Starting phenix.real_space_refine on Fri Aug 22 23:45:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8isz_35701/08_2025/8isz_35701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8isz_35701/08_2025/8isz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8isz_35701/08_2025/8isz_35701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8isz_35701/08_2025/8isz_35701.map" model { file = "/net/cci-nas-00/data/ceres_data/8isz_35701/08_2025/8isz_35701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8isz_35701/08_2025/8isz_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-2.0-5787/lib/python3.9/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: 2.18, per 1000 atoms: 0.26 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: 0.89 Conformation dependent library (CDL) restraints added in 276.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.89 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: 1.40 Time building geometry restraints manager: 1.10 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=" C TYR B 330 " pdb=" N PRO B 331 " ideal model delta sigma weight residual 1.336 1.365 -0.030 1.23e-02 6.61e+03 5.77e+00 bond pdb=" O5' A C 10 " pdb=" C5' A C 10 " ideal model delta sigma weight residual 1.420 1.452 -0.032 1.50e-02 4.44e+03 4.64e+00 bond pdb=" C2 U C 14 " pdb=" N3 U C 14 " ideal model delta sigma weight residual 1.373 1.334 0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" O5' G C 11 " pdb=" C5' G C 11 " ideal model delta sigma weight residual 1.424 1.452 -0.028 1.50e-02 4.44e+03 3.55e+00 bond pdb=" O5' G C 8 " pdb=" C5' G C 8 " ideal model delta sigma weight residual 1.420 1.448 -0.028 1.50e-02 4.44e+03 3.45e+00 ... (remaining 8753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 11783 2.40 - 4.81: 202 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=" C3' U C 9 " pdb=" O3' U C 9 " pdb=" P A C 10 " ideal model delta sigma weight residual 120.20 126.05 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" CA LYS B 302 " pdb=" CB LYS B 302 " pdb=" CG LYS B 302 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 angle pdb=" CB MET B 336 " pdb=" CG MET B 336 " pdb=" SD MET B 336 " ideal model delta sigma weight residual 112.70 123.83 -11.13 3.00e+00 1.11e-01 1.38e+01 ... (remaining 12035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 4875 35.40 - 70.81: 357 70.81 - 106.21: 10 106.21 - 141.61: 0 141.61 - 177.01: 2 Dihedral angle restraints: 5244 sinusoidal: 2549 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 5241 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: 0.770 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.180 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 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= 0.188 Angle : 0.850 12.022 12040 Z= 0.436 Chirality : 0.057 0.557 1319 Planarity : 0.006 0.082 1372 Dihedral : 20.885 177.013 3502 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 aren 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 covalent geometry : bond 0.00378 ( 8758) covalent geometry : angle 0.85035 (12040) hydrogen bonds : bond 0.19088 ( 298) hydrogen bonds : angle 8.33041 ( 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 : 0.352 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: 0.1140 time to fit residues: 24.5567 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 : 0.319 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** 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 = 0.4192 r_free = 0.4192 target = 0.137835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.110642 restraints weight = 22937.960| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 5.69 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1680 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= 0.196 Angle : 0.733 10.186 12040 Z= 0.385 Chirality : 0.047 0.372 1319 Planarity : 0.005 0.069 1372 Dihedral : 19.450 178.373 1597 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.41 % Allowed : 30.24 % Favored : 66.34 % 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 aren not related in a simple way. whole: -1.68 (0.26), residues: 909 helix: 0.14 (0.29), residues: 311 sheet: -1.16 (0.44), residues: 135 loop : -2.03 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 201 TYR 0.021 0.002 TYR A 285 PHE 0.027 0.002 PHE A 503 TRP 0.022 0.002 TRP A 421 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8758) covalent geometry : angle 0.73305 (12040) hydrogen bonds : bond 0.05022 ( 298) hydrogen bonds : angle 6.31078 ( 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 175 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8379 (tp30) cc_final: 0.8098 (tp30) REVERT: A 331 LYS cc_start: 0.9117 (tptp) cc_final: 0.8718 (tptp) REVERT: A 336 LYS cc_start: 0.8645 (pttm) cc_final: 0.8366 (pttm) REVERT: A 397 TYR cc_start: 0.8033 (m-10) cc_final: 0.7545 (m-10) REVERT: B 342 ILE cc_start: 0.9089 (mm) cc_final: 0.8757 (mt) REVERT: B 450 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8496 (tm-30) outliers start: 28 outliers final: 14 residues processed: 164 average time/residue: 0.1136 time to fit residues: 24.7531 Evaluate side-chains 146 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR 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 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 46 TRP Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 311 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: 3.9990 chunk 86 optimal weight: 5.9990 chunk 42 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 80 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 307 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.135753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.108567 restraints weight = 22989.535| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 5.58 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2276 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= 0.170 Angle : 0.689 10.393 12040 Z= 0.361 Chirality : 0.046 0.226 1319 Planarity : 0.005 0.060 1372 Dihedral : 19.570 174.520 1597 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.39 % Allowed : 29.76 % 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 aren not related in a simple way. whole: -1.53 (0.26), residues: 909 helix: 0.29 (0.30), residues: 310 sheet: -1.07 (0.42), residues: 132 loop : -1.95 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 382 TYR 0.021 0.002 TYR A 285 PHE 0.019 0.001 PHE B 60 TRP 0.023 0.002 TRP A 421 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8758) covalent geometry : angle 0.68858 (12040) hydrogen bonds : bond 0.04435 ( 298) hydrogen bonds : angle 5.72313 ( 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 186 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.8011 (p0) cc_final: 0.7533 (p0) REVERT: A 99 GLU cc_start: 0.8474 (tp30) cc_final: 0.8234 (tp30) REVERT: A 267 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8619 (mtmt) REVERT: A 286 LYS cc_start: 0.9210 (tppt) cc_final: 0.8909 (tppt) REVERT: A 303 MET cc_start: 0.7349 (mmm) cc_final: 0.7108 (tpp) REVERT: A 333 LYS cc_start: 0.9130 (mmmt) cc_final: 0.8647 (ptmm) REVERT: A 355 LYS cc_start: 0.8777 (tppt) cc_final: 0.8047 (tppt) REVERT: A 380 ASN cc_start: 0.9373 (p0) cc_final: 0.8711 (p0) REVERT: A 397 TYR cc_start: 0.8272 (m-80) cc_final: 0.7882 (m-10) REVERT: B 179 ILE cc_start: 0.9476 (mm) cc_final: 0.9119 (mp) REVERT: B 287 MET cc_start: 0.5985 (tpt) cc_final: 0.5397 (tpt) REVERT: B 296 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8156 (tm-30) REVERT: B 336 MET cc_start: 0.7741 (ppp) cc_final: 0.7363 (ppp) REVERT: B 392 TYR cc_start: 0.8676 (t80) cc_final: 0.8367 (t80) REVERT: B 400 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8270 (mmmm) REVERT: B 450 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8466 (tm-30) outliers start: 36 outliers final: 20 residues processed: 173 average time/residue: 0.1178 time to fit residues: 26.8314 Evaluate side-chains 160 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 210 LEU 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 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 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 311 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 86 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.130570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.102760 restraints weight = 22884.088| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 5.57 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 8758 Z= 0.237 Angle : 0.733 10.965 12040 Z= 0.384 Chirality : 0.047 0.180 1319 Planarity : 0.005 0.058 1372 Dihedral : 19.737 173.349 1597 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 5.98 % Allowed : 29.39 % Favored : 64.63 % 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 aren not related in a simple way. whole: -1.62 (0.27), residues: 909 helix: 0.26 (0.29), residues: 314 sheet: -1.40 (0.40), residues: 153 loop : -1.96 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 382 TYR 0.015 0.002 TYR A 505 PHE 0.018 0.002 PHE B 223 TRP 0.017 0.002 TRP B 369 HIS 0.005 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 8758) covalent geometry : angle 0.73344 (12040) hydrogen bonds : bond 0.04615 ( 298) hydrogen bonds : angle 5.69851 ( 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 196 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.385 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 67 HIS cc_start: 0.8723 (t70) cc_final: 0.7917 (t70) REVERT: A 69 ASN cc_start: 0.7881 (p0) cc_final: 0.7460 (p0) REVERT: A 74 MET cc_start: 0.7397 (mpp) cc_final: 0.6805 (mpp) REVERT: A 267 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8611 (mtmt) REVERT: A 286 LYS cc_start: 0.9223 (tppt) cc_final: 0.9007 (tppt) REVERT: A 355 LYS cc_start: 0.8975 (tppt) cc_final: 0.8210 (tppt) REVERT: A 380 ASN cc_start: 0.9350 (p0) cc_final: 0.8721 (p0) REVERT: A 397 TYR cc_start: 0.8329 (m-80) cc_final: 0.7880 (m-10) REVERT: A 407 ARG cc_start: 0.8512 (ttm170) cc_final: 0.8250 (ttm170) REVERT: A 444 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8407 (tt0) REVERT: B 54 ARG cc_start: 0.9011 (ptp-110) cc_final: 0.8495 (ptp-110) REVERT: B 92 MET cc_start: 0.9107 (pmm) cc_final: 0.8900 (pmm) REVERT: B 189 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8383 (ptm-80) REVERT: B 287 MET cc_start: 0.6381 (tpt) cc_final: 0.5545 (tpt) REVERT: B 302 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8817 (tppp) REVERT: B 336 MET cc_start: 0.7771 (ppp) cc_final: 0.7319 (ppp) REVERT: B 392 TYR cc_start: 0.8633 (t80) cc_final: 0.8338 (t80) REVERT: B 400 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8276 (mmmm) REVERT: B 450 GLU cc_start: 0.8749 (tm-30) cc_final: 0.8508 (tm-30) outliers start: 49 outliers final: 29 residues processed: 177 average time/residue: 0.1245 time to fit residues: 28.7081 Evaluate side-chains 168 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 115 TYR 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 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 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 332 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 17 optimal weight: 0.0470 chunk 89 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 302 GLN A 329 HIS ** 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 = 0.4117 r_free = 0.4117 target = 0.131990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104254 restraints weight = 22705.580| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 5.54 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3246 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= 0.175 Angle : 0.702 11.599 12040 Z= 0.362 Chirality : 0.045 0.173 1319 Planarity : 0.005 0.055 1372 Dihedral : 19.527 171.366 1597 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.24 % Allowed : 30.24 % 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 aren not related in a simple way. whole: -1.60 (0.27), residues: 909 helix: 0.34 (0.30), residues: 314 sheet: -1.32 (0.40), residues: 140 loop : -2.03 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 275 TYR 0.023 0.002 TYR B 293 PHE 0.028 0.002 PHE A 78 TRP 0.015 0.002 TRP A 86 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8758) covalent geometry : angle 0.70172 (12040) hydrogen bonds : bond 0.04247 ( 298) hydrogen bonds : angle 5.55443 ( 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 187 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.327 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: 0.7472 (pm20) cc_final: 0.7245 (pm20) REVERT: A 39 ILE cc_start: 0.8129 (pt) cc_final: 0.7512 (pt) REVERT: A 69 ASN cc_start: 0.7854 (p0) cc_final: 0.7427 (p0) REVERT: A 95 GLU cc_start: 0.8125 (mp0) cc_final: 0.7648 (mp0) REVERT: A 222 GLN cc_start: 0.8467 (tt0) cc_final: 0.8132 (tt0) REVERT: A 267 LYS cc_start: 0.8961 (mtmt) cc_final: 0.8673 (mtmt) REVERT: A 286 LYS cc_start: 0.9204 (tppt) cc_final: 0.8993 (tppt) REVERT: A 333 LYS cc_start: 0.9119 (tppt) cc_final: 0.8566 (tmmt) REVERT: A 355 LYS cc_start: 0.8967 (tppt) cc_final: 0.8425 (tppt) REVERT: A 380 ASN cc_start: 0.9340 (p0) cc_final: 0.8737 (p0) REVERT: A 397 TYR cc_start: 0.8159 (m-80) cc_final: 0.7711 (m-10) REVERT: A 407 ARG cc_start: 0.8447 (ttm170) cc_final: 0.8157 (ttm170) REVERT: A 476 GLU cc_start: 0.7818 (pm20) cc_final: 