Starting phenix.real_space_refine on Wed Aug 5 04:46:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8isz_35701/08_2026/8isz_35701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8isz_35701/08_2026/8isz_35701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8isz_35701/08_2026/8isz_35701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8isz_35701/08_2026/8isz_35701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8isz_35701/08_2026/8isz_35701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8isz_35701/08_2026/8isz_35701.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8isz_35701/08_2026/8isz_35701.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8isz_35701/08_2026/8isz_35701.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.014 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: 5 Type Number sf(0) Gaussians P 45 5.49 5 S 23 5.16 5 C 5301 2.51 5 N 1418 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 8461 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3771 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 438} Chain breaks: 1 Chain: "B" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3754 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 435} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "C" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 454 Classifications: {'RNAv2': 21} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2} Link IDs: {'rna2p': 18, 'rna3p': 2} Time building chain proxies: 1.72, per 1000 atoms: 0.20 Number of scatterers: 8461 At special positions: 0 Unit cell: (83.2, 91.52, 141.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 45 15.00 O 1674 8.00 N 1418 7.00 C 5301 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: 0.86 Conformation dependent library (CDL) restraints added in 240.8 milliseconds 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1742 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 37.4% alpha, 13.3% beta 6 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 62 removed outlier: 3.565A pdb=" N LYS A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 98 through 106 removed outlier: 3.991A pdb=" N PHE A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 removed outlier: 3.752A pdb=" N ASP A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 removed outlier: 3.581A pdb=" N TYR A 148 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.711A pdb=" N GLN A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 248 through 264 removed outlier: 4.148A pdb=" N LEU A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.687A pdb=" N TRP A 370 " --> pdb=" O ASN A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 Processing helix chain 'A' and resid 477 through 490 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'B' and resid 14 through 28 removed outlier: 3.726A pdb=" N THR B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.567A pdb=" N LEU B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 147 through 158 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 257 through 280 Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.518A pdb=" N ASP B 303 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 368 removed outlier: 3.592A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 384 Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.518A pdb=" N GLU B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU B 438 " --> pdb=" O ASN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 6 removed outlier: 6.621A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA A 361 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 304 " --> pdb=" O TYR A 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.800A pdb=" N GLN A 18 " --> pdb=" O PHE A 14 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.134A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP A 139 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU A 224 " --> pdb=" O TRP A 139 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL A 141 " --> pdb=" O LEU A 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 397 through 398 removed outlier: 3.512A