Starting phenix.real_space_refine on Thu Aug 6 02:32:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vqp_65272/08_2026/9vqp_65272_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vqp_65272/08_2026/9vqp_65272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vqp_65272/08_2026/9vqp_65272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vqp_65272/08_2026/9vqp_65272.map" model { file = "/net/cci-nas-00/data/ceres_data/9vqp_65272/08_2026/9vqp_65272_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vqp_65272/08_2026/9vqp_65272_neut.cif" } resolution = 2.9 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= 0.003 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 8383 2.51 5 N 2030 2.21 5 O 2201 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12732 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3080 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 10, 'TRANS': 375} Chain: "B" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3210 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Chain: "C" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3210 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Chain: "D" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3210 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {' VA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.20, per 1000 atoms: 0.17 Number of scatterers: 12732 At special positions: 0 Unit cell: (119.04, 116.25, 113.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 2201 8.00 N 2030 7.00 C 8383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 538.7 milliseconds 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 3 sheets defined 81.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 8 through 26 Processing helix chain 'A' and resid 39 through 66 Processing helix chain 'A' and resid 71 through 96 removed outlier: 5.140A pdb=" N MET A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N SER A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 116 removed outlier: 4.507A pdb=" N SER A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 160 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 179 through 214 Processing helix chain 'A' and resid 214 through 236 removed outlier: 3.693A pdb=" N ILE A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 292 removed outlier: 5.373A pdb=" N ILE A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N VAL A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 331 removed outlier: 3.523A pdb=" N TYR A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 344 through 355 removed outlier: 3.764A pdb=" N MET A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 391 Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 38 through 67 Processing helix chain 'B' and resid 70 through 97 removed outlier: 3.863A pdb=" N CYS B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 107 through 110 removed outlier: 4.351A pdb=" N GLN B 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 117 through 154 removed outlier: 3.683A pdb=" N THR B 154 " --> pdb=" O TRP B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 246 removed outlier: 4.338A pdb=" N LYS B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 3.681A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 359 Processing helix chain 'B' and resid 359 through 382 removed outlier: 3.721A pdb=" N LEU B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 429 removed outlier: 3.952A pdb=" N PHE B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B 411 " --> pdb=" O HIS B 407 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N MET B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 464 through 486 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 17 through 27 Processing helix chain 'C' and resid 38 through 67 Processing helix chain 'C' and resid 70 through 97 removed outlier: 3.801A pdb=" N CYS C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 117 through 154 removed outlier: 3.826A pdb=" N THR C 154 " --> pdb=" O TRP C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 246 removed outlier: 4.130A pdb=" N LYS C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 328 through 382 removed outlier: 5.364A pdb=" N ALA C 361 " --> pdb=" O ASP C 357 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 428 removed outlier: 3.586A pdb=" N PHE C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE C 411 " --> pdb=" O HIS C 407 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N MET C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU C 424 " --> pdb=" O SER C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 