Starting phenix.real_space_refine on Thu Jul 2 12:01:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8isz_35701/07_2026/8isz_35701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8isz_35701/07_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_35701/07_2026/8isz_35701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8isz_35701/07_2026/8isz_35701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8isz_35701/07_2026/8isz_35701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8isz_35701/07_2026/8isz_35701.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8isz_35701/07_2026/8isz_35701.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8isz_35701/07_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-dev-6108/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: {'RNA': 21} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2} Link IDs: {'rna2p': 18, 'rna3p': 2} Time building chain proxies: 1.81, per 1000 atoms: 0.21 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: 0.74 Conformation dependent library (CDL) restraints added in 445.6 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: 1.02 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: 1.41 Time building geometry restraints manager: 1.02 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: 11767 2.40 - 4.81: 218 4.81 - 7.21: 38 7.21 - 9.62: 11 9.62 - 12.02: 6 Bond angle restraints: 12040 Sorted by residual: angle pdb=" O3' U C 9 " pdb=" C3' U C 9 " pdb=" C2' U C 9 " ideal model delta sigma weight residual 109.50 118.15 -8.65 1.50e+00 4.44e-01 3.32e+01 angle pdb=" C3' A C 7 " pdb=" C2' A C 7 " pdb=" C1' A C 7 " ideal model delta sigma weight residual 101.50 97.02 4.48 1.00e+00 1.00e+00 2.00e+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 ... (remaining 12035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 4828 35.40 - 70.81: 324 70.81 - 106.21: 10 106.21 - 141.61: 0 141.61 - 177.01: 2 Dihedral angle restraints: 5164 sinusoidal: 2469 harmonic: 2695 Sorted by residual: dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual 232.00 54.99 177.01 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' A C 10 " pdb=" C2' A C 10 " pdb=" C1' A C 10 " pdb=" C3' A C 10 " ideal model delta sinusoidal sigma weight residual 25.00 -21.92 46.92 1 8.00e+00 1.56e-02 4.75e+01 dihedral pdb=" C4' A C 10 " pdb=" C3' A C 10 " pdb=" C2' A C 10 " pdb=" C1' A C 10 " ideal model delta sinusoidal sigma weight residual 36.00 -7.55 43.55 1 8.00e+00 1.56e-02 4.13e+01 ... (remaining 5161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1258 0.111 - 0.223: 55 0.223 - 0.334: 0 0.334 - 0.446: 4 0.446 - 0.557: 2 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 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.76e+00 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 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.25e+00 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 2.41 -2.85 -0.44 2.00e-01 2.50e+01 4.92e+00 ... (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: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.910 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.210 ------------------------------------------------------------------------------- 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= 0.270 Angle : 0.866 12.022 12040 Z= 0.491 Chirality : 0.058 0.557 1319 Planarity : 0.006 0.082 1372 Dihedral : 20.300 177.013 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 0.00407 / 0.27 ( 8758) covalent geometry : angle 0.86606 / 0.49 (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 : 0.328 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: 0.1065 time to fit residues: 23.1789 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 : 0.312 ------------------------------------------------------------------------------- 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: 0.0000 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: 1.6108 ------------------------------------------------------------------------------- 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 = 0.4216 r_free = 0.4216 target = 0.139468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.112291 restraints weight = 22947.095| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 5.71 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8758 Z= 0.198 Angle : 0.760 11.500 12040 Z= 0.400 Chirality : 0.047 0.242 1319 Planarity : 0.005 0.064 1372 Dihedral : 17.930 