pdb=" N GLU B 169 " --> pdb=" O GLY B 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 426 Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.518A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.701A pdb=" N MET B 336 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS B 328 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 334 " --> pdb=" O LYS B 328 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 401 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 403 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 210 Processing sheet with id=AA9, first strand: chain 'B' and resid 283 through 286 283 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.46 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1522 1.33 - 1.45: 2415 1.45 - 1.57: 4698 1.57 - 1.69: 88 1.69 - 1.81: 35 Bond restraints: 8758 Sorted by residual: bond pdb=" C6 DA D 32 " pdb=" N1 DA D 32 " ideal model delta sigma weight residual 1.351 1.324 0.027 7.00e-03 2.04e+04 1.51e+01 bond pdb=" C3' DT D 38 " pdb=" C2' DT D 38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" N9 DA D 31 " pdb=" C4 DA D 31 " ideal model delta sigma weight residual 1.374 1.356 0.018 6.00e-03 2.78e+04 9.43e+00 bond pdb=" C6 DA D 36 " pdb=" N1 DA D 36 " ideal model delta sigma weight residual 1.351 1.331 0.020 7.00e-03 2.04e+04 8.35e+00 bond pdb=" N3 DA D 31 " pdb=" C4 DA D 31 " ideal model delta sigma weight residual 1.344 1.327 0.017 6.00e-03 2.78e+04 7.83e+00 ... (remaining 8753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 11655 2.40 - 4.81: 306 4.81 - 7.21: 63 7.21 - 9.62: 10 9.62 - 12.02: 6 Bond angle restraints: 12040 Sorted by residual: angle pdb=" C3' U C 9 " pdb=" O3' U C 9 " pdb=" P A C 10 " ideal model delta sigma weight residual 119.70 126.05 -6.35 1.20e+00 6.94e-01 2.80e+01 angle pdb=" O4' DT D 42 " pdb=" C4' DT D 42 " pdb=" C3' DT D 42 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT D 42 " pdb=" C4 DT D 42 " pdb=" O4 DT D 42 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT D 35 " pdb=" C4 DT D 35 " pdb=" O4 DT D 35 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT D 26 " pdb=" C4 DT D 26 " pdb=" O4 DT D 26 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 12035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 4724 34.50 - 69.01: 410 69.01 - 103.51: 29 103.51 - 138.01: 0 138.01 - 172.51: 1 Dihedral angle restraints: 5164 sinusoidal: 2469 harmonic: 2695 Sorted by residual: dihedral pdb=" C4' A C 7 " pdb=" C3' A C 7 " pdb=" C2' A C 7 " pdb=" C1' A C 7 " ideal model delta sinusoidal sigma weight residual 36.34 -46.07 82.41 1 3.10e+00 1.04e-01 8.67e+02 dihedral pdb=" C4' G C 11 " pdb=" C3' G C 11 " pdb=" C2' G C 11 " pdb=" C1' G C 11 " ideal model delta sinusoidal sigma weight residual 36.35 -43.22 79.57 1 3.10e+00 1.04e-01 8.18e+02 dihedral pdb=" C4' U C 14 " pdb=" C3' U C 14 " pdb=" C2' U C 14 " pdb=" C1' U C 14 " ideal model delta sinusoidal sigma weight residual 36.34 -42.19 78.54 1 3.10e+00 1.04e-01 8.00e+02 ... (remaining 5161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 1252 0.159 - 0.318: 58 0.318 - 0.476: 4 0.476 - 0.635: 0 0.635 - 0.794: 5 Chirality restraints: 1319 Sorted by residual: chirality pdb=" P A C 10 " pdb=" OP1 A C 10 " pdb=" OP2 A C 10 " pdb=" O5' A C 10 " both_signs ideal model delta sigma weight residual True 2.17 -2.97 -0.79 2.00e-01 2.50e+01 1.58e+01 chirality pdb=" P A C 7 " pdb=" OP1 A C 7 " pdb=" OP2 A C 7 " pdb=" O5' A C 7 " both_signs ideal model delta sigma weight residual True 2.17 -2.87 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" P G C 11 " pdb=" OP1 G C 11 " pdb=" OP2 G C 11 " pdb=" O5' G C 11 " both_signs ideal model delta sigma weight residual True 2.17 -2.85 -0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 1316 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 331 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A 332 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 322 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO A 323 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 323 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 323 