435 through 449 Processing helix chain 'C' and resid 464 through 486 Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 17 through 27 Processing helix chain 'D' and resid 38 through 67 Processing helix chain 'D' and resid 70 through 97 removed outlier: 3.808A pdb=" N CYS D 87 " --> pdb=" O PHE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 114 through 116 No H-bonds generated for 'chain 'D' and resid 114 through 116' Processing helix chain 'D' and resid 117 through 156 removed outlier: 3.681A pdb=" N THR D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE D 156 " --> pdb=" O THR D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 246 removed outlier: 4.286A pdb=" N LYS D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix removed outlier: 3.783A pdb=" N SER D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 382 removed outlier: 5.615A pdb=" N ALA D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 429 removed outlier: 3.559A pdb=" N PHE D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE D 411 " --> pdb=" O HIS D 407 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET D 423 " --> pdb=" O SER D 419 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 435 through 450 Processing helix chain 'D' and resid 464 through 486 Processing sheet with id=AA1, first strand: chain 'B' and resid 160 through 165 Processing sheet with id=AA2, first strand: chain 'C' and resid 160 through 165 Processing sheet with id=AA3, first strand: chain 'D' and resid 160 through 165 1060 hydrogen bonds defined for protein. 3147 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: 1.73 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1908 1.31 - 1.44: 3762 1.44 - 1.57: 7179 1.57 - 1.69: 0 1.69 - 1.82: 200 Bond restraints: 13049 Sorted by residual: bond pdb=" C20 VA A 501 " pdb=" O19 VA A 501 " ideal model delta sigma weight residual 1.328 1.410 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C12 VA A 501 " pdb=" C13 VA A 501 " ideal model delta sigma weight residual 1.497 1.560 -0.063 2.00e-02 2.50e+03 9.84e+00 bond pdb=" C10 VA A 501 " pdb=" C11 VA A 501 " ideal model delta sigma weight residual 1.497 1.552 -0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" CA THR A 93 " pdb=" CB THR A 93 " ideal model delta sigma weight residual 1.529 1.562 -0.033 1.64e-02 3.72e+03 4.09e+00 bond pdb=" C MET A 387 " pdb=" O MET A 387 " ideal model delta sigma weight residual 1.236 1.214 0.022 1.15e-02 7.56e+03 3.77e+00 ... (remaining 13044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.03: 17668 6.03 - 12.06: 9 12.06 - 18.09: 0 18.09 - 24.13: 1 24.13 - 30.16: 2 Bond angle restraints: 17680 Sorted by residual: angle pdb=" C11 VA A 501 " pdb=" C12 VA A 501 " pdb=" C13 VA A 501 " ideal model delta sigma weight residual 127.54 157.70 -30.16 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C10 VA A 501 " pdb=" C11 VA A 501 " pdb=" C12 VA A 501 " ideal model delta sigma weight residual 127.47 156.70 -29.23 3.00e+00 1.11e-01 9.49e+01 angle pdb=" C12 VA A 501 " pdb=" C13 VA A 501 " pdb=" C14 VA A 501 " ideal model delta sigma weight residual 112.54 132.23 -19.69 3.00e+00 1.11e-01 4.31e+01 angle pdb=" CB MET B 162 " pdb=" CG MET B 162 " pdb=" SD MET B 162 " ideal model delta sigma weight residual 112.70 124.13 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" N ASP B 466 " pdb=" CA ASP B 466 " pdb=" C ASP B 466 " ideal model delta sigma weight residual 111.07 107.50 3.57 1.07e+00 8.73e-01 1.11e+01 ... (remaining 17675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 6551 17.60 - 35.20: 828 35.20 - 52.80: 205 52.80 - 70.39: 26 70.39 - 87.99: 13 Dihedral angle restraints: 7623 sinusoidal: 2924 harmonic: 4699 Sorted by residual: dihedral pdb=" CA ILE A 266 " pdb=" C ILE A 266 " pdb=" N TYR A 267 " pdb=" CA TYR A 267 " ideal model delta harmonic sigma weight residual -180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB MET A 168 " pdb=" CG MET A 168 " pdb=" SD MET A 168 " pdb=" CE MET A 168 " ideal model delta sinusoidal sigma weight residual 60.00 119.80 -59.80 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS A 341 " pdb=" CB LYS A 341 " pdb=" CG LYS A 341 " pdb=" CD LYS A 341 " ideal model delta sinusoidal sigma weight residual 60.00 118.54 -58.54 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 7620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1519 0.033 - 0.067: 364 0.067 - 0.100: 137 0.100 - 0.133: 26 0.133 - 0.167: 2 Chirality restraints: 2048 Sorted by residual: chirality pdb=" CA ILE D 176 " pdb=" N ILE D 176 " pdb=" C ILE D 176 " pdb=" CB ILE D 176 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ILE