Starting phenix.real_space_refine on Sun Apr 5 21:30:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10ua_75468/04_2026/10ua_75468_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/10ua_75468/04_2026/10ua_75468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10ua_75468/04_2026/10ua_75468_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10ua_75468/04_2026/10ua_75468_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10ua_75468/04_2026/10ua_75468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10ua_75468/04_2026/10ua_75468.map" } resolution = 3.1 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= 0.012 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 Sb 2 10.97 5 S 20 5.16 5 C 4266 2.51 5 N 1046 2.21 5 O 1076 1.98 5 H 6788 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13198 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 6595 Classifications: {'peptide': 428} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'SBO': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 5.67, per 1000 atoms: 0.43 Number of scatterers: 13198 At special positions: 0 Unit cell: (95.55, 113.75, 68.9, 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) Sb 2 50.95 S 20 16.00 O 1076 8.00 N 1046 7.00 C 4266 6.00 H 6788 1.00 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: 0.83 Conformation dependent library (CDL) restraints added in 361.2 milliseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 Processing helix chain 'A' and resid 19 through 22 Processing helix chain 'A' and resid 23 through 38 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 73 removed outlier: 5.393A pdb=" N ASN A 55 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 58 " --> pdb=" O TRP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 90 through 110 removed outlier: 4.154A pdb=" N LEU A 108 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 132 through 150 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 171 through 198 removed outlier: 4.052A pdb=" N VAL A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.798A pdb=" N ALA A 217 " --> pdb=" O GLN A 213 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 218 " --> pdb=" O PRO A 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 218' Processing helix chain 'A' and resid 220 through 240 Processing helix chain 'A' and resid 240 through 245 removed outlier: 4.005A pdb=" N LEU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 267 removed outlier: 3.687A pdb=" N VAL A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N HIS A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 280 through 299 removed outlier: 4.241A pdb=" N VAL A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 314 removed outlier: 4.063A pdb=" N LEU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 336 Processing helix chain 'A' and resid 336 through 350 removed outlier: 3.961A pdb=" N THR A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 342 " --> pdb=" O MET A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 372 Processing helix chain 'A' and resid 373 through 379 Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 380 through 393 Processing helix chain 'A' and resid 398 through 427 Proline residue: A 412 - end of helix Processing helix chain 'B' and resid 2 through 18 Processing helix chain 'B' and resid 19 through 22 Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 45 through 73 removed outlier: 5.393A pdb=" N ASN B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ALA B 56 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 58 " --> pdb=" O TRP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 90 through 110 removed outlier: 4.154A pdb=" N LEU B 108 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 132 through 150 Processing helix chain 'B' and resid 154 through 157 Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 171 through 198 removed outlier: 4.052A pdb=" N VAL B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 213 through 218 removed outlier: 3.798A pdb=" N ALA B 217 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 218 " --> pdb=" O PRO B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 