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U C 14 " 0.012 2.00e-02 2.50e+03 1.53e-02 5.29e+00 pdb=" N1 U C 14 " 0.002 2.00e-02 2.50e+03 pdb=" C2 U C 14 " -0.030 2.00e-02 2.50e+03 pdb=" O2 U C 14 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U C 14 " 0.031 2.00e-02 2.50e+03 pdb=" C4 U C 14 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U C 14 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U C 14 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U C 14 " -0.007 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 60 2.51 - 3.11: 5821 3.11 - 3.71: 14313 3.71 - 4.30: 18986 4.30 - 4.90: 29453 Nonbonded interactions: 68633 Sorted by model distance: nonbonded pdb=" C2 DA D 31 " pdb=" N1 G C 15 " model vdw 1.918 3.420 nonbonded pdb=" OD1 ASP B 44 " pdb=" OG SER B 47 " model vdw 2.233 3.040 nonbonded pdb=" O ASN A 34 " pdb=" OH TYR A 261 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 104 " pdb=" OD1 ASP B 106 " model vdw 2.248 3.040 nonbonded pdb=" O PRO B 182 " pdb=" OG1 THR B 243 " model vdw 2.256 3.040 ... (remaining 68628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.280 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8758 Z= 0.272 Angle : 0.953 12.022 12040 Z= 0.505 Chirality : 0.084 0.794 1319 Planarity : 0.006 0.082 1372 Dihedral : 22.238 172.514 3422 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.12 % Allowed : 31.95 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -2.32 (0.25), residues: 909 helix: -0.54 (0.28), residues: 306 sheet: -1.04 (0.46), residues: 130 loop : -2.43 (0.24), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 113 TYR 0.021 0.001 TYR A 285 PHE 0.013 0.001 PHE A 403 TRP 0.012 0.002 TRP B 369 HIS 0.005 0.001 HIS B 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.27 ( 8758) covalent geometry : angle 0.95344 / 0.50 (12040) hydrogen bonds : bond 0.19088 / 12.50 ( 298) hydrogen bonds : angle 8.33041 / 5.92 ( 828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 380 ASN cc_start: 0.7139 (p0) cc_final: 0.6823 (p0) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.0865 time to fit residues: 18.9800 Evaluate side-chains 135 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0570 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.0570 chunk 74 optimal weight: 3.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 129 ASN ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.139432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.112314 restraints weight = 23150.821| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 5.75 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8758 Z= 0.269 Angle : 1.431 22.820 12040 Z= 0.614 Chirality : 0.160 1.949 1319 Planarity : 0.006 0.064 1372 Dihedral : 19.517 172.732 1517 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.78 % Allowed : 30.49 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.83 (0.26), residues: 909 helix: -0.06 (0.29), residues: 309 sheet: -1.16 (0.43), residues: 132 loop : -2.07 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 407 TYR 0.020 0.002 TYR A 285 PHE 0.025 0.002 PHE A 503 TRP 0.028 0.002 TRP A 421 HIS 0.006 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.27 ( 8758) covalent geometry : angle 1.43083 / 0.61 (12040) hydrogen bonds : bond 0.05619 / 3.87 ( 298) hydrogen bonds : angle 6.57968 / 4.64 ( 828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8364 (tp30) cc_final: 0.8083 (tp30) REVERT: A 422 THR cc_start: 0.8630 (p) cc_final: 0.8416 (p) REVERT: B 250 ARG cc_start: 0.8399 (ptt-90) cc_final: 0.8177 (ptt-90) REVERT: B 392 TYR cc_start: 0.8616 (t80) cc_final: 0.8297 (t80) REVERT: B 450 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8426 (tm-30) outliers start: 31 outliers final: 14 residues processed: 165 average time/residue: 0.0905 time to fit residues: 19.7612 Evaluate side-chains 147 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 48 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** 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 = 0.4207 r_free = 0.4207 target = 0.139169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.112120 restraints weight = 23301.949| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 5.71 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8758 Z= 0.203 Angle : 1.030 19.462 12040 Z= 0.466 Chirality : 0.106 1.591 1319 Planarity : 0.005 0.060 1372 Dihedral : 18.768 170.171 1517 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.78 % Allowed : 30.37 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.60 (0.26), residues: 909 helix: 0.17 (0.29), residues: 312 sheet: -1.01 (0.44), residues: 120 loop : -1.97 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 382 TYR 0.020 0.001 TYR A 285 PHE 0.021 0.001 PHE B 60 TRP 0.035 0.002 TRP A 421 HIS 0.005 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 ( 8758) covalent geometry : angle 1.02989 / 0.47 (12040) hydrogen bonds : bond 0.06083 / 4.18 ( 298) hydrogen bonds : angle 6.10294 / 4.29 ( 828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8360 (tp30) cc_final: 0.8079 (tp30) REVERT: A 267 LYS cc_start: 0.8813 (mtmt) cc_final: 0.8437 (mtmt) REVERT: A 286 LYS cc_start: 0.9136 (tppt) cc_final: 0.8928 (tppt) REVERT: A 397 TYR cc_start: 0.8046 (m-80) cc_final: 0.7508 (m-10) REVERT: B 189 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8119 (ptm-80) REVERT: B 336 MET cc_start: 0.7691 (ppp) cc_final: 0.7290 (ppp) REVERT: B 342 ILE cc_start: 0.9091 (mm) cc_final: 0.8742 (mt) REVERT: B 400 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8431 (mmmm) REVERT: B 450 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8365 (tm-30) outliers start: 31 outliers final: 20 residues processed: 164 average time/residue: 0.0780 time to fit residues: 17.3062 Evaluate side-chains 154 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 400 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 86 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS A 329 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.129802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.102107 restraints weight = 23564.622| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 5.62 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 8758 Z= 0.345 Angle : 1.028 17.626 12040 Z= 0.496 Chirality : 0.088 1.280 1319 Planarity : 0.006 0.059 1372 Dihedral : 18.979 157.421 1517 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.73 % Allowed : 30.12 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.82 (0.27), residues: 909 helix: 0.05 (0.29), residues: 318 sheet: -1.61 (0.40), residues: 149 loop : -2.01 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 152 TYR 0.021 0.003 TYR B 293 PHE 0.021 0.002 PHE A 53 TRP 0.019 0.003 TRP B 369 HIS 0.006 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00750 / 0.34 ( 8758) covalent geometry : angle 1.02791 / 0.50 (12040) hydrogen bonds : bond 0.05854 / 3.89 ( 298) hydrogen bonds : angle 6.06225 / 4.26 ( 828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.7884 (p0) cc_final: 0.7455 (p0) REVERT: A 75 PHE cc_start: 0.8397 (t80) cc_final: 0.7946 (t80) REVERT: A 267 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8593 (mtmt) REVERT: A 286 LYS cc_start: 0.9214 (tppt) cc_final: 0.8953 (tppt) REVERT: A 397 TYR cc_start: 0.8345 (m-80) cc_final: 0.7801 (m-10) REVERT: B 54 ARG cc_start: 0.9115 (ptp-110) cc_final: 0.8892 (ptp-110) REVERT: B 189 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8290 (ptm-80) REVERT: B 231 GLU cc_start: 0.9191 (mp0) cc_final: 0.8957 (mp0) REVERT: B 392 TYR cc_start: 0.8632 (t80) cc_final: 0.8378 (t80) REVERT: B 400 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8366 (mmmm) REVERT: B 450 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8540 (tm-30) outliers start: 47 outliers final: 32 residues processed: 170 average time/residue: 0.0920 time to fit residues: 20.6148 Evaluate side-chains 169 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 33 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.134693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.107179 restraints weight = 22932.115| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 5.61 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8758 Z= 0.174 Angle : 0.926 17.225 12040 