Starting phenix.real_space_refine on Tue Feb 3 20:53:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2i_63586/02_2026/9m2i_63586.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2i_63586/02_2026/9m2i_63586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m2i_63586/02_2026/9m2i_63586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2i_63586/02_2026/9m2i_63586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m2i_63586/02_2026/9m2i_63586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2i_63586/02_2026/9m2i_63586.map" } resolution = 3.19 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 4308 2.51 5 N 1126 2.21 5 O 1280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6758 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3330 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 409} Chain: "B" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3330 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 409} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {' MG': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {' MG': 1, 'NAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.49, per 1000 atoms: 0.22 Number of scatterers: 6758 At special positions: 0 Unit cell: (85.49, 82.17, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1280 8.00 N 1126 7.00 C 4308 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: 0.58 Conformation dependent library (CDL) restraints added in 147.7 milliseconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1636 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 45.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 5 through 11 Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.544A pdb=" N LEU A 37 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.891A pdb=" N CYS A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.521A pdb=" N MET A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 removed outlier: 3.845A pdb=" N GLU A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.795A pdb=" N TYR A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.640A pdb=" N ILE A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 removed outlier: 4.114A pdb=" N ARG A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 removed outlier: 4.165A pdb=" N LEU A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.554A pdb=" N MET A 277 " --> pdb=" O MET A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 removed outlier: 3.616A pdb=" N ALA A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 340 through 345 removed outlier: 3.627A pdb=" N LYS A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.747A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 355 " --> pdb=" O ILE A 351 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 356' Processing helix chain 'A' and resid 387 through 404 removed outlier: 3.998A pdb=" N ALA A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 412 through 426 removed outlier: 4.203A pdb=" N TYR A 416 " --> pdb=" O ASP A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 440 removed outlier: 3.839A pdb=" N ILE A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 43 through 53 removed outlier: 3.912A pdb=" N CYS B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.548A pdb=" N TYR B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 87 through 101 Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 127 through 130 Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.678A pdb=" N TYR B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.557A pdb=" N HIS B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 181 removed outlier: 3.696A pdb=" N ILE B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 197 through 210 removed outlier: 4.061A pdb=" N ALA B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 340 through 354 removed outlier: 3.515A pdb=" N LYS B 344 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 402 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 412 through 426 removed outlier: 3.600A pdb=" N LYS B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 440 removed outlier: 3.902A pdb=" N ILE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 219 removed outlier: 6.574A pdb=" N MET A 190 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N CYS A 219 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL A 192 " --> pdb=" O CYS A 219 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE A 260 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA5, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 193 removed outlier: 6.210A pdb=" N MET B 190 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N CYS B 219 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL B 192 " --> pdb=" O CYS B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 284 through 285 219 hydrogen bonds defined for protein. 