218' Processing helix chain 'B' and resid 220 through 240 Processing helix chain 'B' and resid 240 through 245 removed outlier: 4.006A pdb=" N LEU B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 267 removed outlier: 3.687A pdb=" N VAL B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 280 through 299 removed outlier: 4.241A pdb=" N VAL B 284 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 314 removed outlier: 4.063A pdb=" N LEU B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 336 Processing helix chain 'B' and resid 336 through 350 removed outlier: 3.961A pdb=" N THR B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 372 Processing helix chain 'B' and resid 373 through 379 Proline residue: B 377 - end of helix Processing helix chain 'B' and resid 380 through 393 Processing helix chain 'B' and resid 398 through 427 Proline residue: B 412 - end of helix 525 hydrogen bonds defined for protein. 1545 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: 2.75 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 6788 1.06 - 1.29: 966 1.29 - 1.52: 4318 1.52 - 1.75: 1224 1.75 - 1.98: 46 Bond restraints: 13342 Sorted by residual: bond pdb=" CB VAL B 155 " pdb=" CG1 VAL B 155 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" CB VAL A 155 " pdb=" CG1 VAL A 155 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.09e+00 bond pdb=" CA ILE B 46 " pdb=" CB ILE B 46 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.09e+00 bond pdb=" CB VAL A 160 " pdb=" CG2 VAL A 160 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CB VAL B 160 " pdb=" CG2 VAL B 160 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 ... (remaining 13337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 24263 4.10 - 8.21: 15 8.21 - 12.31: 0 12.31 - 16.41: 2 16.41 - 20.52: 4 Bond angle restraints: 24284 Sorted by residual: angle pdb=" O1 SBO B 501 " pdb="SB SBO B 501 " pdb=" O2 SBO B 501 " ideal model delta sigma weight residual 89.01 109.53 -20.52 3.00e+00 1.11e-01 4.68e+01 angle pdb=" O1 SBO A 501 " pdb="SB SBO A 501 " pdb=" O2 SBO A 501 " ideal model delta sigma weight residual 89.01 109.52 -20.51 3.00e+00 1.11e-01 4.68e+01 angle pdb=" O1 SBO B 501 " pdb="SB SBO B 501 " pdb=" O3 SBO B 501 " ideal model delta sigma weight residual 91.84 109.08 -17.24 3.00e+00 1.11e-01 3.30e+01 angle pdb=" O1 SBO A 501 " pdb="SB SBO A 501 " pdb=" O3 SBO A 501 " ideal model delta sigma weight residual 91.84 109.03 -17.19 3.00e+00 1.11e-01 3.28e+01 angle pdb=" O2 SBO A 501 " pdb="SB SBO A 501 " pdb=" O3 SBO A 501 " ideal model delta sigma weight residual 94.43 109.69 -15.26 3.00e+00 1.11e-01 2.59e+01 ... (remaining 24279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 5308 11.94 - 23.88: 642 23.88 - 35.83: 111 35.83 - 47.77: 49 47.77 - 59.71: 78 Dihedral angle restraints: 6188 sinusoidal: 3296 harmonic: 2892 Sorted by residual: dihedral pdb=" CA LEU A 152 " pdb=" C LEU A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta harmonic sigma weight residual -180.00 -154.85 -25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N PRO B 153 " pdb=" CA PRO B 153 " ideal model delta harmonic sigma weight residual 180.00 -154.88 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CB LYS A 88 " pdb=" CG LYS A 88 " pdb=" CD LYS A 88 " pdb=" CE LYS A 88 " ideal model delta sinusoidal sigma weight residual -180.00 -137.35 -42.65 3 1.50e+01 4.44e-03 7.66e+00 ... (remaining 6185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 568 0.028 - 0.056: 348 0.056 - 0.083: 167 0.083 - 0.111: 39 0.111 - 0.139: 6 Chirality restraints: 1128 Sorted by residual: chirality pdb=" CA PRO B 153 " pdb=" N PRO B 153 " pdb=" C PRO B 153 " pdb=" CB PRO B 153 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA PRO A 153 " pdb=" N PRO A 153 " pdb=" C PRO A 153 " pdb=" CB PRO A 153 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE B 202 " pdb=" N ILE B 202 " pdb=" C ILE B 202 " pdb=" CB ILE B 202 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.27e-01 ... (remaining 1125 not shown) Planarity restraints: 1906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 372 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO A 373 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 372 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 373 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 61 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C ILE B 61 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE B 61 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA B 62 " 0.009 2.00e-02 2.50e+03 ... (remaining 1903 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 774 2.21 - 2.81: 29241 2.81 - 3.40: 37330 3.40 - 4.00: 48763 4.00 - 4.60: 78846 Nonbonded interactions: 194954 Sorted by model distance: nonbonded pdb=" O ALA A 34 " pdb=" HG SER A 38 " model vdw 1.610 2.450 nonbonded pdb=" O ALA B 34 " pdb=" HG SER B 38 " model vdw 1.610 2.450 nonbonded pdb=" O ILE A 348 " pdb=" HG1 THR A 351 " model vdw 1.729 2.450 nonbonded pdb=" O ILE B 348 " pdb=" HG1 THR B 351 " model vdw 1.730 2.450 nonbonded pdb=" O ALA A 177 " pdb="HH21 ARG A 424 " model vdw 1.742 2.450 ... (remaining 194949 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 7.000 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: 0.080 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.520 Find NCS groups from input model: 0.070 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.007 0.043 6554 Z= 0.279 Angle : 0.746 20.515 8972 Z= 0.363 Chirality : 0.042 0.139 1128 Planarity : 0.005 0.043 1082 Dihedral : 9.488 52.550 2196 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.68 (0.24), residues: 852 helix: -1.24 (0.16), residues: 686 sheet: None (None), residues: 0 loop : 0.53 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 424 TYR 0.010 0.002 TYR A 294 PHE 0.022 0.002 PHE A 60 TRP 0.015 0.002 TRP A 228 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00705 ( 6554) covalent geometry : angle 0.74596 ( 8972) hydrogen bonds : bond 0.13890 ( 525) hydrogen bonds : angle 6.41109 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7025 (mmt-90) cc_final: 0.5734 (tpt-90) REVERT: A 314 GLN cc_start: 0.6876 (mt0) cc_final: 0.6383 (mm110) REVERT: B 86 ARG cc_start: 0.7035 (mmt-90) cc_final: 0.5668 (tpt170) REVERT: B 277 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6845 (mm-30) REVERT: B 314 GLN cc_start: 0.6909 (mt0) cc_final: 0.6409 (mm110) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1917 time to fit residues: 14.0791 Evaluate side-chains 48 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.107361 restraints weight = 13642.319| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.62 r_work: 0.3155 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6554 Z= 0.157 Angle : 0.549 5.835 8972 Z= 0.293 Chirality : 0.037 0.127 1128 Planarity : 0.004 0.036 1082 Dihedral : 3.680 25.680 900 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.61 % Allowed : 2.58 % Favored : 96.81 % 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: 0.55 (0.27), residues: 852 helix: 0.54 (0.18), residues: 694 sheet: None (None), residues: 0 loop : 0.13 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.009 0.001 TYR B 290 PHE 0.013 0.001 PHE A 60 TRP 0.015 0.001 TRP A 228 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6554) covalent geometry : angle 0.54946 ( 8972) hydrogen bonds : bond 0.05348 ( 525) hydrogen bonds : angle 4.88567 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.298 Fit side-chains REVERT: A 1 MET cc_start: 0.7671 (tpp) cc_final: 0.7418 (tpp) REVERT: A 86 ARG cc_start: 0.7291 (mmt-90) cc_final: 0.5984 (tpt-90) REVERT: A 314 GLN cc_start: 0.6954 (mt0) cc_final: 0.6510 (mm110) REVERT: B 72 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7388 (mt-10) REVERT: B 86 ARG cc_start: 0.7304 (mmt-90) cc_final: 0.6326 (ttp-110) REVERT: B 277 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6939 (mm-30) REVERT: B 314 GLN cc_start: 0.6995 (mt0) cc_final: 0.6546 (mm110) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.1860 time to fit residues: 14.3967 Evaluate side-chains 60 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106403 restraints weight = 12677.200| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.51 r_work: 0.3028 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6554 Z= 0.153 