Starting phenix.real_space_refine on Thu Feb 13 03:11:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8isz_35701/02_2025/8isz_35701.cif Found real_map, /net/cci-nas-00/data/ceres_data/8isz_35701/02_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_35701/02_2025/8isz_35701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8isz_35701/02_2025/8isz_35701.map" model { file = "/net/cci-nas-00/data/ceres_data/8isz_35701/02_2025/8isz_35701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8isz_35701/02_2025/8isz_35701.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.04, per 1000 atoms: 0.60 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: 2.59 Conformation dependent library (CDL) restraints added in 953.6 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: 2.70 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: 2.43 Time building geometry restraints manager: 2.83 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: 0.550 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.370 Find NCS groups from input model: 0.100 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.590 ------------------------------------------------------------------------------- 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= 0.228 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.002 TRP B 369 HIS 0.005 0.001 HIS B 358 PHE 0.013 0.001 PHE A 403 TYR 0.021 0.001 TYR A 285 ARG 0.007 0.000 ARG A 113 *********************** 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 : 0.851 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: 0.2521 time to fit residues: 53.4451 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 : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 0.0010 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.140373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.113261 restraints weight = 22616.449| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 5.69 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8758 Z= 0.226 Angle : 0.717 10.226 12040 Z= 0.375 Chirality : 0.046 0.292 1319 Planarity : 0.005 0.067 1372 Dihedral : 19.396 177.825 1597 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.17 % Allowed : 29.76 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.26), residues: 909 helix: 0.10 (0.29), residues: 310 sheet: -1.43 (0.40), residues: 158 loop : -2.03 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 421 HIS 0.006 0.001 HIS A 329 PHE 0.030 0.001 PHE A 503 TYR 0.020 0.001 TYR A 285 ARG 0.004 0.001 ARG B 201 *********************** 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: 26 poor density : 149 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8368 (tp30) cc_final: 0.8065 (tp30) REVERT: A 202 TYR cc_start: 0.7536 (m-80) cc_final: 0.6655 (m-80) REVERT: A 285 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7465 (t80) REVERT: A 331 LYS cc_start: 0.9077 (tptp) cc_final: 0.8730 (tptp) REVERT: A 355 LYS cc_start: 0.8630 (tppt) cc_final: 0.8412 (tppt) REVERT: A 397 TYR cc_start: 0.8087 (m-10) cc_final: 0.7617 (m-10) REVERT: A 422 THR cc_start: 0.8698 (p) cc_final: 0.8361 (p) REVERT: B 251 TYR cc_start: 0.7560 (t80) cc_final: 0.7320 (t80) REVERT: B 270 ASN cc_start: 0.9100 (m-40) cc_final: 0.8864 (m-40) REVERT: B 342 ILE cc_start: 0.9043 (mm) cc_final: 0.8701 (mt) REVERT: B 450 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8389 (tm-30) outliers start: 26 outliers final: 10 residues processed: 164 average time/residue: 0.2610 time to fit residues: 56.0514 Evaluate side-chains 144 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 285 TYR 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 140 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 266 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 307 ASN ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.134021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.106996 restraints weight = 23365.964| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 5.67 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2390 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= 0.268 Angle : 0.708 10.079 12040 Z= 0.372 Chirality : 0.046 0.212 1319 Planarity : 0.005 0.063 1372 Dihedral : 19.641 174.947 1597 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.24 % Allowed : 29.