633 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: 0.59 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1167 1.29 - 1.42: 1544 1.42 - 1.55: 4110 1.55 - 1.68: 9 1.68 - 1.81: 60 Bond restraints: 6890 Sorted by residual: bond pdb=" C PRO B 386 " pdb=" O PRO B 386 " ideal model delta sigma weight residual 1.235 1.157 0.078 1.30e-02 5.92e+03 3.63e+01 bond pdb=" C LEU B 388 " pdb=" O LEU B 388 " ideal model delta sigma weight residual 1.235 1.176 0.059 1.03e-02 9.43e+03 3.25e+01 bond pdb=" C PRO A 386 " pdb=" O PRO A 386 " ideal model delta sigma weight residual 1.235 1.175 0.060 1.30e-02 5.92e+03 2.12e+01 bond pdb=" C LEU A 388 " pdb=" O LEU A 388 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.16e-02 7.43e+03 1.86e+01 bond pdb=" N PRO A 386 " pdb=" CA PRO A 386 " ideal model delta sigma weight residual 1.469 1.418 0.050 1.28e-02 6.10e+03 1.55e+01 ... (remaining 6885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 9083 2.09 - 4.18: 220 4.18 - 6.26: 49 6.26 - 8.35: 11 8.35 - 10.44: 7 Bond angle restraints: 9370 Sorted by residual: angle pdb=" N VAL A 390 " pdb=" CA VAL A 390 " pdb=" C VAL A 390 " ideal model delta sigma weight residual 113.39 103.93 9.46 1.47e+00 4.63e-01 4.14e+01 angle pdb=" N ARG B 387 " pdb=" CA ARG B 387 " pdb=" C ARG B 387 " ideal model delta sigma weight residual 114.09 104.12 9.97 1.55e+00 4.16e-01 4.13e+01 angle pdb=" C PRO B 386 " pdb=" CA PRO B 386 " pdb=" CB PRO B 386 " ideal model delta sigma weight residual 111.56 101.12 10.44 1.65e+00 3.67e-01 4.00e+01 angle pdb=" N LEU A 388 " pdb=" CA LEU A 388 " pdb=" C LEU A 388 " ideal model delta sigma weight residual 111.14 105.27 5.87 1.08e+00 8.57e-01 2.96e+01 angle pdb=" C PRO B 383 " pdb=" N PHE B 384 " pdb=" CA PHE B 384 " ideal model delta sigma weight residual 122.79 114.88 7.91 1.63e+00 3.76e-01 2.35e+01 ... (remaining 9365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 3702 17.49 - 34.98: 453 34.98 - 52.47: 119 52.47 - 69.96: 25 69.96 - 87.46: 11 Dihedral angle restraints: 4310 sinusoidal: 1776 harmonic: 2534 Sorted by residual: dihedral pdb=" C PRO B 386 " pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" CB PRO B 386 " ideal model delta harmonic sigma weight residual -120.70 -106.90 -13.80 0 2.50e+00 1.60e-01 3.05e+01 dihedral pdb=" CA CYS A 323 " pdb=" C CYS A 323 " pdb=" N PHE A 324 " pdb=" CA PHE A 324 " ideal model delta harmonic sigma weight residual -180.00 -156.31 -23.69 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" C ARG B 387 " pdb=" N ARG B 387 " pdb=" CA ARG B 387 " pdb=" CB ARG B 387 " ideal model delta harmonic sigma weight residual -122.60 -110.81 -11.79 0 2.50e+00 1.60e-01 2.22e+01 ... (remaining 4307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 872 0.063 - 0.126: 187 0.126 - 0.189: 21 0.189 - 0.253: 3 0.253 - 0.316: 1 Chirality restraints: 1084 Sorted by residual: chirality pdb=" CA ARG B 387 " pdb=" N ARG B 387 " pdb=" C ARG B 387 " pdb=" CB ARG B 387 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ASP B 385 " pdb=" N ASP B 385 " pdb=" C ASP B 385 " pdb=" CB ASP B 385 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB VAL A 390 " pdb=" CA VAL A 390 " pdb=" CG1 VAL A 390 " pdb=" CG2 VAL A 390 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1081 not shown) Planarity restraints: 1214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 388 " 0.020 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" C LEU A 388 " -0.072 2.00e-02 2.50e+03 pdb=" O LEU A 388 " 0.027 2.00e-02 2.50e+03 pdb=" N ILE A 389 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 388 " 0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU B 388 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU B 388 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE B 389 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 40 " -0.048 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO B 41 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 41 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 41 " -0.040 5.00e-02 4.00e+02 ... (remaining 1211 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 61 2.57 - 3.15: 5837 3.15 - 3.74: 10721 3.74 - 4.32: 14811 4.32 - 4.90: 24195 Nonbonded interactions: 55625 Sorted by model distance: nonbonded pdb=" OD1 ASP B 137 " pdb="MG MG B 502 " model vdw 1.989 2.170 nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A 502 " model vdw 2.059 2.170 nonbonded pdb=" OD2 ASP B 137 " pdb="MG MG B 502 " model vdw 2.139 2.170 nonbonded pdb=" O ALA A 167 " pdb=" OG1 THR A 171 " model vdw 2.210 3.040 nonbonded pdb=" NZ LYS B 183 " pdb=" OD2 ASP B 258 " model vdw 2.224 3.120 ... (remaining 55620 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: 8.