Angle : 0.505 4.821 8972 Z= 0.270 Chirality : 0.036 0.124 1128 Planarity : 0.004 0.037 1082 Dihedral : 3.576 25.300 900 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.91 % Allowed : 2.74 % Favored : 96.35 % 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: 1.51 (0.28), residues: 852 helix: 1.35 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -0.28 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 297 TYR 0.006 0.001 TYR B 290 PHE 0.019 0.001 PHE A 60 TRP 0.014 0.001 TRP B 228 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6554) covalent geometry : angle 0.50475 ( 8972) hydrogen bonds : bond 0.04703 ( 525) hydrogen bonds : angle 4.54899 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.352 Fit side-chains REVERT: A 1 MET cc_start: 0.7792 (tpp) cc_final: 0.7589 (tpp) REVERT: A 86 ARG cc_start: 0.7406 (mmt-90) cc_final: 0.6505 (ttp-170) REVERT: A 314 GLN cc_start: 0.6995 (mt0) cc_final: 0.6568 (mm110) REVERT: B 86 ARG cc_start: 0.7388 (mmt-90) cc_final: 0.6467 (ttp-170) REVERT: B 314 GLN cc_start: 0.7050 (mt0) cc_final: 0.6611 (mm110) outliers start: 6 outliers final: 5 residues processed: 68 average time/residue: 0.1722 time to fit residues: 16.2863 Evaluate side-chains 62 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104251 restraints weight = 12533.142| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.42 r_work: 0.3061 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6554 Z= 0.170 Angle : 0.507 5.554 8972 Z= 0.273 Chirality : 0.036 0.127 1128 Planarity : 0.004 0.039 1082 Dihedral : 3.555 24.084 900 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.52 % Allowed : 3.34 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.28), residues: 852 helix: 1.46 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -0.39 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 199 TYR 0.010 0.001 TYR A 290 PHE 0.020 0.001 PHE A 60 TRP 0.014 0.001 TRP B 228 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6554) covalent geometry : angle 0.50730 ( 8972) hydrogen bonds : bond 0.04687 ( 525) hydrogen bonds : angle 4.46232 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.320 Fit side-chains REVERT: A 86 ARG cc_start: 0.7455 (mmt-90) cc_final: 0.6593 (ttp-170) REVERT: A 314 GLN cc_start: 0.6974 (mt0) cc_final: 0.6665 (mm110) REVERT: B 86 ARG cc_start: 0.7452 (mmt-90) cc_final: 0.6550 (ttp-170) REVERT: B 314 GLN cc_start: 0.7054 (mt0) cc_final: 0.6637 (mm110) outliers start: 10 outliers final: 9 residues processed: 68 average time/residue: 0.1528 time to fit residues: 14.4501 Evaluate side-chains 68 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 397 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.102750 restraints weight = 12549.189| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.44 r_work: 0.3011 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6554 Z= 0.188 Angle : 0.513 5.268 8972 Z= 0.278 Chirality : 0.037 0.130 1128 Planarity : 0.004 0.038 1082 Dihedral : 3.587 23.745 900 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.22 % Allowed : 4.56 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.28), residues: 852 helix: 1.49 (0.19), residues: 692 sheet: None (None), residues: 0 loop : -0.53 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 424 TYR 0.011 0.001 TYR B 290 PHE 0.020 0.001 PHE A 60 TRP 0.015 0.001 TRP B 228 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 6554) covalent geometry : angle 0.51345 ( 8972) hydrogen bonds : bond 0.04763 ( 525) hydrogen bonds : angle 4.42724 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.348 Fit side-chains REVERT: A 86 ARG cc_start: 0.7469 (mmt-90) cc_final: 0.6594 (ttp-170) REVERT: A 314 GLN cc_start: 0.7042 (mt0) cc_final: 0.6704 (mm110) REVERT: B 314 GLN cc_start: 0.7053 (mt0) cc_final: 0.6717 (mm110) outliers start: 8 outliers final: 5 residues processed: 71 average time/residue: 0.1435 time to fit residues: 14.8386 Evaluate side-chains 68 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.100659 restraints weight = 13020.054| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.61 r_work: 0.2951 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6554 Z= 