178.172 1517 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.66 % Allowed : 30.49 % Favored : 65.85 % 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: -1.81 (0.26), residues: 909 helix: -0.03 (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 0.024 0.002 TYR A 285 PHE 0.028 0.002 PHE A 503 TRP 0.020 0.002 TRP A 421 HIS 0.006 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 ( 8758) covalent geometry : angle 0.75968 / 0.40 (12040) hydrogen bonds : bond 0.05489 / 3.69 ( 298) hydrogen bonds : angle 6.54769 / 4.61 ( 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 173 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8365 (tp30) cc_final: 0.8078 (tp30) REVERT: A 331 LYS cc_start: 0.9071 (tptp) cc_final: 0.8708 (tptp) REVERT: A 333 LYS cc_start: 0.9085 (mmmt) cc_final: 0.8870 (mmmt) REVERT: A 422 THR cc_start: 0.8657 (p) cc_final: 0.8453 (p) REVERT: B 189 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7753 (ptm-80) REVERT: B 250 ARG cc_start: 0.8413 (ptt-90) cc_final: 0.8185 (ptt-90) REVERT: B 392 TYR cc_start: 0.8606 (t80) cc_final: 0.8290 (t80) REVERT: B 450 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8425 (tm-30) outliers start: 30 outliers final: 14 residues processed: 163 average time/residue: 0.0986 time to fit residues: 21.2770 Evaluate side-chains 148 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 113 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 189 ARG 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: 7.9990 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4181 r_free = 0.4181 target = 0.137170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.109845 restraints weight = 22969.642| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 5.67 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8758 Z= 0.182 Angle : 0.724 11.175 12040 Z= 0.381 Chirality : 0.047 0.201 1319 Planarity : 0.005 0.058 1372 Dihedral : 17.955 177.500 1517 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.90 % Allowed : 30.49 % Favored : 65.61 % 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: -1.59 (0.26), residues: 909 helix: 0.16 (0.29), residues: 312 sheet: -0.95 (0.45), residues: 120 loop : -1.98 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 382 TYR 0.021 0.002 TYR A 285 PHE 0.021 0.001 PHE B 60 TRP 0.021 0.002 TRP A 421 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 ( 8758) covalent geometry : angle 0.72424 / 0.38 (12040) hydrogen bonds : bond 0.04969 / 3.35 ( 298) hydrogen bonds : angle 6.10893 / 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 177 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 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: 0.8400 (tp30) cc_final: 0.8126 (tp30) REVERT: A 267 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8482 (mtmt) REVERT: A 286 LYS cc_start: 0.9201 (tppt) cc_final: 0.8989 (tppt) REVERT: A 397 TYR cc_start: 0.8103 (m-80) cc_final: 0.7583 (m-10) REVERT: B 160 HIS cc_start: 0.9239 (t70) cc_final: 0.9027 (t-90) REVERT: B 336 MET cc_start: 0.7704 (ppp) cc_final: 0.7271 (ppp) REVERT: B 342 ILE cc_start: 0.9093 (mm) cc_final: 0.8723 (mt) REVERT: B 400 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8420 (mmmm) REVERT: B 450 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8455 (tm-30) outliers start: 32 outliers final: 20 residues processed: 163 average time/residue: 0.0810 time to fit residues: 17.8887 Evaluate side-chains 154 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 279 CYS 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 153 LEU Chi-restraints excluded: chain B residue 184 GLU 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 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: 0.9990 chunk 28 optimal weight: 0.2980 chunk 5 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS A 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.136755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.109724 restraints weight = 23124.847| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 5.58 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8758 Z= 0.159 Angle : 0.706 12.239 12040 Z= 0.371 Chirality : 0.046 0.186 1319 Planarity : 0.005 0.058 1372 Dihedral : 17.910 174.747 1517 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.15 % Allowed : 30.85 % Favored : 65.00 % 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: -1.54 (0.27), residues: 909 helix: 0.32 (0.30), residues: 312 sheet: -1.22 (0.41), residues: 133 loop : -1.94 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 382 TYR 0.018 0.001 TYR B 392 PHE 0.014 0.001 PHE A 403 TRP 0.034 0.002 TRP A 421 HIS 0.002 0.001 HIS B 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 8758) covalent geometry : angle 0.70645 / 0.37 (12040) hydrogen bonds : bond 0.04484 / 3.09 ( 298) hydrogen bonds : angle 5.79853 / 4.05 ( 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 179 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.213 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: 0.7983 (p0) cc_final: 0.7708 (p0) REVERT: A 74 MET cc_start: 0.7065 (mpp) cc_final: 0.6748 (mpp) REVERT: A 75 PHE cc_start: 0.8172 (t80) cc_final: 0.7623 (t80) REVERT: A 99 GLU cc_start: 0.8405 (tp30) cc_final: 0.8129 (tp30) REVERT: A 146 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: A 267 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8551 (mtmt) REVERT: A 336 LYS cc_start: 0.8579 (pttm) cc_final: 0.8319 (pttm) REVERT: A 355 LYS cc_start: 0.8635 (tppt) cc_final: 0.8004 (tppt) REVERT: A 380 ASN cc_start: 0.9336 (p0) cc_final: 0.8870 (p0) REVERT: A 397 TYR cc_start: 0.8257 (m-80) cc_final: 0.7821 (m-10) REVERT: B 160 HIS cc_start: 0.9250 (t70) cc_final: 0.9038 (t-90) REVERT: B 179 ILE cc_start: 0.9475 (mm) cc_final: 0.9064 (mp) REVERT: B 287 MET cc_start: 0.5465 (tpt) cc_final: 0.4687 (tpt) REVERT: B 296 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8211 (tm-30) REVERT: B 342 ILE cc_start: 0.9121 (mm) cc_final: 0.8770 (mt) REVERT: B 392 TYR cc_start: 0.8639 (t80) cc_final: 0.8361 (t80) REVERT: B 400 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8338 (mmmm) REVERT: B 450 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8445 (tm-30) outliers start: 34 outliers final: 20 residues processed: 164 average time/residue: 0.0904 time to fit residues: 20.0631 Evaluate side-chains 158 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL 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 307 ASN 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 11 THR Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 46 TRP Chi-restraints excluded: chain B residue 66 THR 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 400 LYS 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: 0.0670 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4188 r_free = 0.4188 target = 0.137302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.110243 restraints weight = 22891.061| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 5.56 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8758 Z= 0.141 Angle : 0.702 12.670 12040 Z= 0.366 Chirality : 0.046 0.184 1319 Planarity : 0.005 0.053 1372 Dihedral : 17.859 173.378 1517 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.39 % Allowed : 31.10 % Favored : 64.51 % 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: -1.46 (0.27), residues: 909 helix: 0.33 (0.30), residues: 318 sheet: -1.19 (0.41), residues: 143 loop : -1.88 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 275 TYR 0.021 0.001 TYR B 293 PHE 0.018 0.001 PHE B 223 TRP 0.014 0.001 TRP A 421 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 8758) covalent geometry : angle 0.70234 / 0.37 (12040) hydrogen bonds : bond 0.04271 / 2.95 ( 298) hydrogen bonds : angle 5.70726 / 3.99 ( 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 181 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.7972 (p0) cc_final: 0.7565 (p0) REVERT: A 75 PHE cc_start: 0.8214 (t80) cc_final: 0.7699 (t80) REVERT: A 99 GLU cc_start: 0.8400 (tp30) cc_final: 0.8120 (tp30) REVERT: A 267 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8555 (mtmt) REVERT: A 275 ARG cc_start: 0.8846 (mmm160) cc_final: 0.8590 (mmm160) REVERT: A 355 LYS cc_start: 0.8697 (tppt) cc_final: 0.7893 (tppt) REVERT: A 380 ASN cc_start: 0.9339 (p0) cc_final: 0.8723 (p0) REVERT: A 397 TYR cc_start: 0.8191 (m-80) cc_final: 0.7774 (m-10) REVERT: A 444 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8387 (tt0) REVERT: A 465 LEU cc_start: 0.6492 (mp) cc_final: 0.6282 (mp) REVERT: B 179 ILE cc_start: 0.9480 (mm) cc_final: 0.9131 (mp) REVERT: B 189 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8267 (ptm-80) REVERT: B 250 ARG cc_start: 0.8479 (ptt-90) cc_final: 0.8220 (ptt-90) REVERT: B 287 MET cc_start: 0.5794 (tpt) cc_final: 0.5185 (tpt) REVERT: B 342 ILE cc_start: 0.9069 (mm) cc_final: 0.8698 (mt) REVERT: B 400 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8348 (mmmm) REVERT: B 450 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8384 (tm-30) outliers start: 36 outliers final: 23 residues processed: 167 average time/residue: 0.0976 time to fit residues: 21.5960 Evaluate side-chains 166 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 92 VAL 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 307 ASN 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 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 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: 9.