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.100 Find NCS groups from input model: 0.060 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:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.005 0.078 6890 Z= 0.278 Angle : 0.840 10.440 9370 Z= 0.468 Chirality : 0.052 0.316 1084 Planarity : 0.006 0.071 1214 Dihedral : 16.860 87.455 2674 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.27 % Favored : 90.27 % Rotamer: Outliers : 1.98 % Allowed : 18.22 % Favored : 79.80 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.45 % 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: -2.22 (0.28), residues: 874 helix: -0.45 (0.28), residues: 352 sheet: -2.92 (0.51), residues: 82 loop : -2.04 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 387 TYR 0.010 0.001 TYR A 226 PHE 0.017 0.002 PHE A 159 HIS 0.004 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 6890) covalent geometry : angle 0.83990 ( 9370) hydrogen bonds : bond 0.21733 ( 219) hydrogen bonds : angle 7.72931 ( 633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: B 79 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8394 (mm) outliers start: 14 outliers final: 8 residues processed: 111 average time/residue: 0.0437 time to fit residues: 7.4412 Evaluate side-chains 102 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 414 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 0.0070 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.179696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139443 restraints weight = 8922.055| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.49 r_work: 0.3546 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6890 Z= 0.154 Angle : 0.686 9.568 9370 Z= 0.342 Chirality : 0.048 0.167 1084 Planarity : 0.005 0.068 1214 Dihedral : 9.713 59.892 1079 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.78 % Favored : 91.88 % Rotamer: Outliers : 4.10 % Allowed : 16.53 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.47 (0.29), residues: 874 helix: 0.57 (0.30), residues: 340 sheet: -2.72 (0.53), residues: 82 loop : -1.90 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 63 TYR 0.018 0.001 TYR B 314 PHE 0.026 0.002 PHE A 12 HIS 0.003 0.001 HIS B 160 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6890) covalent geometry : angle 0.68632 ( 9370) hydrogen bonds : bond 0.04254 ( 219) hydrogen bonds : angle 4.93101 ( 633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.248 Fit side-chains REVERT: A 367 TYR cc_start: 0.6710 (OUTLIER) cc_final: 0.5903 (m-10) REVERT: B 79 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8433 (mm) REVERT: B 333 ASP cc_start: 0.8321 (m-30) cc_final: 0.8066 (m-30) outliers start: 29 outliers final: 8 residues processed: 119 average time/residue: 0.0466 time to fit residues: 8.6020 Evaluate side-chains 97 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 414 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.179968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140126 restraints weight = 8945.267| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.46 r_work: 0.3550 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6890 Z= 0.141 Angle : 0.658 8.706 9370 Z= 0.328 Chirality : 0.047 0.167 1084 Planarity : 0.005 0.067 1214 Dihedral : 9.181 58.168 1072 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.01 % Favored : 91.65 % Rotamer: Outliers : 3.81 % Allowed : 19.21 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.28 (0.29), residues: 874 helix: 0.66 (0.30), residues: 346 sheet: -2.57 (0.53), residues: 82 loop : -1.77 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.009 0.001 TYR B 314 PHE 0.024 0.002 PHE A 12 HIS 0.003 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6890) covalent geometry : angle 0.65843 ( 9370) hydrogen bonds : bond 0.03572 ( 219) hydrogen bonds : angle 4.45240 ( 633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.218 Fit side-chains REVERT: B 51 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7267 (tp30) REVERT: B 333 ASP cc_start: 0.8285 (m-30) cc_final: 0.8022 (m-30) outliers start: 27 outliers final: 13 residues processed: 114 average time/residue: 0.0576 time to fit residues: 9.4384 Evaluate side-chains 96 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 414 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 11 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.178903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139357 