B 176 " pdb=" N ILE B 176 " pdb=" C ILE B 176 " pdb=" CB ILE B 176 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE A 172 " pdb=" N ILE A 172 " pdb=" C ILE A 172 " pdb=" CB ILE A 172 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 2045 not shown) Planarity restraints: 2141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 215 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 216 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 424 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" CD GLU D 424 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU D 424 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU D 424 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 306 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C ILE A 306 " -0.027 2.00e-02 2.50e+03 pdb=" O ILE A 306 " 0.010 2.00e-02 2.50e+03 pdb=" N THR A 307 " 0.009 2.00e-02 2.50e+03 ... (remaining 2138 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 492 2.72 - 3.26: 14059 3.26 - 3.81: 23040 3.81 - 4.35: 25585 4.35 - 4.90: 45715 Nonbonded interactions: 108891 Sorted by model distance: nonbonded pdb=" N GLU A 342 " pdb=" OE1 GLU A 342 " model vdw 2.172 3.120 nonbonded pdb=" N GLU A 8 " pdb=" OE1 GLU A 8 " model vdw 2.193 3.120 nonbonded pdb=" OE1 GLN A 85 " pdb=" OG1 THR A 277 " model vdw 2.205 3.040 nonbonded pdb=" OE2 GLU B 70 " pdb=" ND2 ASN B 72 " model vdw 2.226 3.120 nonbonded pdb=" O ASP C 16 " pdb=" NH1 ARG C 133 " model vdw 2.263 3.120 ... (remaining 108886 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.200 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 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 : 0.003 0.082 13049 Z= 0.178 Angle : 0.660 30.157 17680 Z= 0.325 Chirality : 0.035 0.167 2048 Planarity : 0.004 0.053 2141 Dihedral : 16.364 87.992 4587 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.14 % Allowed : 23.02 % Favored : 76.83 % 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: 3.01 (0.20), residues: 1578 helix: 2.69 (0.14), residues: 1241 sheet: -0.22 (0.79), residues: 42 loop : -0.85 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 133 TYR 0.009 0.001 TYR B 427 PHE 0.017 0.001 PHE B 137 TRP 0.007 0.001 TRP A 39 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.18 (13049) covalent geometry : angle 0.66038 / 0.33 (17680) hydrogen bonds : bond 0.09726 / 6.82 ( 1060) hydrogen bonds : angle 4.51436 / 3.36 ( 3147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.324 Fit side-chains REVERT: A 205 ASP cc_start: 0.9121 (m-30) cc_final: 0.8716 (m-30) REVERT: A 261 GLN cc_start: 0.8780 (mt0) cc_final: 0.8304 (mt0) REVERT: B 210 MET cc_start: 0.8974 (mtp) cc_final: 0.8442 (mtm) REVERT: B 238 MET cc_start: 0.9174 (tpp) cc_final: 0.8677 (ttp) REVERT: B 367 MET cc_start: 0.9071 (tpp) cc_final: 0.8826 (tpp) REVERT: B 433 ASP cc_start: 0.9306 (m-30) cc_final: 0.9021 (m-30) REVERT: C 9 LYS cc_start: 0.8825 (pttt) cc_final: 0.8562 (mppt) REVERT: C 22 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7784 (mtm180) REVERT: C 41 MET cc_start: 0.8294 (tpp) cc_final: 0.7989 (mmm) REVERT: D 448 GLN cc_start: 0.8737 (mm110) cc_final: 0.8508 (mm-40) outliers start: 2 outliers final: 5 residues processed: 203 average time/residue: 0.5689 time to fit residues: 124.8730 Evaluate side-chains 177 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 172 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 203 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 163 GLN A 355 ASN B 106 ASN B 109 ASN B 232 GLN C 380 GLN C 484 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.075304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.060886 restraints weight = 28413.319| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.69 r_work: 0.2708 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13049 Z= 0.133 Angle : 0.503 7.288 17680 Z= 0.264 Chirality : 0.037 0.170 2048 Planarity : 0.004 0.041 2141 Dihedral : 4.630 48.281 1732 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.30 % Allowed : 21.01 % Favored : 76.69 % 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: 3.48 (0.20), residues: 1578 helix: 3.03 (0.14), residues: 1249 sheet: -0.46 (0.80), residues: 36 loop : -0.81 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 335 TYR 0.011 0.001 TYR A 114 PHE 0.020 0.001 PHE B 137 TRP 0.009 0.001 TRP A 39 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13049) covalent geometry : angle 0.50337 / 0.26 (17680) hydrogen bonds : bond 0.04776 / 3.17 ( 1060) hydrogen bonds : angle 3.43578 / 2.53 ( 3147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.366 