Z= 0.439 Chirality : 0.079 0.893 1319 Planarity : 0.005 0.057 1372 Dihedral : 18.881 163.597 1517 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.39 % Allowed : 31.46 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.27), residues: 909 helix: 0.22 (0.29), residues: 314 sheet: -1.51 (0.40), residues: 155 loop : -1.89 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 201 TYR 0.014 0.001 TYR A 262 PHE 0.035 0.002 PHE A 78 TRP 0.012 0.002 TRP B 369 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 8758) covalent geometry : angle 0.92560 / 0.44 (12040) hydrogen bonds : bond 0.05159 / 3.41 ( 298) hydrogen bonds : angle 5.84135 / 4.10 ( 828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.7905 (p0) cc_final: 0.7656 (p0) REVERT: A 74 MET cc_start: 0.7163 (mpp) cc_final: 0.6662 (mpp) REVERT: A 75 PHE cc_start: 0.8377 (t80) cc_final: 0.8003 (t80) REVERT: A 95 GLU cc_start: 0.7999 (mp0) cc_final: 0.7550 (mp0) REVERT: A 267 LYS cc_start: 0.8866 (mtmt) cc_final: 0.8612 (mtmt) REVERT: A 286 LYS cc_start: 0.9191 (tppt) cc_final: 0.8883 (tppt) REVERT: A 380 ASN cc_start: 0.9323 (p0) cc_final: 0.8759 (p0) REVERT: A 397 TYR cc_start: 0.8242 (m-80) cc_final: 0.7668 (m-10) REVERT: A 444 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8376 (tt0) REVERT: B 1 MET cc_start: 0.9410 (ppp) cc_final: 0.9121 (ppp) REVERT: B 55 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8902 (mm-30) REVERT: B 179 ILE cc_start: 0.9477 (mm) cc_final: 0.9076 (mp) REVERT: B 231 GLU cc_start: 0.9173 (mp0) cc_final: 0.8934 (mp0) REVERT: B 296 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 307 LYS cc_start: 0.9377 (mmmm) cc_final: 0.9121 (mmmm) REVERT: B 336 MET cc_start: 0.7676 (ppp) cc_final: 0.7278 (ppp) REVERT: B 342 ILE cc_start: 0.9139 (mm) cc_final: 0.8789 (mt) REVERT: B 392 TYR cc_start: 0.8612 (t80) cc_final: 0.8367 (t80) REVERT: B 400 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8335 (mmmm) REVERT: B 450 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8466 (tm-30) outliers start: 36 outliers final: 25 residues processed: 165 average time/residue: 0.0775 time to fit residues: 17.3486 Evaluate side-chains 160 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 329 HIS Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 57 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.0370 chunk 10 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** 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 = 0.4180 r_free = 0.4180 target = 0.136368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.109232 restraints weight = 23160.923| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 5.59 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8758 Z= 0.161 Angle : 0.893 16.906 12040 Z= 0.419 Chirality : 0.073 0.714 1319 Planarity : 0.005 0.057 1372 Dihedral : 18.940 170.375 1517 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.02 % Allowed : 31.46 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.45 (0.28), residues: 909 helix: 0.35 (0.30), residues: 319 sheet: -1.45 (0.40), residues: 154 loop : -1.77 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 275 TYR 0.025 0.001 TYR B 330 PHE 0.029 0.002 PHE B 60 TRP 0.029 0.002 TRP A 421 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 8758) covalent geometry : angle 0.89319 / 0.42 (12040) hydrogen bonds : bond 0.04840 / 3.17 ( 298) hydrogen bonds : angle 5.64783 / 3.94 ( 828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.7894 (p0) cc_final: 0.7530 (p0) REVERT: A 74 MET cc_start: 0.7019 (mpp) cc_final: 0.6782 (mpp) REVERT: A 75 PHE cc_start: 0.8347 (t80) cc_final: 0.7899 (t80) REVERT: A 95 GLU cc_start: 0.8005 (mp0) cc_final: 0.7542 (mp0) REVERT: A 203 ASP cc_start: 0.6260 (OUTLIER) cc_final: 0.5785 (t70) REVERT: A 267 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8569 (mtmt) REVERT: A 286 LYS cc_start: 0.9133 (tppt) cc_final: 0.8787 (tppt) REVERT: A 333 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8613 (ptmm) REVERT: A 380 ASN cc_start: 0.9311 (p0) cc_final: 0.8754 (p0) REVERT: A 397 TYR cc_start: 0.8160 (m-80) cc_final: 0.7738 (m-10) REVERT: A 457 LYS