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS A 222 GLN ** 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 = 0.4100 r_free = 0.4100 target = 0.129846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.102827 restraints weight = 23295.150| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 5.55 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 8758 Z= 0.283 Angle : 0.800 10.913 12040 Z= 0.420 Chirality : 0.048 0.201 1319 Planarity : 0.006 0.054 1372 Dihedral : 18.012 173.686 1517 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 5.61 % Allowed : 30.12 % Favored : 64.27 % 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: -1.64 (0.27), residues: 909 helix: 0.28 (0.29), residues: 308 sheet: -1.53 (0.39), residues: 155 loop : -1.92 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 382 TYR 0.027 0.002 TYR B 293 PHE 0.016 0.002 PHE A 403 TRP 0.019 0.002 TRP B 369 HIS 0.005 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.28 ( 8758) covalent geometry : angle 0.80014 / 0.42 (12040) hydrogen bonds : bond 0.04958 / 3.34 ( 298) hydrogen bonds : angle 5.76781 / 4.03 ( 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 187 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7842 (pm20) cc_final: 0.7552 (pm20) REVERT: A 67 HIS cc_start: 0.8692 (t70) cc_final: 0.7923 (t70) REVERT: A 69 ASN cc_start: 0.8004 (p0) cc_final: 0.7751 (p0) REVERT: A 74 MET cc_start: 0.7339 (mpp) cc_final: 0.6952 (mpp) REVERT: A 75 PHE cc_start: 0.8308 (t80) cc_final: 0.7869 (t80) REVERT: A 95 GLU cc_start: 0.8090 (mp0) cc_final: 0.7873 (mp0) REVERT: A 267 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8652 (mtmt) REVERT: A 275 ARG cc_start: 0.8949 (mmm160) cc_final: 0.8522 (mmm160) REVERT: A 355 LYS cc_start: 0.8945 (tppt) cc_final: 0.8188 (tppt) REVERT: A 380 ASN cc_start: 0.9373 (p0) cc_final: 0.8712 (p0) REVERT: A 397 TYR cc_start: 0.8282 (m-80) cc_final: 0.7788 (m-10) REVERT: A 444 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8440 (tt0) REVERT: B 179 ILE cc_start: 0.9482 (mm) cc_final: 0.9072 (mp) REVERT: B 189 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8303 (ptm-80) REVERT: B 287 MET cc_start: 0.6223 (tpt) cc_final: 0.5297 (tpt) REVERT: B 392 TYR cc_start: 0.8638 (t80) cc_final: 0.8311 (t80) REVERT: B 400 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8232 (mmmm) REVERT: B 450 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8468 (tm-30) outliers start: 46 outliers final: 31 residues processed: 171 average time/residue: 0.1107 time to fit residues: 25.1145 Evaluate side-chains 168 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 222 GLN 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 288 ILE Chi-restraints excluded: chain A residue 307 ASN 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 437 VAL Chi-restraints excluded: chain B residue 14 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.0870 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 GLN ** 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 = 0.4140 r_free = 0.4140 target = 0.133858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.106841 restraints weight = 22807.276| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 5.50 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8758 Z= 0.154 Angle : 0.760 13.249 12040 Z= 0.392 Chirality : 0.046 0.178 1319 Planarity : 0.005 0.053 1372 Dihedral : 18.053 172.411 1517 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.15 % Allowed : 32.32 % 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: -1.58 (0.27), residues: 909 helix: 0.27 (0.29), residues: 317 sheet: -1.51 (0.40), residues: 154 loop : -1.88 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 54 TYR 0.020 0.001 TYR B 293 PHE 0.031 0.002 PHE A 78 TRP 0.013 0.002 TRP B 369 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 8758) covalent geometry : angle 0.76037 / 0.39 (12040) hydrogen bonds : bond 0.04311 / 2.99 ( 298) hydrogen bonds : angle 5.79059 / 4.03 ( 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 180 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 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: A 3 GLU cc_start: 0.7657 (pm20) cc_final: 0.7371 (pm20) REVERT: A 69 ASN cc_start: 0.7935 (p0) cc_final: 0.7570 (p0) REVERT: A 74 MET cc_start: 0.7087 (mpp) cc_final: 0.6864 (mpp) REVERT: A 75 PHE cc_start: 0.8349 (t80) cc_final: 0.7925 (t80) REVERT: A 95 GLU cc_start: 0.8043 (mp0) cc_final: 0.7558 (mp0) REVERT: A 267 LYS cc_start: 0.8903 (mtmt) cc_final: 0.8630 (mtmt) REVERT: A 275 ARG cc_start: 0.8865 (mmm160) cc_final: 0.8585 (mmm160) REVERT: A 285 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.8288 (t80) REVERT: A 353 TYR cc_start: 0.8763 (p90) cc_final: 0.8556 (p90) REVERT: A 355 LYS cc_start: 0.8879 (tppt) cc_final: 0.8153 (tppt) REVERT: A 380 ASN cc_start: 0.9321 (p0) cc_final: 0.8823 (p0) REVERT: A 397 TYR cc_start: 0.8238 (m-80) cc_final: 0.7810 (m-10) REVERT: A 444 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8388 (tt0) REVERT: B 55 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9012 (mp0) REVERT: B 179 ILE cc_start: 0.9491 (mm) cc_final: 0.9131 (mp) REVERT: B 189 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8326 (ptm-80) REVERT: B 301 GLU cc_start: 0.9294 (tp30) cc_final: 0.9025 (tp30) REVERT: B 307 LYS cc_start: 0.9387 (mmmm) cc_final: 0.9177 (mmmm) REVERT: B 342 ILE cc_start: 0.9164 (mm) cc_final: 0.8769 (mt) REVERT: B 392 TYR cc_start: 0.8667 (t80) cc_final: 0.8340 (t80) REVERT: B 400 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8141 (mmmm) REVERT: B 450 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8398 (tm-30) outliers start: 34 outliers final: 23 residues processed: 166 average time/residue: 0.1138 time to fit residues: 25.0298 Evaluate side-chains 165 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL 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 271 LEU Chi-restraints excluded: chain A residue 285 TYR 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 14 ASP 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 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: 5.9990 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS A 222 GLN ** 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 = 0.4136 r_free = 0.4136 target = 0.133527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.106444 restraints weight = 22884.192| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 5.51 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8758 Z= 0.171 Angle : 0.772 13.056 12040 Z= 0.397 Chirality : 0.047 0.271 1319 Planarity : 0.005 0.051 1372 Dihedral : 18.042 171.848 1517 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.27 % Allowed : 32.56 % Favored : 63.17 % 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: -1.52 (0.27), residues: 909 helix: 0.35 (0.29), residues: 316 sheet: -1.46 (0.41), residues: 154 loop : -1.87 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 481 TYR 0.023 0.002 TYR B 330 PHE 0.037 0.001 PHE A 78 TRP 0.013 0.002 TRP B 369 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 8758) covalent geometry : angle 0.77232 / 0.40 (12040) hydrogen bonds : bond 0.04223 / 2.90 ( 298) hydrogen bonds : angle 5.78036 / 4.04 ( 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 180 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7601 (pm20) cc_final: 0.7316 (pm20) REVERT: A 69 ASN cc_start: 0.7916 (p0) cc_final: 0.7563 (p0) REVERT: A 74 MET cc_start: 0.7110 (mpp) cc_final: 0.6884 (mpp) REVERT: A 75 PHE cc_start: 0.8393 (t80) cc_final: 0.7949 (t80) REVERT: A 203 ASP cc_start: 0.6279 (OUTLIER) cc_final: 0.5809 (t70) REVERT: A 222 GLN cc_start: 0.6801 (OUTLIER) cc_final: 0.6433 (tm-30) REVERT: A 267 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8619 (mtmt) REVERT: A 275 ARG cc_start: 0.8908 (mmm160) cc_final: 0.8615 (mmm160) REVERT: A 285 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8293 (t80) REVERT: A 303 MET cc_start: 0.7004 (mmm) cc_final: 0.6774 (tpp) REVERT: A 355 LYS cc_start: 0.8878 (tppt) cc_final: 0.8175 (tppt) REVERT: A 380 ASN cc_start: 0.9326 (p0) cc_final: 0.8851 (p0) REVERT: A 397 TYR cc_start: 0.8223 (m-80) cc_final: 0.7826 (m-10) REVERT: A 457 LYS cc_start: 0.7624 (mtmm) cc_final: 0.7364 (mppt) REVERT: B 55 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9009 (mp0) REVERT: B 179 ILE cc_start: 0.9523 (mm) cc_final: 0.9291 (mp) REVERT: B 189 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8273 (ptm-80) REVERT: B 307 LYS cc_start: 0.9394 (mmmm) cc_final: 0.9184 (mmmm) REVERT: B 392 TYR cc_start: 0.8645 (t80) cc_final: 0.8305 (t80) REVERT: B 400 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8130 (mmmm) REVERT: B 450 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8399 (tm-30) outliers start: 35 outliers final: 24 residues processed: 168 average time/residue: 0.1104 time to fit residues: 24.6399 Evaluate side-chains 169 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 222 GLN 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 285 TYR 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 66 THR 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 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 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: 0.6980 chunk 28 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** A 222 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 = 0.4132 r_free = 0.4132 target = 0.133194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.106045 restraints weight = 23006.784| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 5.54 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8758 Z= 0.181 Angle : 0.793 13.198 12040 Z= 0.405 Chirality : 0.047 0.208 1319 Planarity : 0.005 0.051 1372 Dihedral : 18.017 171.300 1517 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.02 % Allowed : 33.05 % Favored : 62.93 % 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: -1.55 (0.27), residues: 909 helix: 0.30 (0.29), residues: 318 sheet: -1.43 (0.41), residues: 154 loop : -1.89 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 54 TYR 0.043 0.002 TYR B 330 PHE 0.031 0.002 PHE A 78 TRP 0.013 0.002 TRP B 369 HIS 0.003 0.001 HIS B 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 8758) covalent geometry : angle 0.79254 / 0.40 (12040) hydrogen bonds : bond 0.04319 / 2.93 ( 298) hydrogen bonds : angle 5.77261 / 4.04 ( 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 177 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7652 (pm20) cc_final: 0.7354 (pm20) REVERT: A 69 ASN cc_start: 0.7938 (p0) cc_final: 0.7566 (p0) REVERT: A 74 MET cc_start: 0.7217 (mpp) cc_final: 0.6978 (mpp) REVERT: A 75 PHE cc_start: 0.8379 (t80) cc_final: 0.7986 (t80) REVERT: A 95 GLU cc_start: 0.8054 (mp0) cc_final: 0.7557 (mp0) REVERT: A 146 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: A 203 ASP cc_start: 0.6348 (OUTLIER) cc_final: 0.5876 (t70) REVERT: A 267 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8644 (mtmt) REVERT: A 285 TYR cc_start: 0.8621 (OUTLIER) cc_final: 0.8242 (t80) REVERT: A 286 LYS cc_start: 0.9174 (tppt) cc_final: 0.8856 (tppt) REVERT: A 333 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8428 (ptmm) REVERT: A 336 LYS cc_start: 0.8391 (pttm) cc_final: 0.7851 (pttm) REVERT: A 353 TYR cc_start: 0.8846 (p90) cc_final: 0.8622 (p90) REVERT: A 355 LYS cc_start: 0.8916 (tppt) cc_final: 0.8180 (tppt) REVERT: A 380 ASN cc_start: 0.9359 (p0) cc_final: 0.8746 (p0) REVERT: A 397 TYR cc_start: 0.8290 (m-80) cc_final: 0.7904 (m-10) REVERT: A 457 LYS cc_start: 0.7702 (mtmm) cc_final: 0.7413 (mppt) REVERT: B 55 GLU cc_start: 0.9337 (mm-30) cc_final: 0.9129 (mm-30) REVERT: B 179 ILE cc_start: 0.9523 (mm) cc_final: 0.9316 (mp) REVERT: B 189 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8268 (ptm-80) REVERT: B 287 MET cc_start: 0.5951 (tpt) cc_final: 0.5072 (tpt) REVERT: B 301 GLU cc_start: 0.9263 (tp30) cc_final: 0.9035 (tp30) REVERT: B 392 TYR cc_start: 0.8628 (t80) cc_final: 0.8308 (t80) REVERT: B 400 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8140 (mmmm) REVERT: B 450 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8408 (tm-30) outliers start: 33 outliers final: 25 residues processed: 166 average time/residue: 0.1117 time to fit residues: 24.6325 Evaluate side-chains 168 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 243 ARG Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 307 ASN 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 66 THR 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 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 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: 0.9990 chunk 48 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 44 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 91 