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.26), residues: 909 helix: 0.26 (0.29), residues: 312 sheet: -1.46 (0.41), residues: 139 loop : -1.84 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 421 HIS 0.005 0.001 HIS A 207 PHE 0.021 0.002 PHE B 223 TYR 0.019 0.002 TYR B 293 ARG 0.006 0.001 ARG B 382 *********************** 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 196 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASN cc_start: 0.7990 (p0) cc_final: 0.7521 (p0) REVERT: A 75 PHE cc_start: 0.8338 (t80) cc_final: 0.7845 (t80) REVERT: A 99 GLU cc_start: 0.8478 (tp30) cc_final: 0.8252 (tp30) REVERT: A 267 LYS cc_start: 0.8855 (mtmt) cc_final: 0.8524 (mtmt) REVERT: A 303 MET cc_start: 0.7167 (mmm) cc_final: 0.6867 (tpp) REVERT: A 355 LYS cc_start: 0.8885 (tppt) cc_final: 0.8146 (tppt) REVERT: A 380 ASN cc_start: 0.9407 (p0) cc_final: 0.8649 (p0) REVERT: A 397 TYR cc_start: 0.8224 (m-80) cc_final: 0.7803 (m-10) REVERT: A 407 ARG cc_start: 0.8453 (ttm170) cc_final: 0.8233 (ttm-80) REVERT: A 465 LEU cc_start: 0.6796 (mp) cc_final: 0.6584 (mp) REVERT: B 156 GLN cc_start: 0.9049 (pp30) cc_final: 0.8847 (pp30) REVERT: B 179 ILE cc_start: 0.9476 (mm) cc_final: 0.9063 (mp) REVERT: B 189 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8391 (ptm-80) REVERT: B 287 MET cc_start: 0.6163 (tpt) cc_final: 0.5443 (tpt) REVERT: B 296 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8166 (tm-30) REVERT: B 336 MET cc_start: 0.7776 (ppp) cc_final: 0.7419 (ppp) REVERT: B 392 TYR cc_start: 0.8670 (t80) cc_final: 0.8383 (t80) REVERT: B 400 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8293 (mmmm) REVERT: B 450 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8479 (tm-30) outliers start: 43 outliers final: 21 residues processed: 180 average time/residue: 0.2572 time to fit residues: 60.1301 Evaluate side-chains 166 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 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 40 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.133386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.106382 restraints weight = 23005.876| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 5.56 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2848 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= 0.253 Angle : 0.708 11.154 12040 Z= 0.367 Chirality : 0.046 0.182 1319 Planarity : 0.005 0.056 1372 Dihedral : 19.657 172.473 1597 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.37 % Allowed : 30.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.27), residues: 909 helix: 0.35 (0.29), residues: 316 sheet: -1.65 (0.39), residues: 158 loop : -1.79 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 369 HIS 0.004 0.001 HIS B 9 PHE 0.021 0.002 PHE A 482 TYR 0.023 0.002 TYR A 285 ARG 0.005 0.001 ARG B 382 *********************** 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 192 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.861 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: 0.7582 (p0) REVERT: A 74 MET cc_start: 0.7311 (mpp) cc_final: 0.6870 (mpp) REVERT: A 75 PHE cc_start: 0.8375 (t80) cc_final: 0.8122 (t80) REVERT: A 267 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8652 (mtmt) REVERT: A 303 MET cc_start: 0.7418 (mmm) cc_final: 0.7109 (tpp) REVERT: A 355 LYS cc_start: 0.8943 (tppt) cc_final: 0.8288 (tppt) REVERT: A 380 ASN cc_start: 0.9394 (p0) cc_final: 0.8590 (p0) REVERT: A 397 TYR cc_start: 0.8185 (m-80) cc_final: 0.7743 (m-10) REVERT: A 407 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8144 (ttm170) REVERT: B 92 MET cc_start: 0.9148 (pmm) cc_final: 0.8937 (pmm) REVERT: B 179 ILE cc_start: 0.9488 (mm) cc_final: 0.9143 (mp) REVERT: B 287 MET cc_start: 0.6344 (tpt) cc_final: 0.5588 (tpt) REVERT: B 307 LYS cc_start: 0.9380 (mmmm) cc_final: 0.9116 (mmmm) REVERT: B 392 TYR cc_start: 0.8630 (t80) cc_final: 0.8319 (t80) REVERT: B 400 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8271 (mmmm) REVERT: B 450 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8456 (tm-30) outliers start: 44 outliers final: 29 residues processed: 174 average time/residue: 0.2650 time to fit residues: 60.0209 Evaluate side-chains 165 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 207 HIS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 223 ILE 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 307 ASN 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS 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 = 0.132513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.105547 restraints weight = 22993.439| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 5.54 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8758 Z= 0.248 Angle : 0.707 11.021 12040 Z= 0.365 Chirality : 0.045 0.170 1319 Planarity : 0.005 0.054 1372 Dihedral : 19.466 171.193 1597 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.00 % Allowed : 31.10 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.27), residues: 909 helix: 0.54 (0.30), residues: 308 sheet: -1.51 (0.40), residues: 148 loop : -1.88 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 421 HIS 0.004 0.001 HIS A 329 PHE 0.016 0.001 PHE A 403 TYR 0.022 0.002 TYR B 293 ARG 0.007 0.001 ARG A 481 *********************** 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 186 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7552 (pm20) cc_final: 0.7327 (pm20) REVERT: A 69 ASN cc_start: 0.7818 (p0) cc_final: 0.7372 (p0) REVERT: A 267 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8620 (mtmt) REVERT: A 355 LYS cc_start: 0.8990 (tppt) cc_final: 0.8358 (tppt) REVERT: A 380 ASN cc_start: 0.9336 (p0) cc_final: 0.8601 (p0) REVERT: A 397 TYR cc_start: 0.8214 (m-80) cc_final: 0.7783 (m-10) REVERT: A 407 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.8161 (ttm170) REVERT: B 54 ARG cc_start: 0.8997 (ptp-110) cc_final: 0.8478 (ptp-110) REVERT: B 70 LYS cc_start: 0.9123 (mmmt) cc_final: 0.8891 (pttm) REVERT: B 92 MET cc_start: 0.9091 (pmm) cc_final: 0.8866 (pmm) REVERT: B 179 ILE cc_start: 0.9488 (mm) cc_final: 0.9091 (mp) REVERT: B 189 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8232 (ptm-80) REVERT: B 287 MET cc_start: 0.6125 (tpt) cc_final: 0.5355 (tpt) REVERT: B 296 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 314 GLN cc_start: 0.8647 (pp30) cc_final: 0.8042 (pp30) REVERT: B 392 TYR cc_start: 0.8646 (t80) cc_final: 0.8353 (t80) REVERT: B 400 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8213 (mmmm) REVERT: B 450 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8460 (tm-30) outliers start: 41 outliers final: 22 residues processed: 167 average time/residue: 0.2613 time to fit residues: 56.9242 Evaluate side-chains 169 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL 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 281 LEU 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 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 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 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 53 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 7 optimal weight: 0.0670 chunk 94 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.128348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.099936 restraints weight = 22806.311| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 5.56 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 8758 Z= 0.371 Angle : 0.764 11.160 12040 Z= 0.396 Chirality : 0.047 0.173 1319 Planarity : 0.006 0.055 1372 Dihedral : 19.376 170.850 1597 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 6.10 % Allowed : 29.51 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.27), residues: 909 helix: 0.23 (0.29), residues: 319 sheet: -1.42 (0.42), residues: 132 loop : -2.06 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 369 HIS 0.005 0.002 HIS B 9 PHE 0.029 0.002 PHE A 78 TYR 0.024 0.002 TYR B 293 ARG 0.006 0.001 ARG A 481 *********************** 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 193 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7675 (pm20) cc_final: 0.7423 (pm20) REVERT: A 39 ILE cc_start: 0.8138 (pt) cc_final: 0.7576 (pt) REVERT: A 69 ASN cc_start: 0.7672 (p0) cc_final: 0.7205 (p0) REVERT: A 95 GLU cc_start: 0.8225 (mp0) cc_final: 0.7987 (mp0) REVERT: A 203 ASP cc_start: 0.6578 (OUTLIER) cc_final: 0.6036 (t70) REVERT: A 222 GLN cc_start: 0.8409 (tt0) cc_final: 0.7863 (tt0) REVERT: A 243 ARG cc_start: 0.5365 (OUTLIER) cc_final: 0.5102 (mmt180) REVERT: A 267 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8641 (mtmt) REVERT: A 286 LYS cc_start: 0.9255 (tppt) cc_final: 0.9052 (tppt) REVERT: A 355 LYS cc_start: 0.9087 (tppt) cc_final: 0.8497 (tppt) REVERT: A 380 ASN cc_start: 0.9400 (p0) cc_final: 0.8746 (p0) REVERT: A 397 