cc_start: 0.7521 (mppt) cc_final: 0.7309 (mtmm) REVERT: B 160 HIS cc_start: 0.9292 (t-90) cc_final: 0.8985 (t-90) REVERT: B 179 ILE cc_start: 0.9498 (mm) cc_final: 0.9067 (mp) REVERT: B 189 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8224 (ptm-80) REVERT: B 231 GLU cc_start: 0.9184 (mp0) cc_final: 0.8940 (mp0) REVERT: B 284 GLU cc_start: 0.7384 (pp20) cc_final: 0.7137 (pp20) REVERT: B 301 GLU cc_start: 0.9286 (tp30) cc_final: 0.9000 (tp30) REVERT: B 307 LYS cc_start: 0.9381 (mmmm) cc_final: 0.9109 (mmmm) REVERT: B 342 ILE cc_start: 0.9118 (mm) cc_final: 0.8730 (mt) REVERT: B 346 ASP cc_start: 0.9033 (m-30) cc_final: 0.8730 (t70) REVERT: B 392 TYR cc_start: 0.8660 (t80) cc_final: 0.8401 (t80) REVERT: B 400 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8286 (mmmm) REVERT: B 450 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8365 (tm-30) outliers start: 33 outliers final: 23 residues processed: 168 average time/residue: 0.0845 time to fit residues: 19.1379 Evaluate side-chains 161 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.3980 chunk 78 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 84 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.135828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.108268 restraints weight = 23017.104| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 5.63 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8758 Z= 0.168 Angle : 0.878 16.984 12040 Z= 0.418 Chirality : 0.070 0.714 1319 Planarity : 0.005 0.052 1372 Dihedral : 18.846 174.897 1517 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.63 % Allowed : 31.34 % Favored : 64.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.34 (0.28), residues: 909 helix: 0.42 (0.30), residues: 318 sheet: -1.37 (0.41), residues: 154 loop : -1.68 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 382 TYR 0.020 0.001 TYR B 330 PHE 0.022 0.001 PHE A 78 TRP 0.014 0.002 TRP A 421 HIS 0.002 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 8758) covalent geometry : angle 0.87761 / 0.42 (12040) hydrogen bonds : bond 0.04777 / 3.06 ( 298) hydrogen bonds : angle 5.61293 / 3.92 ( 828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7543 (pm20) cc_final: 0.7271 (pm20) REVERT: A 69 ASN cc_start: 0.7952 (p0) cc_final: 0.7591 (p0) REVERT: A 74 MET cc_start: 0.7021 (mpp) cc_final: 0.6756 (mpp) REVERT: A 75 PHE cc_start: 0.8160 (t80) cc_final: 0.7711 (t80) REVERT: A 267 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8616 (mtmt) REVERT: A 286 LYS cc_start: 0.9175 (tppt) cc_final: 0.8834 (tppt) REVERT: A 333 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8654 (ptmm) REVERT: A 336 LYS cc_start: 0.8628 (pttm) cc_final: 0.8140 (pttm) REVERT: A 380 ASN cc_start: 0.9332 (p0) cc_final: 0.8816 (p0) REVERT: A 397 TYR cc_start: 0.8157 (m-80) cc_final: 0.7777 (m-10) REVERT: A 457 LYS cc_start: 0.7575 (mppt) cc_final: 0.7364 (mtmm) REVERT: B 179 ILE cc_start: 0.9539 (mm) cc_final: 0.9317 (mp) REVERT: B 189 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8230 (ptm-80) REVERT: B 296 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8331 (tm-30) REVERT: B 307 LYS cc_start: 0.9406 (mmmm) cc_final: 0.9158 (mmmm) REVERT: B 392 TYR cc_start: 0.8637 (t80) cc_final: 0.8373 (t80) REVERT: B 400 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8282 (mmmm) outliers start: 38 outliers final: 26 residues processed: 169 average time/residue: 0.0858 time to fit residues: 19.6836 Evaluate side-chains 168 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS A 302 GLN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.134746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.107441 restraints weight = 22883.821| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 5.52 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8758 Z= 0.183 Angle : 0.890 17.260 12040 Z= 0.422 Chirality : 0.068 0.717 1319 Planarity : 0.005 0.050 1372 Dihedral : 18.881 177.664 1517 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.76 % Allowed : 31.71 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.37 (0.28), residues: 909 helix: 0.47 (0.30), residues: 