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN ** A 222 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 = 0.4143 r_free = 0.4143 target = 0.133968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.106955 restraints weight = 22650.010| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 5.47 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.3381 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= 0.168 Angle : 0.808 13.634 12040 Z= 0.409 Chirality : 0.047 0.246 1319 Planarity : 0.005 0.051 1372 Dihedral : 18.022 170.396 1517 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.02 % Allowed : 32.93 % Favored : 63.05 % 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: -1.56 (0.27), residues: 909 helix: 0.27 (0.29), residues: 315 sheet: -1.44 (0.41), residues: 154 loop : -1.85 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 54 TYR 0.035 0.001 TYR B 330 PHE 0.021 0.001 PHE A 78 TRP 0.013 0.002 TRP B 369 HIS 0.003 0.001 HIS B 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 8758) covalent geometry : angle 0.80785 / 0.41 (12040) hydrogen bonds : bond 0.04164 / 2.88 ( 298) hydrogen bonds : angle 5.73277 / 4.02 ( 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 178 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7537 (pm20) cc_final: 0.7242 (pm20) REVERT: A 69 ASN cc_start: 0.7981 (p0) cc_final: 0.7620 (p0) REVERT: A 74 MET cc_start: 0.7181 (mpp) cc_final: 0.6949 (mpp) REVERT: A 75 PHE cc_start: 0.8404 (t80) cc_final: 0.7985 (t80) REVERT: A 95 GLU cc_start: 0.8027 (mp0) cc_final: 0.7538 (mp0) REVERT: A 146 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: A 203 ASP cc_start: 0.6217 (OUTLIER) cc_final: 0.5746 (t70) REVERT: A 267 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8630 (mtmt) REVERT: A 285 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.8274 (t80) REVERT: A 286 LYS cc_start: 0.9189 (tppt) cc_final: 0.8869 (tppt) REVERT: A 333 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8430 (ptmm) REVERT: A 336 LYS cc_start: 0.8411 (pttm) cc_final: 0.7906 (pttm) REVERT: A 355 LYS cc_start: 0.8897 (tppt) cc_final: 0.8192 (tppt) REVERT: A 380 ASN cc_start: 0.9352 (p0) cc_final: 0.8756 (p0) REVERT: A 397 TYR cc_start: 0.8225 (m-80) cc_final: 0.7856 (m-10) REVERT: A 457 LYS cc_start: 0.7690 (mtmm) cc_final: 0.7400 (mppt) REVERT: B 189 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8193 (ptm-80) REVERT: B 287 MET cc_start: 0.6016 (tpt) cc_final: 0.5107 (tpt) REVERT: B 336 MET cc_start: 0.7739 (ppp) cc_final: 0.7370 (ppp) REVERT: B 392 TYR cc_start: 0.8640 (t80) cc_final: 0.8330 (t80) REVERT: B 400 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8159 (mmmm) outliers start: 33 outliers final: 25 residues processed: 168 average time/residue: 0.1126 time to fit residues: 24.8909 Evaluate side-chains 166 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 HIS 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 243 ARG Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 307 ASN 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 66 THR 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 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 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 0 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS ** A 222 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 = 0.4153 r_free = 0.4153 target = 0.134632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.107550 restraints weight = 22823.908| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 5.51 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8758 Z= 0.162 Angle : 0.821 14.305 12040 Z= 0.416 Chirality : 0.047 0.240 1319 Planarity : 0.005 0.051 1372 Dihedral : 18.055 169.876 1517 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.66 % Allowed : 33.90 % Favored : 62.44 % 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: -1.62 (0.28), residues: 909 helix: 0.27 (0.29), residues: 315 sheet: -1.68 (0.40), residues: 163 loop : -1.84 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 54 TYR 0.030 0.001 TYR B 330 PHE 0.017 0.001 PHE A 482 TRP 0.016 0.002 TRP A 421 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 8758) covalent geometry : angle 0.82073 / 0.42 (12040) hydrogen bonds : bond 0.04185 / 2.88 ( 298) hydrogen bonds : angle 5.78333 / 4.06 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.39 seconds wall clock time: 31 minutes 43.82 seconds (1903.82 seconds total)