0.7588 (pm20) REVERT: B 54 ARG cc_start: 0.8968 (ptp-110) cc_final: 0.8436 (ptp-110) REVERT: B 92 MET cc_start: 0.9111 (pmm) cc_final: 0.8871 (pmm) REVERT: B 179 ILE cc_start: 0.9517 (mm) cc_final: 0.9113 (mp) REVERT: B 189 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8216 (ptm-80) REVERT: B 287 MET cc_start: 0.6218 (tpt) cc_final: 0.5407 (tpt) REVERT: B 296 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8257 (tm-30) REVERT: B 342 ILE cc_start: 0.9142 (mm) cc_final: 0.8773 (mt) REVERT: B 392 TYR cc_start: 0.8624 (t80) cc_final: 0.8332 (t80) REVERT: B 400 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8214 (mmmm) REVERT: B 450 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8478 (tm-30) outliers start: 43 outliers final: 25 residues processed: 174 average time/residue: 0.1150 time to fit residues: 26.3809 Evaluate side-chains 170 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 288 ILE Chi-restraints excluded: chain A residue 363 THR 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 43 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 266 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 334 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 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: 2.9990 chunk 21 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.124407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097089 restraints weight = 23083.409| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 5.38 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.155 8758 Z= 0.370 Angle : 0.867 11.046 12040 Z= 0.449 Chirality : 0.049 0.170 1319 Planarity : 0.007 0.055 1372 Dihedral : 19.553 171.503 1597 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 24.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 6.34 % Allowed : 29.15 % 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 aren not related in a simple way. whole: -1.97 (0.26), residues: 909 helix: -0.08 (0.28), residues: 318 sheet: -1.75 (0.44), residues: 114 loop : -2.09 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 481 TYR 0.027 0.003 TYR B 293 PHE 0.025 0.003 PHE A 403 TRP 0.024 0.003 TRP B 369 HIS 0.006 0.002 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00831 ( 8758) covalent geometry : angle 0.86652 (12040) hydrogen bonds : bond 0.05499 ( 298) hydrogen bonds : angle 6.00681 ( 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 197 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7964 (pm20) cc_final: 0.7708 (pm20) REVERT: A 47 GLN cc_start: 0.9418 (pm20) cc_final: 0.9213 (pm20) REVERT: A 95 GLU cc_start: 0.8264 (mp0) cc_final: 0.8007 (mp0) REVERT: A 203 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6345 (t70) REVERT: A 243 ARG cc_start: 0.5665 (OUTLIER) cc_final: 0.5317 (mmt180) REVERT: A 267 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8762 (mtmt) REVERT: A 355 LYS cc_start: 0.9145 (tppt) cc_final: 0.8621 (tppt) REVERT: A 380 ASN cc_start: 0.9420 (p0) cc_final: 0.8804 (p0) REVERT: A 397 TYR cc_start: 0.8469 (m-80) cc_final: 0.7890 (m-10) REVERT: A 407 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8155 (ttm170) REVERT: A 466 ASN cc_start: 0.8970 (t0) cc_final: 0.8697 (t0) REVERT: B 54 ARG cc_start: 0.9073 (ptp-110) cc_final: 0.8824 (ptp-110) REVERT: B 92 MET cc_start: 0.9059 (pmm) cc_final: 0.8786 (pmm) REVERT: B 189 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8031 (ptm-80) REVERT: B 287 MET cc_start: 0.7056 (tpt) cc_final: 0.6148 (tpt) REVERT: B 410 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: B 447 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6906 (mt-10) outliers start: 52 outliers final: 33 residues processed: 178 average time/residue: 0.1200 time to fit residues: 27.8923 Evaluate side-chains 179 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 115 TYR 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 279 CYS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain B residue 14 ASP Chi-restraints excluded: chain B residue 43 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 153 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain B residue 232 THR 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 353 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 410 PHE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 447 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 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 = 0.4108 