Fit side-chains REVERT: A 33 ASP cc_start: 0.8779 (t0) cc_final: 0.8310 (t0) REVERT: A 69 ASP cc_start: 0.8022 (t0) cc_final: 0.7654 (t70) REVERT: A 70 LEU cc_start: 0.8553 (mt) cc_final: 0.7826 (tt) REVERT: A 176 ASP cc_start: 0.8122 (t0) cc_final: 0.7783 (t0) REVERT: A 205 ASP cc_start: 0.9163 (m-30) cc_final: 0.8691 (m-30) REVERT: A 238 ASP cc_start: 0.8460 (t0) cc_final: 0.7840 (t0) REVERT: A 245 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8543 (mtp) REVERT: B 123 ARG cc_start: 0.8827 (ttp80) cc_final: 0.8542 (ttp80) REVERT: B 232 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8708 (tp40) REVERT: B 367 MET cc_start: 0.9063 (tpp) cc_final: 0.8816 (tpp) REVERT: B 433 ASP cc_start: 0.9364 (m-30) cc_final: 0.8984 (m-30) REVERT: C 9 LYS cc_start: 0.8870 (pttt) cc_final: 0.8610 (mppt) REVERT: C 22 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7631 (mtm180) REVERT: C 41 MET cc_start: 0.8276 (tpp) cc_final: 0.8027 (mmm) outliers start: 32 outliers final: 8 residues processed: 218 average time/residue: 0.4608 time to fit residues: 109.5041 Evaluate side-chains 175 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 245 MET Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 124 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 163 GLN A 177 HIS A 374 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.062931 restraints weight = 28718.663| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.71 r_work: 0.2750 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13049 Z= 0.122 Angle : 0.484 8.087 17680 Z= 0.251 Chirality : 0.036 0.168 2048 Planarity : 0.003 0.037 2141 Dihedral : 4.298 51.305 1726 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.73 % Allowed : 20.65 % Favored : 76.62 % 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: 3.60 (0.20), residues: 1578 helix: 3.13 (0.13), residues: 1252 sheet: -0.56 (0.73), residues: 48 loop : -0.84 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 335 TYR 0.010 0.001 TYR A 114 PHE 0.015 0.001 PHE B 194 TRP 0.008 0.001 TRP A 40 HIS 0.006 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13049) covalent geometry : angle 0.48423 / 0.25 (17680) hydrogen bonds : bond 0.04487 / 2.99 ( 1060) hydrogen bonds : angle 3.31431 / 2.44 ( 3147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8623 (mt) cc_final: 0.7878 (tt) REVERT: A 100 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8758 (mtm) REVERT: A 205 ASP cc_start: 0.9162 (m-30) cc_final: 0.8592 (m-30) REVERT: A 207 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.7402 (t80) REVERT: A 238 ASP cc_start: 0.8405 (t0) cc_final: 0.7881 (t0) REVERT: A 291 MET cc_start: 0.8818 (mtm) cc_final: 0.8445 (mtp) REVERT: B 93 TYR cc_start: 0.9112 (t80) cc_final: 0.8811 (t80) REVERT: B 123 ARG cc_start: 0.8904 (ttp80) cc_final: 0.8613 (ttp80) REVERT: B 330 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: B 367 MET cc_start: 0.9078 (tpp) cc_final: 0.8870 (tpp) REVERT: B 433 ASP cc_start: 0.9335 (m-30) cc_final: 0.8968 (m-30) REVERT: C 9 LYS cc_start: 0.8806 (pttt) cc_final: 0.8578 (mppt) REVERT: C 22 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7769 (mtm180) REVERT: C 41 MET cc_start: 0.8296 (tpp) cc_final: 0.8075 (mmm) outliers start: 38 outliers final: 9 residues processed: 203 average time/residue: 0.4980 time to fit residues: 109.9376 Evaluate side-chains 183 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN B 56 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN D 448 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.073287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.059233 restraints weight = 29351.947| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.69 r_work: 0.2674 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13049 Z= 0.242 Angle : 0.534 7.604 17680 Z= 0.281 Chirality : 0.040 0.189 2048 Planarity : 0.003 0.036 2141 Dihedral : 4.244 43.845 1722 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.09 % Allowed : 20.58 % Favored : 76.33 % 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: 3.44 (0.20), residues: 1578 helix: 3.01 (0.13), residues: 1252 sheet: -0.60 (0.71), residues: 48 loop : -0.87 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 414 TYR 0.011 0.001 TYR A 256 PHE 0.019 0.002 PHE A 139 TRP 0.009 0.001 TRP A 40 HIS 0.004 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 (13049) covalent geometry : angle 0.53407 / 0.28 (17680) hydrogen bonds : bond 0.04859 / 3.23 ( 1060) hydrogen bonds : angle 3.41301 / 2.51 ( 3147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 167 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8740 (t80) cc_final: 0.8068 (t80) REVERT: A 70 LEU cc_start: 0.8651 (mt) cc_final: 0.7885 (tt) REVERT: A 85 GLN cc_start: 0.8693 (mt0) cc_final: 0.8410 (mt0) REVERT: A 100 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.8868 (mtm) REVERT: A 205 ASP cc_start: 0.9184 (m-30) cc_final: 0.8719 (m-30) REVERT: A 207 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.7414 (t80) REVERT: A 238 ASP cc_start: 0.8469 (t0) cc_final: 0.7939 (t70) REVERT: A 291 MET cc_start: 0.8896 (mtm) cc_final: 0.8500 (mtp) REVERT: B 41 MET cc_start: 0.8327 (mmt) cc_final: 0.8071 (mmm) REVERT: B 175 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: B 238 MET cc_start: 0.9235 (tpp) cc_final: 0.8801 (ttp) REVERT: B 330 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: B 433 ASP cc_start: 0.9381 (m-30) cc_final: 0.9041 (m-30) REVERT: C 9 LYS cc_start: 0.8817 (pttt) cc_final: 0.8612 (mppt) REVERT: C 22 ARG cc_start: 0.8274 (mtp85) cc_final: 0.7926 (mtm180) REVERT: C 41 MET cc_start: 0.8385 (tpp) cc_final: 0.8134 (mpp) REVERT: C 359 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: D 448 GLN cc_start: 0.9086 (tp40) cc_final: 0.8809 (tm-30) outliers start: 43 outliers final: 12 residues processed: 191 average time/residue: 0.5046 time to fit residues: 104.6718 Evaluate side-chains 175 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 94 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.076196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.062216 restraints weight = 28789.350| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.65 r_work: 0.2745 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13049 Z= 0.119 Angle : 0.490 9.423 17680 Z= 0.252 Chirality : 0.036 0.171 2048 Planarity : 0.003 0.038 2141 Dihedral : 4.113 45.662 1722 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.23 % Allowed : 21.51 % Favored : 76.26 % 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: 3.59 (0.20), residues: 1578 helix: 3.11 (0.13), residues: 1253 sheet: -0.66 (0.70), residues: 48 loop : -0.80 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 335 TYR 0.010 0.001 TYR A 114 PHE 0.017 0.001 PHE D 84 TRP 0.007 0.001 TRP A 39 HIS 0.004 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (13049) covalent geometry : angle 0.48991 / 0.25 (17680) hydrogen bonds : bond 0.04443 / 2.96 ( 1060) hydrogen bonds : angle 3.28904 / 2.43 ( 3147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.8634 (mt) cc_final: 0.7868 (tt) REVERT: A 85 GLN cc_start: 0.8650 (mt0) cc_final: 0.8342 (mt0) REVERT: A 100 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8849 (mtm) REVERT: A 207 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.7400 (t80) REVERT: A 231 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8755 (tm-30) REVERT: A 238 ASP cc_start: 0.8393 (t0) cc_final: 0.7883 (t0) REVERT: A 291 MET cc_start: 0.8779 (mtm) cc_final: 0.8355 (mtp) REVERT: A 385 MET cc_start: 0.8165 (tpp) cc_final: 0.7960 (tpt) REVERT: B 41 MET cc_start: 0.8316 (mmt) cc_final: 0.8068 (mmm) REVERT: B 123 ARG cc_start: 0.8883 (ttp80) cc_final: 0.8608 (ttp80) REVERT: B 330 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: B 333 MET cc_start: 0.9058 (tpt) cc_final: 0.8624 (tpp) REVERT: B 433 ASP cc_start: 0.9318 (m-30) cc_final: 0.8946 (m-30) REVERT: C 9 LYS cc_start: 0.8810 (pttt) cc_final: 0.8605 (mppt) REVERT: C 22 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7906 (mtm180) REVERT: C 41 MET cc_start: 0.8353 (tpp) cc_final: 0.8137 (mpp) REVERT: C 423 MET cc_start: 0.8918 (tmm) cc_final: 0.8537 (tpp) REVERT: D 448 GLN cc_start: 0.9071 (tp40) cc_final: 0.8835 (tm-30) outliers start: 31 outliers final: 12 residues processed: 202 average time/residue: 0.4848 time to fit residues: 106.4776 Evaluate side-chains 184 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain D residue 107 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.075346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.061510 restraints weight = 28852.992| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 2.63 r_work: 0.2731 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13049 Z= 0.142 Angle : 0.501 9.888 17680 Z= 0.258 Chirality : 0.037 0.189 2048 Planarity : 0.003 0.038 2141 Dihedral : 4.076 48.793 1722 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.73 % Allowed : 21.73 % Favored : 75.54 % 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: 3.60 (0.20), residues: 1578 helix: 3.13 (0.13), residues: 1252 sheet: -0.80 (0.68), residues: 48 loop : -0.80 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 335 TYR 0.022 0.001 TYR B 93 PHE 0.028 0.001 PHE B 137 TRP 