) hydrogen bonds : angle 4.02606 / 2.79 ( 873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7407 (tp30) cc_final: 0.6717 (mt-10) REVERT: A 52 TYR cc_start: 0.7418 (m-80) cc_final: 0.7172 (m-80) REVERT: A 129 ASN cc_start: 0.7142 (t0) cc_final: 0.6738 (t0) REVERT: A 186 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6639 (mt-10) REVERT: A 295 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.6989 (mp) REVERT: B 243 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6667 (mm-30) REVERT: B 336 GLU cc_start: 0.7070 (pm20) cc_final: 0.6713 (pm20) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.0561 time to fit residues: 7.5011 Evaluate side-chains 99 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 67 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.0570 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6300 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.156989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.132988 restraints weight = 6500.389| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.84 r_work: 0.3482 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5832 Z= 0.132 Angle : 0.483 6.607 7905 Z= 0.257 Chirality : 0.042 0.127 885 Planarity : 0.004 0.059 1004 Dihedral : 8.085 81.390 841 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.25 % Allowed : 13.64 % Favored : 84.11 % 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: 1.93 (0.32), residues: 703 helix: 1.72 (0.26), residues: 382 sheet: 1.18 (0.65), residues: 69 loop : 0.81 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 154 TYR 0.013 0.001 TYR A 42 PHE 0.023 0.002 PHE A 24 TRP 0.008 0.002 TRP B 358 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 5832) covalent geometry : angle 0.48300 / 0.26 ( 7905) hydrogen bonds : bond 0.03426 / 2.25 ( 315) hydrogen bonds : angle 3.98938 / 2.76 ( 873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7384 (tp30) cc_final: 0.6719 (mt-10) REVERT: A 52 TYR cc_start: 0.7385 (m-80) cc_final: 0.6855 (m-10) REVERT: A 129 ASN cc_start: 0.7155 (t0) cc_final: 0.6754 (t0) REVERT: A 186 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: A 295 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7008 (mp) REVERT: B 95 GLU cc_start: 0.6977 (mm-30) cc_final: 0.5875 (mm-30) REVERT: B 243 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6651 (mm-30) REVERT: B 336 GLU cc_start: 0.7069 (pm20) cc_final: 0.6714 (pm20) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.0534 time to fit residues: 7.2879 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 68 optimal weight: 0.0000 chunk 14 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 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 = 0.3861 r_free = 0.3861 target = 0.156132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.133636 restraints weight = 6608.813| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.70 r_work: 0.3493 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5832 Z= 0.129 Angle : 0.483 6.900 7905 Z= 0.258 Chirality : 0.042 0.126 885 Planarity : 0.004 0.059 1004 Dihedral : 7.986 81.523 841 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.09 % Allowed : 14.13 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.32), residues: 703 helix: 1.73 (0.26), residues: 382 sheet: 1.15 (0.64), residues: 69 loop : 0.84 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 154 TYR 0.013 0.001 TYR A 42 PHE 0.037 0.002 PHE A 31 TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5832) covalent geometry : angle 0.48298 / 0.26 ( 7905) hydrogen bonds : bond 0.03440 / 2.26 ( 315) hydrogen bonds : angle 3.98773 / 2.77 ( 873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1406 Ramachandran restraints generated. 703 Oldfield, 0 Emsley, 703 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7404 (tp30) cc_final: 0.6747 (mt-10) REVERT: A 52 TYR cc_start: 0.7408 (m-80) cc_final: 0.6871 (m-10) REVERT: A 129 ASN cc_start: 0.7152 (t0) cc_final: 0.6747 (t0) REVERT: A 186 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6073 (mp0) REVERT: A 295 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.6993 (mp) REVERT: B 95 GLU cc_start: 0.6941 (mm-30) cc_final: 0.5962 (mm-30) REVERT: B 243 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6627 (mm-30) REVERT: B 336 GLU cc_start: 0.7052 (pm20) cc_final: 0.6691 (pm20) outliers start: 13 outliers final: 10 residues processed: 96 average time/residue: 0.0564 time to fit residues: 7.5053 Evaluate side-chains 98 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 259 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 19 optimal weight: 0.0050 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 166 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 = 0.3872 r_free = 0.3872 target = 0.157375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.134178 restraints weight = 6426.781| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.75 r_work: 0.3498 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5832 Z= 0.129 Angle : 0.478 4.772 7905 Z= 0.256 Chirality : 0.042 0.126 885 Planarity : 0.004 0.059 1004 Dihedral : 7.901 81.757 841 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.93 % Allowed : 14.61 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.32), residues: 703 helix: 1.72 (0.26), residues: 382 sheet: 1.11 (0.63), residues: 69 loop : 0.81 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 154 TYR 0.013 0.001 TYR A 42 PHE 0.041 0.002 PHE A 31 TRP 0.009 0.002 TRP A 277 HIS 0.003 0.001 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 5832) covalent geometry : angle 0.47825 / 0.26 ( 7905) hydrogen bonds : bond 0.03415 / 2.24 ( 315) hydrogen bonds : angle 3.99216 / 2.78 ( 873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1246.93 seconds wall clock time: 22 minutes 5.43 seconds (1325.43 seconds total)