r_free = 0.4108 target = 0.131248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.103814 restraints weight = 22861.584| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 5.45 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3963 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 : 0.762 13.484 12040 Z= 0.387 Chirality : 0.046 0.177 1319 Planarity : 0.005 0.053 1372 Dihedral : 19.405 170.844 1597 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.66 % Allowed : 31.71 % Favored : 64.63 % 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 aren not related in a simple way. whole: -1.67 (0.27), residues: 909 helix: 0.25 (0.29), residues: 315 sheet: -1.62 (0.42), residues: 135 loop : -1.96 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 481 TYR 0.025 0.001 TYR B 330 PHE 0.018 0.002 PHE A 403 TRP 0.017 0.002 TRP A 421 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8758) covalent geometry : angle 0.76164 (12040) hydrogen bonds : bond 0.04239 ( 298) hydrogen bonds : angle 5.66155 ( 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 185 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.299 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: 0.7506 (pm20) cc_final: 0.7255 (pm20) REVERT: A 95 GLU cc_start: 0.8234 (mp0) cc_final: 0.7742 (mp0) REVERT: A 203 ASP cc_start: 0.6352 (OUTLIER) cc_final: 0.5929 (t70) REVERT: A 267 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8641 (mtmt) REVERT: A 285 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.7903 (t80) REVERT: A 302 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7604 (mp10) REVERT: A 329 HIS cc_start: 0.7954 (m-70) cc_final: 0.7570 (m-70) REVERT: A 355 LYS cc_start: 0.9090 (tppt) cc_final: 0.8644 (tppt) REVERT: A 380 ASN cc_start: 0.9287 (p0) cc_final: 0.8802 (p0) REVERT: A 397 TYR cc_start: 0.8256 (m-80) cc_final: 0.7679 (m-10) REVERT: A 466 ASN cc_start: 0.8991 (t0) cc_final: 0.8734 (t0) REVERT: B 60 PHE cc_start: 0.9199 (t80) cc_final: 0.8957 (t80) REVERT: B 92 MET cc_start: 0.9026 (pmm) cc_final: 0.8748 (pmm) REVERT: B 287 MET cc_start: 0.6206 (tpt) cc_final: 0.5801 (tpt) REVERT: B 296 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8316 (tm-30) REVERT: B 314 GLN cc_start: 0.8517 (pp30) cc_final: 0.7899 (pp30) outliers start: 30 outliers final: 20 residues processed: 176 average time/residue: 0.1256 time to fit residues: 28.7067 Evaluate side-chains 161 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS 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 281 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 302 GLN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ILE 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 261 CYS 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 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: 0.8980 chunk 90 optimal weight: 0.4980 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** 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 = 0.4114 r_free = 0.4114 target = 0.131717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.104417 restraints weight = 22845.041| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 5.57 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8758 Z= 0.160 Angle : 0.771 13.431 12040 Z= 0.392 Chirality : 0.045 0.176 1319 Planarity : 0.005 0.054 1372 Dihedral : 19.359 170.436 1597 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.90 % Allowed : 32.56 % 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 aren not related in a simple way. whole: -1.67 (0.27), residues: 909 helix: 0.25 (0.29), residues: 316 sheet: -1.65 (0.42), residues: 137 loop : -1.93 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 407 TYR 0.021 0.001 TYR B 330 PHE 0.022 0.002 PHE A 482 TRP 0.016 0.002 TRP A 421 HIS 0.003 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 8758) covalent geometry : angle 0.77095 (12040) hydrogen bonds : bond 0.04241 ( 298) hydrogen bonds : angle 5.67940 ( 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 176 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.335 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: 0.7496 (pm20) cc_final: 0.7247 (pm20) REVERT: A 72 ARG cc_start: 0.5567 (tpp-160) cc_final: 0.5184 (tpp-160) REVERT: A 74 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6994 (mpp) REVERT: A 95 GLU cc_start: 0.8256 (mp0) cc_final: 0.7750 (mp0) REVERT: A 267 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8592 (mtmt) REVERT: A 285 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7935 (t80) REVERT: A 286 LYS cc_start: 0.9184 (tppt) cc_final: 0.8864 (tppt) REVERT: A 302 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: A 329 HIS cc_start: 0.7951 (m-70) cc_final: 0.7519 (m-70) REVERT: A 355 LYS cc_start: 0.9080 (tppt) cc_final: 0.8627 (tppt) REVERT: A 380 ASN cc_start: 0.9275 (p0) cc_final: 0.8782 (p0) REVERT: A 397 TYR cc_start: 0.8283 (m-80) cc_final: 0.7730 (m-10) REVERT: A 466 ASN cc_start: 0.8957 (t0) cc_final: 0.8676 (t0) REVERT: B 92 MET cc_start: 0.9060 (pmm) cc_final: 0.8766 (pmm) REVERT: B 287 MET cc_start: 0.6051 (tpt) cc_final: 0.5530 (tpt) REVERT: B 296 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8325 (tm-30) REVERT: B 314 GLN cc_start: 0.8496 (pp30) cc_final: 0.7886 (pp30) REVERT: B 336 MET cc_start: 0.7671 (ppp) cc_final: 0.7340 (tmm) outliers start: 32 outliers final: 28 residues processed: 165 average time/residue: 0.1226 time to fit residues: 26.4379 Evaluate side-chains 171 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 74 MET 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 223 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 302 GLN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain B residue 43 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 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 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 433 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 302 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** 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 = 0.4105 r_free = 0.4105 target = 0.131375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.104036 restraints weight = 22761.999| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 5.51 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8758 Z= 0.168 Angle : 0.764 13.410 12040 Z= 0.387 Chirality : 0.045 0.177 1319 Planarity : 0.005 0.055 1372 Dihedral : 19.356 169.643 1597 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.39 % Allowed : 32.68 % 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 aren not related in a simple way. whole: -1.61 (0.27), residues: 909 helix: 0.31 (0.29), residues: 310 sheet: -1.35 (0.43), residues: 130 loop : -1.98 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 407 TYR 0.022 0.001 TYR B 330 PHE 0.017 0.002 PHE A 482 TRP 0.014 0.002 TRP A 421 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8758) covalent geometry : angle 0.76431 (12040) hydrogen bonds : bond 0.04253 ( 298) hydrogen bonds : angle 5.64018 ( 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 173 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.327 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: 0.7442 (pm20) cc_final: 0.7193 (pm20) REVERT: A 74 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7035 (mpp) REVERT: A 95 GLU cc_start: 0.8233 (mp0) cc_final: 0.7727 (mp0) REVERT: A 203 ASP cc_start: 0.6258 (OUTLIER) cc_final: 0.5783 (t70) REVERT: A 222 GLN cc_start: 0.8470 (tt0) cc_final: 0.7996 (tm-30) REVERT: A 267 LYS cc_start: 0.8979 (mtmt) cc_final: 0.8630 (mtmt) REVERT: A 285 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.7928 (t80) REVERT: A 286 LYS cc_start: 0.9186 (tppt) cc_final: 0.8953 (tppt) REVERT: A 329 HIS cc_start: 0.7963 (m-70) cc_final: 0.7498 (m-70) REVERT: A 355 LYS cc_start: 0.9075 (tppt) cc_final: 0.8625 (tppt) REVERT: A 380 ASN cc_start: 0.9281 (p0) cc_final: 0.8789 (p0) REVERT: A 397 TYR cc_start: 0.8257 (m-80) cc_final: 0.7702 (m-10) REVERT: A 466 ASN cc_start: 0.8893 (t0) cc_final: 0.8575 (t0) REVERT: A 481 ARG cc_start: 0.8552 (ttm110) cc_final: 0.8306 (ttm110) REVERT: B 54 ARG cc_start: 0.8929 (ptp-110) cc_final: 0.8537 (ptp90) REVERT: B 92 MET cc_start: 0.9063 (pmm) cc_final: 0.8751 (pmm) REVERT: B 287 MET cc_start: 0.6059 (tpt) cc_final: 0.5418 (tpt) REVERT: B 296 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 314 GLN cc_start: 0.8530 (pp30) cc_final: 0.7911 (pp30) REVERT: B 336 MET cc_start: 0.7635 (ppp) cc_final: 0.7286 (ppp) outliers start: 36 outliers final: 29 residues processed: 160 average time/residue: 0.1185 time to fit residues: 24.8738 Evaluate side-chains 165 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 115 TYR 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 281 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 388 ILE 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 A residue 441 