restraints weight = 8844.836| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.47 r_work: 0.3542 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6890 Z= 0.140 Angle : 0.659 8.739 9370 Z= 0.325 Chirality : 0.047 0.167 1084 Planarity : 0.005 0.067 1214 Dihedral : 8.901 59.149 1068 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.35 % Favored : 91.30 % Rotamer: Outliers : 3.67 % Allowed : 21.75 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.25 (0.29), residues: 874 helix: 0.65 (0.30), residues: 346 sheet: -2.54 (0.54), residues: 82 loop : -1.71 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.012 0.001 TYR B 314 PHE 0.027 0.002 PHE A 12 HIS 0.003 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6890) covalent geometry : angle 0.65860 ( 9370) hydrogen bonds : bond 0.03385 ( 219) hydrogen bonds : angle 4.39986 ( 633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.205 Fit side-chains REVERT: A 306 ILE cc_start: 0.8447 (mm) cc_final: 0.8208 (mm) REVERT: B 150 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8028 (mt) REVERT: B 273 MET cc_start: 0.7277 (ptp) cc_final: 0.6928 (ptm) REVERT: B 333 ASP cc_start: 0.8315 (m-30) cc_final: 0.8020 (m-30) REVERT: B 379 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8444 (tt) outliers start: 26 outliers final: 13 residues processed: 114 average time/residue: 0.0464 time to fit residues: 7.9111 Evaluate side-chains 101 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 414 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 53 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN B 22 GLN B 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.178659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139764 restraints weight = 8897.119| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.44 r_work: 0.3519 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6890 Z= 0.155 Angle : 0.674 11.429 9370 Z= 0.332 Chirality : 0.048 0.167 1084 Planarity : 0.005 0.066 1214 Dihedral : 8.754 59.734 1068 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.04 % Favored : 90.62 % Rotamer: Outliers : 4.38 % Allowed : 21.05 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.30 (0.29), residues: 874 helix: 0.55 (0.29), residues: 346 sheet: -2.50 (0.55), residues: 82 loop : -1.70 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 387 TYR 0.009 0.001 TYR B 226 PHE 0.030 0.002 PHE A 12 HIS 0.004 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 6890) covalent geometry : angle 0.67425 ( 9370) hydrogen bonds : bond 0.03493 ( 219) hydrogen bonds : angle 4.38995 ( 633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 90 time to evaluate : 0.255 Fit side-chains REVERT: A 306 ILE cc_start: 0.8652 (mm) cc_final: 0.8403 (mm) REVERT: A 367 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.5919 (m-10) REVERT: B 150 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8054 (mt) REVERT: B 273 MET cc_start: 0.7344 (ptp) cc_final: 0.6956 (ptm) REVERT: B 372 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6831 (pp) REVERT: B 379 ILE cc_start: 0.8631 (tp) cc_final: 0.8418 (tt) outliers start: 31 outliers final: 19 residues processed: 115 average time/residue: 0.0512 time to fit residues: 8.6979 Evaluate side-chains 109 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 367 TYR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 414 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 chunk 50 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN B 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.178548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139747 restraints weight = 8888.865| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.44 r_work: 0.3527 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6890 Z= 0.144 Angle : 0.676 9.866 9370 Z= 0.332 Chirality : 0.048 0.163 1084 Planarity : 0.005 0.065 1214 Dihedral : 8.589 59.704 1068 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.81 % Favored : 90.85 % Rotamer: Outliers : 4.10 % Allowed : 22.18 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.27 (0.29), residues: 874 helix: 0.52 (0.29), residues: 350 sheet: -2.42 (0.56), residues: 82 loop : -1.66 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 329 TYR 0.008 0.001 TYR A 226 PHE 0.029 0.002 PHE A 12 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6890) covalent geometry : angle 0.67633 ( 9370) hydrogen bonds : bond 0.03301 ( 219) hydrogen bonds : angle 4.27066 ( 633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.146 Fit side-chains REVERT: A 306 ILE cc_start: 0.8677 (mm) cc_final: 0.8443 (mm) REVERT: A 324 