0.146 Angle : 0.482 5.345 8972 Z= 0.260 Chirality : 0.036 0.125 1128 Planarity : 0.003 0.037 1082 Dihedral : 3.550 24.217 900 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.22 % Allowed : 5.32 % Favored : 93.47 % 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: 1.88 (0.28), residues: 852 helix: 1.67 (0.20), residues: 692 sheet: None (None), residues: 0 loop : -0.48 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 199 TYR 0.010 0.001 TYR A 290 PHE 0.018 0.001 PHE A 60 TRP 0.015 0.001 TRP B 228 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6554) covalent geometry : angle 0.48248 ( 8972) hydrogen bonds : bond 0.04492 ( 525) hydrogen bonds : angle 4.32547 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.310 Fit side-chains REVERT: A 86 ARG cc_start: 0.7361 (mmt-90) cc_final: 0.6429 (ttp-170) REVERT: A 314 GLN cc_start: 0.7043 (mt0) cc_final: 0.6669 (mm110) REVERT: B 314 GLN cc_start: 0.7079 (mt0) cc_final: 0.6700 (mm110) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.1411 time to fit residues: 14.3614 Evaluate side-chains 70 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 397 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 76 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100517 restraints weight = 13053.063| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.59 r_work: 0.2970 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6554 Z= 0.151 Angle : 0.482 5.251 8972 Z= 0.260 Chirality : 0.036 0.123 1128 Planarity : 0.003 0.036 1082 Dihedral : 3.520 23.789 900 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.76 % Allowed : 5.93 % Favored : 93.31 % 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 (0.28), residues: 852 helix: 1.71 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -0.46 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 199 TYR 0.010 0.001 TYR A 290 PHE 0.019 0.001 PHE A 60 TRP 0.014 0.001 TRP B 228 HIS 0.002 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6554) covalent geometry : angle 0.48222 ( 8972) hydrogen bonds : bond 0.04488 ( 525) hydrogen bonds : angle 4.29059 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.265 Fit side-chains REVERT: A 199 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.6749 (ptt-90) REVERT: A 314 GLN cc_start: 0.7058 (mt0) cc_final: 0.6700 (mm110) REVERT: B 199 ARG cc_start: 0.7571 (ttp-110) cc_final: 0.6833 (ptt-90) REVERT: B 314 GLN cc_start: 0.7065 (mt0) cc_final: 0.6700 (mm110) outliers start: 5 outliers final: 4 residues processed: 71 average time/residue: 0.1569 time to fit residues: 15.7169 Evaluate side-chains 66 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.099933 restraints weight = 12954.711| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.61 r_work: 0.2938 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6554 Z= 0.131 Angle : 0.470 5.159 8972 Z= 0.253 Chirality : 0.036 0.124 1128 Planarity : 0.003 0.035 1082 Dihedral : 3.492 24.104 900 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.76 % Allowed : 6.23 % Favored : 93.01 % 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: 2.13 (0.28), residues: 852 helix: 1.83 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -0.40 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 199 TYR 0.011 0.001 TYR A 290 PHE 0.018 0.001 PHE A 60 TRP 0.014 0.001 TRP B 228 HIS 0.002 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6554) covalent geometry : angle 0.47002 ( 8972) hydrogen bonds : bond 0.04339 ( 525) hydrogen bonds : angle 4.24522 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.323 Fit side-chains REVERT: A 314 GLN cc_start: 0.7051 (mt0) cc_final: 0.6677 (mm110) REVERT: B 199 ARG cc_start: 0.7536 (ttp-110) cc_final: 0.6807 (ptt-90) REVERT: B 314 GLN cc_start: 0.7071 (mt0) cc_final: 0.6691 (mm110) outliers start: 5 outliers final: 4 residues processed: 70 average time/residue: 0.1332 time to fit residues: 13.7736 Evaluate side-chains 69 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.099369 restraints weight = 14493.830| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.51 r_work: 0.3083 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6554 Z= 0.209 Angle : 0.523 