ILE Chi-restraints excluded: chain B residue 43 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 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 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 443 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** 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 = 0.4052 r_free = 0.4052 target = 0.127476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.099991 restraints weight = 22634.150| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 5.36 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 8758 Z= 0.242 Angle : 0.806 12.808 12040 Z= 0.411 Chirality : 0.047 0.175 1319 Planarity : 0.006 0.054 1372 Dihedral : 19.590 168.582 1597 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 3.90 % Allowed : 33.54 % Favored : 62.56 % 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 aren not related in a simple way. whole: -1.81 (0.27), residues: 909 helix: 0.12 (0.29), residues: 311 sheet: -1.61 (0.42), residues: 136 loop : -2.03 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 407 TYR 0.022 0.002 TYR B 330 PHE 0.020 0.002 PHE A 403 TRP 0.019 0.002 TRP B 369 HIS 0.004 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00554 ( 8758) covalent geometry : angle 0.80574 (12040) hydrogen bonds : bond 0.04776 ( 298) hydrogen bonds : angle 5.81133 ( 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 166 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.328 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: 0.7347 (pm20) REVERT: A 74 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7043 (mpp) REVERT: A 95 GLU cc_start: 0.8246 (mp0) cc_final: 0.7758 (mp0) REVERT: A 203 ASP cc_start: 0.6437 (OUTLIER) cc_final: 0.5938 (t70) REVERT: A 267 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8646 (mtmt) REVERT: A 285 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.7946 (t80) REVERT: A 329 HIS cc_start: 0.8011 (m-70) cc_final: 0.7408 (m-70) REVERT: A 333 LYS cc_start: 0.9154 (tppt) cc_final: 0.8702 (ttpp) REVERT: A 355 LYS cc_start: 0.9114 (tppt) cc_final: 0.8656 (tppt) REVERT: A 380 ASN cc_start: 0.9309 (p0) cc_final: 0.8820 (p0) REVERT: A 397 TYR cc_start: 0.8313 (m-80) cc_final: 0.7678 (m-10) REVERT: A 466 ASN cc_start: 0.8875 (t0) cc_final: 0.8597 (t0) REVERT: B 54 ARG cc_start: 0.9103 (ptp-110) cc_final: 0.8681 (ptp90) REVERT: B 92 MET cc_start: 0.9060 (pmm) cc_final: 0.8741 (pmm) REVERT: B 287 MET cc_start: 0.6434 (tpt) cc_final: 0.5552 (tpt) REVERT: B 296 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8287 (tm-30) REVERT: B 336 MET cc_start: 0.7625 (ppp) cc_final: 0.7252 (ppp) outliers start: 32 outliers final: 26 residues processed: 154 average time/residue: 0.1161 time to fit residues: 23.5318 Evaluate side-chains 158 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 115 TYR 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 281 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 388 ILE 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 A residue 441 ILE Chi-restraints excluded: chain B residue 43 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 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 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 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: 6.9990 chunk 92 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.138222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.112588 restraints weight = 24342.487| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 5.24 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8758 Z= 0.161 Angle : 0.797 13.901 12040 Z= 0.402 Chirality : 0.045 0.177 1319 Planarity : 0.005 0.075 1372 Dihedral : 19.597 169.364 1597 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.66 % Allowed : 34.51 % Favored : 61.83 % 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 aren not related in a simple way. whole: -1.72 (0.27), residues: 909 helix: 0.21 (0.29), residues: 309 sheet: -1.58 (0.43), residues: 137 loop : -1.98 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 382 TYR 0.021 0.001 TYR B 293 PHE 0.018 0.002 PHE A 403 TRP 0.017 0.002 TRP A 421 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8758) covalent geometry : angle 0.79670 (12040) hydrogen bonds : bond 0.04377 ( 298) hydrogen bonds : angle 5.66310 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1953.89 seconds wall clock time: 34 minutes 37.45 seconds (2077.45 seconds total)