PHE cc_start: 0.7373 (m-80) cc_final: 0.7131 (m-10) REVERT: B 150 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8046 (mt) REVERT: B 209 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8648 (tt) REVERT: B 273 MET cc_start: 0.7335 (ptp) cc_final: 0.6939 (ptm) REVERT: B 333 ASP cc_start: 0.8338 (m-30) cc_final: 0.8124 (m-30) REVERT: B 372 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6379 (mt) outliers start: 29 outliers final: 20 residues processed: 120 average time/residue: 0.0386 time to fit residues: 7.1074 Evaluate side-chains 112 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 414 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 0.0870 chunk 19 optimal weight: 0.3980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.179160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139177 restraints weight = 8862.754| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.51 r_work: 0.3518 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6890 Z= 0.140 Angle : 0.674 11.259 9370 Z= 0.331 Chirality : 0.047 0.161 1084 Planarity : 0.005 0.064 1214 Dihedral : 8.445 59.774 1068 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.70 % Favored : 90.96 % Rotamer: Outliers : 4.38 % Allowed : 22.60 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.24 (0.29), residues: 874 helix: 0.54 (0.29), residues: 350 sheet: -2.42 (0.56), residues: 82 loop : -1.65 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 387 TYR 0.007 0.001 TYR A 226 PHE 0.021 0.002 PHE A 12 HIS 0.002 0.001 HIS B 13 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6890) covalent geometry : angle 0.67370 ( 9370) hydrogen bonds : bond 0.03224 ( 219) hydrogen bonds : angle 4.20391 ( 633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.267 Fit side-chains REVERT: A 306 ILE cc_start: 0.8676 (mm) cc_final: 0.8457 (mm) REVERT: A 324 PHE cc_start: 0.7351 (m-80) cc_final: 0.7138 (m-10) REVERT: B 150 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8052 (mt) REVERT: B 273 MET cc_start: 0.7341 (ptp) cc_final: 0.6944 (ptm) REVERT: B 294 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7041 (mm) REVERT: B 333 ASP cc_start: 0.8315 (m-30) cc_final: 0.8082 (m-30) REVERT: B 372 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6407 (mt) REVERT: B 417 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8654 (mm) outliers start: 31 outliers final: 21 residues processed: 117 average time/residue: 0.0455 time to fit residues: 8.1357 Evaluate side-chains 113 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 51 optimal weight: 0.0050 chunk 15 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.177389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.138263 restraints weight = 8819.819| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.48 r_work: 0.3519 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6890 Z= 0.147 Angle : 0.684 11.297 9370 Z= 0.336 Chirality : 0.048 0.180 1084 Planarity : 0.005 0.064 1214 Dihedral : 8.313 58.076 1068 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.04 % Favored : 90.62 % Rotamer: Outliers : 3.95 % Allowed : 23.02 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.26 (0.29), residues: 874 helix: 0.53 (0.29), residues: 350 sheet: -2.40 (0.57), residues: 82 loop : -1.67 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 329 TYR 0.007 0.001 TYR A 226 PHE 0.023 0.002 PHE A 12 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6890) covalent geometry : angle 0.68411 ( 9370) hydrogen bonds : bond 0.03295 ( 219) hydrogen bonds : angle 4.25617 ( 633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.185 Fit side-chains REVERT: A 306 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8491 (mm) REVERT: A 324 PHE cc_start: 0.7355 (m-80) cc_final: 0.7154 (m-10) REVERT: B 150 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8052 (mt) REVERT: B 294 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7066 (mm) REVERT: B 333 ASP cc_start: 0.8327 (m-30) cc_final: 0.8079 (m-30) REVERT: B 372 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6418 (mt) REVERT: B 417 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8662 (mm) outliers start: 28 outliers final: 20 residues processed: 113 average time/residue: 0.0570 time to fit residues: 9.3481 Evaluate side-chains 113 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 0.0970 chunk 81 optimal weight: 0.0670 chunk 64 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 0.0870 overall best weight: 0.3094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN B 356 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.180718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141910 