316 sheet: -1.24 (0.42), residues: 142 loop : -1.83 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 382 TYR 0.035 0.001 TYR B 330 PHE 0.022 0.002 PHE B 198 TRP 0.014 0.002 TRP A 421 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 8758) covalent geometry : angle 0.89001 / 0.42 (12040) hydrogen bonds : bond 0.04772 / 3.04 ( 298) hydrogen bonds : angle 5.56661 / 3.88 ( 828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7564 (pm20) cc_final: 0.7282 (pm20) REVERT: A 69 ASN cc_start: 0.7941 (p0) cc_final: 0.7582 (p0) REVERT: A 74 MET cc_start: 0.7081 (mpp) cc_final: 0.6795 (mpp) REVERT: A 75 PHE cc_start: 0.8232 (t80) cc_final: 0.7828 (t80) REVERT: A 95 GLU cc_start: 0.8027 (mp0) cc_final: 0.7549 (mp0) REVERT: A 203 ASP cc_start: 0.6251 (OUTLIER) cc_final: 0.5760 (t70) REVERT: A 267 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8624 (mtmt) REVERT: A 286 LYS cc_start: 0.9179 (tppt) cc_final: 0.8870 (tppt) REVERT: A 353 TYR cc_start: 0.8834 (p90) cc_final: 0.8631 (p90) REVERT: A 380 ASN cc_start: 0.9337 (p0) cc_final: 0.8789 (p0) REVERT: A 397 TYR cc_start: 0.8165 (m-80) cc_final: 0.7685 (m-10) REVERT: B 54 ARG cc_start: 0.9212 (ptp-170) cc_final: 0.8911 (ptp-110) REVERT: B 179 ILE cc_start: 0.9516 (mm) cc_final: 0.9313 (mp) REVERT: B 189 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8249 (ptm-80) REVERT: B 296 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 301 GLU cc_start: 0.9312 (tp30) cc_final: 0.9080 (tp30) REVERT: B 307 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9195 (mtmm) REVERT: B 392 TYR cc_start: 0.8647 (t80) cc_final: 0.8372 (t80) REVERT: B 400 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8279 (mmmm) REVERT: B 450 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8368 (tm-30) outliers start: 39 outliers final: 29 residues processed: 168 average time/residue: 0.0974 time to fit residues: 21.9597 Evaluate side-chains 172 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 15 optimal weight: 0.0270 chunk 13 optimal weight: 0.8980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN A 217 HIS A 302 GLN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.136213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.109176 restraints weight = 23121.965| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 5.58 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8758 Z= 0.159 Angle : 0.878 17.335 12040 Z= 0.416 Chirality : 0.065 0.696 1319 Planarity : 0.005 0.052 1372 Dihedral : 18.919 179.789 1517 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.90 % Allowed : 31.71 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.40 (0.28), residues: 909 helix: 0.38 (0.29), residues: 321 sheet: -1.14 (0.42), residues: 146 loop : -1.86 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 382 TYR 0.028 0.001 TYR B 330 PHE 0.018 0.001 PHE B 198 TRP 0.018 0.002 TRP A 421 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 8758) covalent geometry : angle 0.87826 / 0.42 (12040) hydrogen bonds : bond 0.04758 / 3.01 ( 298) hydrogen bonds : angle 5.58954 / 3.90 ( 828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7420 (pm20) cc_final: 0.7142 (pm20) REVERT: A 69 ASN cc_start: 0.7960 (p0) cc_final: 0.7592 (p0) REVERT: A 75 PHE cc_start: 0.8240 (t80) cc_final: 0.7875 (t80) REVERT: A 95 GLU cc_start: 0.8013 (mp0) cc_final: 0.7521 (mp0) REVERT: A 267 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8574 (mtmt) REVERT: A 286 LYS cc_start: 0.9112 (tppt) cc_final: 0.8796 (tppt) REVERT: A 333 LYS cc_start: 0.9085 (mmmt) cc_final: 0.8604 (ptmm) REVERT: A 380 ASN cc_start: 0.9336 (p0) cc_final: 0.8841 (p0) REVERT: A 397 TYR cc_start: 0.8177 (m-80) cc_final: 0.7818 (m-10) REVERT: A 457 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7506 (mptt) REVERT: B 287 MET cc_start: 0.6614 (tpt) cc_final: 0.6124 (tpt) REVERT: B 296 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8273 (tm-30) REVERT: B 301 GLU cc_start: 0.9341 (tp30) cc_final: 0.9080 (tp30) REVERT: B 307 LYS cc_start: 0.9418 (mmmm) cc_final: 0.9190 (mtmm) REVERT: B 314 GLN cc_start: 0.8634 (pp30) cc_final: 0.7972 (pp30) REVERT: B 392 TYR cc_start: 0.8661 (t80) cc_final: 0.8402 (t80) REVERT: B 400 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8285 (mmmm) outliers start: 32 outliers final: 27 residues processed: 164 average time/residue: 0.0901 time to fit residues: 20.0475 Evaluate side-chains 169 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 81 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 91 optimal weight: 30.