0.007 0.001 TRP A 40 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (13049) covalent geometry : angle 0.50069 / 0.26 (17680) hydrogen bonds : bond 0.04447 / 2.96 ( 1060) hydrogen bonds : angle 3.29758 / 2.44 ( 3147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8739 (t80) cc_final: 0.7947 (t80) REVERT: A 70 LEU cc_start: 0.8651 (mt) cc_final: 0.7881 (tt) REVERT: A 100 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8676 (mtm) REVERT: A 205 ASP cc_start: 0.9199 (m-30) cc_final: 0.8722 (m-30) REVERT: A 207 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.7459 (t80) REVERT: A 238 ASP cc_start: 0.8400 (t0) cc_final: 0.7885 (t0) REVERT: A 291 MET cc_start: 0.8798 (mtm) cc_final: 0.8373 (mtp) REVERT: B 41 MET cc_start: 0.8329 (mmt) cc_final: 0.8076 (mmm) REVERT: B 123 ARG cc_start: 0.8882 (ttp80) cc_final: 0.8592 (ttp80) REVERT: B 165 ASP cc_start: 0.8290 (t0) cc_final: 0.7669 (p0) REVERT: B 175 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: B 330 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: B 433 ASP cc_start: 0.9335 (m-30) cc_final: 0.8968 (m-30) REVERT: C 22 ARG cc_start: 0.8298 (mtp85) cc_final: 0.7937 (mtm180) REVERT: C 41 MET cc_start: 0.8337 (tpp) cc_final: 0.8000 (mmt) REVERT: C 359 TYR cc_start: 0.8614 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: C 423 MET cc_start: 0.8890 (tmm) cc_final: 0.8600 (tpp) REVERT: D 480 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8296 (mmm) outliers start: 38 outliers final: 12 residues processed: 197 average time/residue: 0.5073 time to fit residues: 108.8270 Evaluate side-chains 183 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 131 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 374 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.075917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.062063 restraints weight = 28876.906| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.65 r_work: 0.2739 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13049 Z= 0.133 Angle : 0.532 11.442 17680 Z= 0.266 Chirality : 0.037 0.178 2048 Planarity : 0.003 0.038 2141 Dihedral : 4.065 49.408 1722 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.73 % Allowed : 22.37 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.20), residues: 1578 helix: 3.15 (0.13), residues: 1254 sheet: -0.78 (0.70), residues: 48 loop : -0.85 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 335 TYR 0.024 0.001 TYR B 93 PHE 0.021 0.001 PHE D 84 TRP 0.007 0.001 TRP A 39 HIS 0.003 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13049) covalent geometry : angle 0.53163 / 0.27 (17680) hydrogen bonds : bond 0.04392 / 2.93 ( 1060) hydrogen bonds : angle 3.28338 / 2.42 ( 3147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8750 (t80) cc_final: 0.7937 (t80) REVERT: A 70 LEU cc_start: 0.8655 (mt) cc_final: 0.7879 (tt) REVERT: A 100 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8746 (mtm) REVERT: A 131 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8792 (mp) REVERT: A 207 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.7488 (t80) REVERT: A 238 ASP cc_start: 0.8389 (t0) cc_final: 0.8054 (t0) REVERT: A 291 MET cc_start: 0.8811 (mtm) cc_final: 0.8383 (mtp) REVERT: B 41 MET cc_start: 0.8329 (mmt) cc_final: 0.8056 (mmm) REVERT: B 123 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8585 (ttp80) REVERT: B 175 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: B 238 MET cc_start: 0.9157 (tpp) cc_final: 0.8867 (ttt) REVERT: B 330 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: B 333 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8638 (tpp) REVERT: B 433 ASP cc_start: 0.9325 (m-30) cc_final: 0.8946 (m-30) REVERT: C 22 ARG cc_start: 0.8293 (mtp85) cc_final: 0.7928 (mtm180) REVERT: C 41 MET cc_start: 0.8337 (tpp) cc_final: 0.8001 (mmt) REVERT: C 359 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8168 (m-80) outliers start: 38 outliers final: 17 residues processed: 199 average time/residue: 0.5005 time to fit residues: 108.5101 Evaluate side-chains 193 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 207 TYR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain D residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 89 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 163 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.075790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.062139 restraints weight = 28623.726| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.62 r_work: 0.2743 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13049 Z= 0.137 Angle : 0.538 12.818 17680 Z= 0.270 