5.353 8972 Z= 0.283 Chirality : 0.037 0.130 1128 Planarity : 0.004 0.035 1082 Dihedral : 3.623 24.657 900 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.76 % Allowed : 6.23 % Favored : 93.01 % 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: 1.81 (0.28), residues: 852 helix: 1.62 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -0.56 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 424 TYR 0.013 0.001 TYR A 290 PHE 0.022 0.001 PHE A 60 TRP 0.013 0.001 TRP A 228 HIS 0.003 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 6554) covalent geometry : angle 0.52256 ( 8972) hydrogen bonds : bond 0.04798 ( 525) hydrogen bonds : angle 4.35019 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.7595 (mmt-90) cc_final: 0.6703 (ttp-170) REVERT: A 199 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.6862 (ptt-90) REVERT: A 200 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7868 (mtt-85) REVERT: A 314 GLN cc_start: 0.7117 (mt0) cc_final: 0.6792 (mm110) REVERT: B 199 ARG cc_start: 0.7681 (ttp-110) cc_final: 0.6969 (ptt-90) REVERT: B 200 ARG cc_start: 0.8181 (mmm-85) cc_final: 0.7851 (mtt-85) REVERT: B 314 GLN cc_start: 0.7140 (mt0) cc_final: 0.6813 (mm110) outliers start: 5 outliers final: 5 residues processed: 78 average time/residue: 0.1950 time to fit residues: 20.2685 Evaluate side-chains 81 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.119195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100592 restraints weight = 14370.377| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.50 r_work: 0.3102 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 6554 Z= 0.159 Angle : 0.488 5.293 8972 Z= 0.265 Chirality : 0.036 0.128 1128 Planarity : 0.003 0.037 1082 Dihedral : 3.566 24.553 900 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.76 % Allowed : 6.53 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.28), residues: 852 helix: 1.75 (0.19), residues: 694 sheet: None (None), residues: 0 loop : -0.48 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 199 TYR 0.010 0.001 TYR B 290 PHE 0.019 0.001 PHE A 60 TRP 0.015 0.001 TRP A 228 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6554) covalent geometry : angle 0.48841 ( 8972) hydrogen bonds : bond 0.04559 ( 525) hydrogen bonds : angle 4.29594 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.366 Fit side-chains REVERT: A 199 ARG cc_start: 0.7618 (ttp-110) cc_final: 0.6879 (ptt-90) REVERT: A 200 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.7846 (mtt-85) REVERT: A 314 GLN cc_start: 0.7129 (mt0) cc_final: 0.6809 (mm110) REVERT: B 199 ARG cc_start: 0.7674 (ttp-110) cc_final: 0.6956 (ptt-90) REVERT: B 200 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7861 (mtt-85) REVERT: B 314 GLN cc_start: 0.7128 (mt0) cc_final: 0.6806 (mm110) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.1801 time to fit residues: 18.5280 Evaluate side-chains 77 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 41 optimal weight: 0.0470 chunk 61 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 18 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.127172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.108936 restraints weight = 12767.596| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.45 r_work: 0.2954 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6554 Z= 0.115 Angle : 0.461 5.037 8972 Z= 0.248 Chirality : 0.035 0.125 1128 Planarity : 0.003 0.038 1082 Dihedral : 3.460 23.782 900 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.61 % Allowed : 6.84 % Favored : 92.55 % 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 (0.29), residues: 852 helix: 2.03 (0.20), residues: 694 sheet: None (None), residues: 0 loop : -0.34 (0.45), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 85 TYR 0.011 0.001 TYR A 290 PHE 0.017 0.001 PHE A 60 TRP 0.015 0.001 TRP B 228 HIS 0.001 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6554) covalent geometry : angle 0.46079 ( 8972) hydrogen bonds : bond 0.04220 ( 525) hydrogen bonds : angle 4.20067 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2957.50 seconds wall clock time: 50 minutes 44.42 seconds (3044.42 seconds total)