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.131499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.104172 restraints weight = 22874.577| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 5.44 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 8758 Z= 0.243 Angle : 0.924 17.581 12040 Z= 0.444 Chirality : 0.066 0.696 1319 Planarity : 0.006 0.051 1372 Dihedral : 19.030 177.996 1517 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.90 % Allowed : 31.71 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.53 (0.27), residues: 909 helix: 0.31 (0.29), residues: 321 sheet: -1.23 (0.42), residues: 141 loop : -1.96 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 407 TYR 0.026 0.002 TYR B 330 PHE 0.018 0.002 PHE A 482 TRP 0.018 0.002 TRP B 368 HIS 0.004 0.001 HIS B 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.24 ( 8758) covalent geometry : angle 0.92450 / 0.44 (12040) hydrogen bonds : bond 0.05120 / 3.21 ( 298) hydrogen bonds : angle 5.57345 / 3.92 ( 828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7682 (pm20) cc_final: 0.7392 (pm20) REVERT: A 69 ASN cc_start: 0.7915 (p0) cc_final: 0.7525 (p0) REVERT: A 75 PHE cc_start: 0.8409 (t80) cc_final: 0.8099 (t80) REVERT: A 95 GLU cc_start: 0.8074 (mp0) cc_final: 0.7844 (mp0) REVERT: A 203 ASP cc_start: 0.6493 (OUTLIER) cc_final: 0.6031 (t70) REVERT: A 222 GLN cc_start: 0.8259 (tt0) cc_final: 0.7982 (tt0) REVERT: A 267 LYS cc_start: 0.8889 (mtmt) cc_final: 0.8632 (mtmt) REVERT: A 286 LYS cc_start: 0.9262 (tppt) cc_final: 0.9024 (tppt) REVERT: A 303 MET cc_start: 0.7170 (mmm) cc_final: 0.6899 (tpp) REVERT: A 333 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8730 (tmmt) REVERT: A 380 ASN cc_start: 0.9343 (p0) cc_final: 0.8947 (p0) REVERT: A 397 TYR cc_start: 0.8218 (m-80) cc_final: 0.7753 (m-10) REVERT: A 457 LYS cc_start: 0.7700 (mtmm) cc_final: 0.7421 (mptt) REVERT: B 54 ARG cc_start: 0.9240 (ptp-170) cc_final: 0.8953 (ptp-110) REVERT: B 189 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8156 (ptm-80) REVERT: B 287 MET cc_start: 0.7335 (tpt) cc_final: 0.7002 (tpt) REVERT: B 296 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 392 TYR cc_start: 0.8656 (t80) cc_final: 0.8330 (t80) REVERT: B 400 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8253 (mmmm) outliers start: 32 outliers final: 24 residues processed: 165 average time/residue: 0.0810 time to fit residues: 18.1081 Evaluate side-chains 168 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 116 ASN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 357 GLN ** 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 = 0.4148 r_free = 0.4148 target = 0.133472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.106379 restraints weight = 22986.174| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 5.52 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8758 Z= 0.178 Angle : 0.904 17.399 12040 Z= 0.434 Chirality : 0.064 0.661 1319 Planarity : 0.005 0.050 1372 Dihedral : 18.987 176.384 1517 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.29 % Allowed : 33.29 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.58 (0.27), residues: 909 helix: 0.28 (0.29), residues: 313 sheet: -1.31 (0.42), residues: 142 loop : -1.94 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 407 TYR 0.026 0.001 TYR B 330 PHE 0.018 0.002 PHE B 198 TRP 0.015 0.002 TRP A 421 HIS 0.004 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 8758) covalent geometry : angle 0.90426 / 0.43 (12040) hydrogen bonds : bond 0.04943 / 3.11 ( 298) hydrogen bonds : angle 5.55489 / 3.91 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1616.08 seconds wall clock time: 28 minutes 31.78 seconds (1711.78 seconds total)