Chirality : 0.037 0.199 2048 Planarity : 0.003 0.038 2141 Dihedral : 4.053 50.134 1722 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.73 % Allowed : 23.53 % Favored : 73.74 % 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: 3.63 (0.20), residues: 1578 helix: 3.16 (0.13), residues: 1254 sheet: -0.68 (0.72), residues: 48 loop : -0.88 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.023 0.001 TYR B 93 PHE 0.021 0.001 PHE C 84 TRP 0.007 0.001 TRP A 39 HIS 0.004 0.001 HIS D 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13049) covalent geometry : angle 0.53802 / 0.27 (17680) hydrogen bonds : bond 0.04390 / 2.92 ( 1060) hydrogen bonds : angle 3.28986 / 2.43 ( 3147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.418 Fit side-chains REVERT: A 26 PHE cc_start: 0.8752 (t80) cc_final: 0.7914 (t80) REVERT: A 70 LEU cc_start: 0.8663 (mt) cc_final: 0.7877 (tt) REVERT: A 131 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8737 (mp) REVERT: A 206 MET cc_start: 0.9082 (mmm) cc_final: 0.8815 (mmp) REVERT: A 238 ASP cc_start: 0.8353 (t0) cc_final: 0.8029 (t0) REVERT: A 291 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8403 (mtp) REVERT: A 387 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8358 (mtp) REVERT: B 41 MET cc_start: 0.8316 (mmt) cc_final: 0.8057 (mmm) REVERT: B 123 ARG cc_start: 0.8851 (ttp80) cc_final: 0.8561 (ttp80) REVERT: B 165 ASP cc_start: 0.8257 (t0) cc_final: 0.7677 (p0) REVERT: B 175 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: B 193 MET cc_start: 0.8347 (ppp) cc_final: 0.8086 (ppp) REVERT: B 238 MET cc_start: 0.9107 (tpp) cc_final: 0.8614 (ttp) REVERT: B 330 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: B 333 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8635 (tpp) REVERT: B 433 ASP cc_start: 0.9304 (m-30) cc_final: 0.8921 (m-30) REVERT: C 22 ARG cc_start: 0.8259 (mtp85) cc_final: 0.7894 (mtm180) REVERT: C 41 MET cc_start: 0.8337 (tpp) cc_final: 0.8001 (mmt) REVERT: C 243 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8760 (mp0) REVERT: C 359 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: D 150 TRP cc_start: 0.5284 (t-100) cc_final: 0.4356 (t60) REVERT: D 480 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8311 (mmm) outliers start: 38 outliers final: 18 residues processed: 201 average time/residue: 0.5003 time to fit residues: 109.9208 Evaluate side-chains 198 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.0470 chunk 16 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 163 GLN A 374 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN D 450 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.075716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.062088 restraints weight = 28967.693| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.64 r_work: 0.2737 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13049 Z= 0.146 Angle : 0.573 13.463 17680 Z= 0.282 Chirality : 0.038 0.209 2048 Planarity : 0.003 0.038 2141 Dihedral : 4.070 50.782 1722 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.73 % Allowed : 23.74 % Favored : 73.53 % 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: 3.56 (0.20), residues: 1578 helix: 3.11 (0.13), residues: 1256 sheet: -0.77 (0.72), residues: 48 loop : -0.91 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.012 0.001 TYR C 204 PHE 0.022 0.001 PHE C 84 TRP 0.007 0.001 TRP A 39 HIS 0.004 0.001 HIS D 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (13049) covalent geometry : angle 0.57322 / 0.28 (17680) hydrogen bonds : bond 0.04398 / 2.93 ( 1060) hydrogen bonds : angle 3.30209 / 2.44 ( 3147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.453 Fit side-chains REVERT: A 26 PHE cc_start: 0.8771 (t80) cc_final: 0.7946 (t80) REVERT: A 70 LEU cc_start: 0.8681 (mt) cc_final: 0.7893 (tt) REVERT: A 131 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8739 (mp) REVERT: A 206 MET cc_start: 0.9100 (mmm) cc_final: 0.8835 (mmp) REVERT: A 238 ASP cc_start: 0.8293 (t0) cc_final: 0.7982 (t0) REVERT: A 291 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8448 (mtp) REVERT: B 41 MET cc_start: 0.8316 (mmt) cc_final: 0.8052 (mmm) REVERT: B 165 ASP cc_start: 0.8235 (t0) cc_final: 0.7616 (p0) REVERT: B 175 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: B 238 MET cc_start: 0.9061 (tpp) cc_final: 0.8784 (ttt) REVERT: B 330 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7349 (tt0) REVERT: B 333 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8650 (tpp) REVERT: B 433 ASP cc_start: 0.9338 (m-30) cc_final: 0.8991 (m-30) REVERT: C 22 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7940 (mtm180) REVERT: C 41 MET cc_start: 0.8344 (tpp) cc_final: 0.8022 (mmt) REVERT: C 359 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.8167 (m-80) REVERT: C 451 LYS cc_start: 0.9180 (mmmm) cc_final: 0.8725 (mmmt) REVERT: D 150 TRP cc_start: 0.5346 (t-100) cc_final: 0.4409 (t60) REVERT: D 480 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8353 (mmm) outliers start: 38 outliers final: 17 residues processed: 196 average time/residue: 0.5032 time to fit residues: 107.6200 Evaluate side-chains 190 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 163 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.076519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.062099 restraints weight = 28700.234| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.73 r_work: 0.2758 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13049 Z= 0.132 Angle : 0.588 13.806 17680 Z= 0.287 Chirality : 0.037 0.200 2048 Planarity : 0.003 0.038 2141 Dihedral : 4.088 50.226 1722 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.09 % Allowed : 24.82 % Favored : 73.09 % 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: 3.60 (0.20), residues: 1578 helix: 3.12 (0.13), residues: 1250 sheet: -0.85 (0.72), residues: 48 loop : -0.75 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 123 TYR 0.010 0.001 TYR A 300 PHE 0.020 0.001 PHE C 84 TRP 0.006 0.001 TRP A 39 HIS 0.004 0.001 HIS D 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13049) covalent geometry : angle 0.58760 / 0.29 (17680) hydrogen bonds : bond 0.04351 / 2.89 ( 1060) hydrogen bonds : angle 3.30622 / 2.44 ( 3147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.315 Fit side-chains REVERT: A 70 LEU cc_start: 0.8690 (mt) cc_final: 0.7883 (tt) REVERT: A 131 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8680 (mp) REVERT: A 206 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8816 (mmp) REVERT: A 238 ASP cc_start: 0.8268 (t0) cc_final: 0.7999 (t0) REVERT: A 291 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8407 (mtp) REVERT: B 41 MET cc_start: 0.8304 (mmt) cc_final: 0.8040 (mmm) REVERT: B 165 ASP cc_start: 0.8213 (t0) cc_final: 0.7567 (p0) REVERT: B 175 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8345 (tm-30) REVERT: B 238 MET cc_start: 0.8984 (tpp) cc_final: 0.8774 (ttt) REVERT: B 330 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: B 333 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8584 (tpp) REVERT: B 335 ARG cc_start: 0.8620 (ttp80) cc_final: 0.8387 (ttp80) REVERT: B 433 ASP cc_start: 0.9324 (m-30) cc_final: 0.8949 (m-30) REVERT: C 22 ARG cc_start: 0.8268 (mtp85) cc_final: 0.7887 (mtm180) REVERT: C 41 MET cc_start: 0.8319 (tpp) cc_final: 0.7999 (mmt) REVERT: C 243 GLU cc_start: 0.8857 (mp0) cc_final: 0.8236 (mp0) REVERT: C 359 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: C 451 LYS cc_start: 0.9167 (mmmm) cc_final: 0.8713 (mmmt) REVERT: D 150 TRP cc_start: 0.5257 (t-100) cc_final: 0.4327 (t60) REVERT: D 343 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8828 (mm-30) outliers start: 29 outliers final: 14 residues processed: 197 average time/residue: 0.4915 time to fit residues: 105.3668 Evaluate side-chains 193 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 417 GLU Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 203 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 66 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN A 163 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.077039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.062820 restraints weight = 28669.585| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.75 r_work: 0.2773 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13049 Z= 0.125 Angle : 0.580 13.713 17680 Z= 0.282 Chirality : 0.037 0.205 2048 Planarity : 0.003 0.038 2141 Dihedral : 4.059 49.115 1722 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.09 % Allowed : 24.96 % Favored : 72.95 % 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: 3.58 (0.20), residues: 1578 helix: 3.12 (0.13), residues: 1255 sheet: -0.87 (0.71), residues: 48 loop : -0.88 (0.34), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 335 TYR 0.013 0.001 TYR B 93 PHE 0.023 0.001 PHE A 290 TRP 0.006 0.001 TRP A 39 HIS 0.005 0.001 HIS D 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (13049) covalent geometry : angle 0.58048 / 0.28 (17680) hydrogen bonds : bond 0.04284 / 2.85 ( 1060) hydrogen bonds : angle 3.28726 / 2.42 ( 3147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2941.94 seconds wall clock time: 51 minutes 20.57 seconds (3080.57 seconds total)