TYR cc_start: 0.8329 (m-80) cc_final: 0.7776 (m-10) REVERT: A 407 ARG cc_start: 0.8397 (ttm-80) cc_final: 0.7966 (ttm170) REVERT: A 457 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7236 (mtmm) REVERT: A 466 ASN cc_start: 0.8904 (t0) cc_final: 0.8566 (t0) REVERT: B 92 MET cc_start: 0.9033 (pmm) cc_final: 0.8781 (pmm) REVERT: B 189 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8166 (ptm-80) REVERT: B 287 MET cc_start: 0.6648 (tpt) cc_final: 0.5697 (tpt) REVERT: B 392 TYR cc_start: 0.8633 (t80) cc_final: 0.8265 (t80) REVERT: B 400 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8165 (mmtt) REVERT: B 450 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8541 (tm-30) outliers start: 50 outliers final: 30 residues processed: 174 average time/residue: 0.2542 time to fit residues: 57.5708 Evaluate side-chains 174 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 27 LEU 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 208 ASP 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 307 ASN 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 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 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 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 433 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS 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 = 0.4102 r_free = 0.4102 target = 0.130734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.103337 restraints weight = 22834.315| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 5.53 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3825 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= 0.250 Angle : 0.738 12.725 12040 Z= 0.377 Chirality : 0.045 0.174 1319 Planarity : 0.005 0.051 1372 Dihedral : 19.319 170.438 1597 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.12 % Allowed : 31.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.27), residues: 909 helix: 0.29 (0.29), residues: 316 sheet: -1.56 (0.45), residues: 113 loop : -1.93 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 369 HIS 0.004 0.001 HIS A 329 PHE 0.021 0.001 PHE A 78 TYR 0.021 0.002 TYR B 293 ARG 0.008 0.001 ARG A 275 *********************** 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 193 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.858 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: 0.7569 (pm20) cc_final: 0.7318 (pm20) REVERT: A 39 ILE cc_start: 0.8377 (pt) cc_final: 0.7934 (pt) REVERT: A 95 GLU cc_start: 0.8221 (mp0) cc_final: 0.7963 (mp0) REVERT: A 203 ASP cc_start: 0.6452 (OUTLIER) cc_final: 0.6014 (t70) REVERT: A 222 GLN cc_start: 0.8543 (tt0) cc_final: 0.7963 (tt0) REVERT: A 267 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8631 (mtmt) REVERT: A 286 LYS cc_start: 0.9219 (tppt) cc_final: 0.8944 (tppt) REVERT: A 355 LYS cc_start: 0.9085 (tppt) cc_final: 0.8615 (tppt) REVERT: A 380 ASN cc_start: 0.9339 (p0) cc_final: 0.8842 (p0) REVERT: A 397 TYR cc_start: 0.8301 (m-80) cc_final: 0.7820 (m-10) REVERT: A 407 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7866 (ttm170) REVERT: A 466 ASN cc_start: 0.8938 (t0) cc_final: 0.8574 (t0) REVERT: B 55 GLU cc_start: 0.9353 (mm-30) cc_final: 0.9040 (mp0) REVERT: B 92 MET cc_start: 0.9016 (pmm) cc_final: 0.8763 (pmm) REVERT: B 179 ILE cc_start: 0.9521 (mm) cc_final: 0.9142 (mp) REVERT: B 287 MET cc_start: 0.6144 (tpt) cc_final: 0.5521 (tpt) REVERT: B 296 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8301 (tm-30) REVERT: B 314 GLN cc_start: 0.8594 (pp30) cc_final: 0.8003 (pp30) REVERT: B 336 MET cc_start: 0.7710 (ppp) cc_final: 0.7303 (ppp) REVERT: B 392 TYR cc_start: 0.8670 (t80) cc_final: 0.8405 (t80) REVERT: B 400 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8202 (mmmm) REVERT: B 450 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8512 (tm-30) outliers start: 42 outliers final: 28 residues processed: 178 average time/residue: 0.2664 time to fit residues: 60.8532 Evaluate side-chains 174 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 127 THR 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 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 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 311 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.139092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.113458 restraints weight = 