restraints weight = 8917.440| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.45 r_work: 0.3577 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6890 Z= 0.125 Angle : 0.669 11.848 9370 Z= 0.328 Chirality : 0.047 0.172 1084 Planarity : 0.005 0.064 1214 Dihedral : 8.070 56.745 1068 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.58 % Favored : 91.08 % Rotamer: Outliers : 3.53 % Allowed : 23.31 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.12 (0.29), residues: 874 helix: 0.66 (0.30), residues: 350 sheet: -2.30 (0.58), residues: 82 loop : -1.61 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 387 TYR 0.007 0.001 TYR B 226 PHE 0.035 0.002 PHE B 324 HIS 0.002 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 6890) covalent geometry : angle 0.66924 ( 9370) hydrogen bonds : bond 0.02910 ( 219) hydrogen bonds : angle 4.14958 ( 633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.253 Fit side-chains REVERT: A 91 MET cc_start: 0.8307 (mmt) cc_final: 0.7872 (mmt) REVERT: A 402 GLU cc_start: 0.7655 (tp30) cc_final: 0.7454 (tp30) REVERT: B 150 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8132 (mt) REVERT: B 273 MET cc_start: 0.7317 (ptp) cc_final: 0.6905 (ptm) REVERT: B 294 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.7008 (mm) REVERT: B 333 ASP cc_start: 0.8259 (m-30) cc_final: 0.8040 (m-30) REVERT: B 372 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6302 (mt) REVERT: B 417 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8609 (mm) outliers start: 25 outliers final: 17 residues processed: 113 average time/residue: 0.0615 time to fit residues: 10.2472 Evaluate side-chains 112 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 0.8980 chunk 81 optimal weight: 0.0980 chunk 37 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 76 optimal weight: 0.6980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.181108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.142475 restraints weight = 8821.070| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.42 r_work: 0.3576 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6890 Z= 0.128 Angle : 0.686 11.737 9370 Z= 0.335 Chirality : 0.048 0.194 1084 Planarity : 0.005 0.064 1214 Dihedral : 7.934 55.804 1066 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.58 % Favored : 91.08 % Rotamer: Outliers : 2.97 % Allowed : 23.87 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.12 (0.29), residues: 874 helix: 0.67 (0.29), residues: 350 sheet: -2.31 (0.58), residues: 82 loop : -1.62 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 329 TYR 0.006 0.001 TYR B 226 PHE 0.020 0.001 PHE A 12 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6890) covalent geometry : angle 0.68618 ( 9370) hydrogen bonds : bond 0.02934 ( 219) hydrogen bonds : angle 4.14221 ( 633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.212 Fit side-chains REVERT: B 150 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8199 (mt) REVERT: B 273 MET cc_start: 0.7290 (ptp) cc_final: 0.6876 (ptm) REVERT: B 294 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7063 (mm) REVERT: B 372 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6333 (mt) REVERT: B 417 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8604 (mm) outliers start: 21 outliers final: 15 residues processed: 107 average time/residue: 0.0509 time to fit residues: 8.1110 Evaluate side-chains 111 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 12 PHE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.0470 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.179435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.140445 restraints weight = 8858.783| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.44 r_work: 0.3557 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6890 Z= 0.147 Angle : 0.702 11.640 9370 Z= 0.345 Chirality : 0.049 0.201 1084 Planarity : 0.005 0.063 1214 Dihedral : 7.903 56.484 1064 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.92 % Favored : 90.73 % Rotamer: Outliers : 2.54 % Allowed : 25.00 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.22 (0.29), residues: 874 helix: 0.54 (0.29), residues: 350 sheet: -2.44 (0.57), residues: 82 loop : -1.62 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 387 TYR 0.006 0.001 TYR A 226 PHE 0.023 0.002 PHE A 12 HIS 0.003 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6890) covalent geometry : angle 0.70214 ( 9370) hydrogen bonds : bond 0.03248 ( 219) hydrogen bonds : angle 4.22230 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1553.76 seconds wall clock time: 27 minutes 18.15 seconds (1638.15 seconds total)