24446.702| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 5.29 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8758 Z= 0.234 Angle : 0.752 12.621 12040 Z= 0.383 Chirality : 0.046 0.231 1319 Planarity : 0.005 0.050 1372 Dihedral : 19.282 170.015 1597 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.39 % Allowed : 32.93 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.27), residues: 909 helix: 0.40 (0.30), residues: 316 sheet: -1.68 (0.43), residues: 126 loop : -1.93 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 369 HIS 0.004 0.001 HIS B 9 PHE 0.017 0.001 PHE A 403 TYR 0.022 0.001 TYR B 330 ARG 0.007 0.001 ARG B 250 *********************** 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 182 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 0.908 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: 0.7492 (pm20) cc_final: 0.7242 (pm20) REVERT: A 95 GLU cc_start: 0.8157 (mp0) cc_final: 0.7638 (mp0) REVERT: A 203 ASP cc_start: 0.6290 (OUTLIER) cc_final: 0.5831 (t70) REVERT: A 267 LYS cc_start: 0.8881 (mtmt) cc_final: 0.8634 (mtmt) REVERT: A 286 LYS cc_start: 0.9229 (tppt) cc_final: 0.8944 (tppt) REVERT: A 355 LYS cc_start: 0.9070 (tppt) cc_final: 0.8615 (tppt) REVERT: A 380 ASN cc_start: 0.9311 (p0) cc_final: 0.8816 (p0) REVERT: A 397 TYR cc_start: 0.8267 (m-80) cc_final: 0.7783 (m-10) REVERT: A 407 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7903 (ttm170) REVERT: A 415 GLU cc_start: 0.8985 (mp0) cc_final: 0.8655 (mp0) REVERT: B 92 MET cc_start: 0.9017 (pmm) cc_final: 0.8717 (pmm) REVERT: B 179 ILE cc_start: 0.9540 (mm) cc_final: 0.9137 (mp) REVERT: B 287 MET cc_start: 0.6224 (tpt) cc_final: 0.5277 (tpt) REVERT: B 296 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8252 (tm-30) REVERT: B 314 GLN cc_start: 0.8549 (pp30) cc_final: 0.7936 (pp30) REVERT: B 336 MET cc_start: 0.7611 (ppp) cc_final: 0.7302 (tmm) REVERT: B 392 TYR cc_start: 0.8643 (t80) cc_final: 0.8375 (t80) REVERT: B 400 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8226 (mmmm) outliers start: 36 outliers final: 27 residues processed: 169 average time/residue: 0.2676 time to fit residues: 58.5583 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 : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 ASP 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 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 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 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 217 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.131756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.104705 restraints weight = 23072.970| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 5.55 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4068 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= 0.258 Angle : 0.772 13.187 12040 Z= 0.392 Chirality : 0.046 0.223 1319 Planarity : 0.005 0.050 1372 Dihedral : 19.342 169.297 1597 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.02 % Allowed : 32.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.27), residues: 909 helix: 0.41 (0.30), residues: 309 sheet: -1.62 (0.47), residues: 105 loop : -1.86 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 369 HIS 0.004 0.001 HIS B 9 PHE 0.017 0.001 PHE A 403 TYR 0.020 0.001 TYR B 330 ARG 0.010 0.001 ARG A 275 *********************** 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 179 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.983 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: 0.7475 (pm20) cc_final: 0.7228 (pm20) REVERT: A 69 ASN cc_start: 0.7685 (p0) cc_final: 0.7162 (p0) REVERT: A 74 MET cc_start: 0.7524 (mpp) cc_final: 0.7047 (mpp) REVERT: A 95 GLU cc_start: 0.8200 (mp0) cc_final: 0.7696 (mp0) REVERT: A 203 ASP cc_start: 0.6192 (OUTLIER) cc_final: 0.5720 (t70) REVERT: A 267 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8670 (mtmt) REVERT: A 286 LYS cc_start: 0.9250 (tppt) cc_final: 0.8905 (tppt) REVERT: A 355 LYS cc_start: 0.9097 (tppt) cc_final: 0.8647 (tppt) REVERT: A 380 ASN cc_start: 0.9312 (p0) cc_final: 0.8839 (p0) REVERT: A 397 TYR cc_start: 0.8266 (m-80) cc_final: 0.7795 (m-10) REVERT: A 415 GLU cc_start: 0.8993 (mp0) cc_final: 0.8668 (mp0) REVERT: B 55 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9058 (mp0) REVERT: B 92 MET cc_start: 0.9011 (pmm) cc_final: 0.8716 (pmm) REVERT: B 111 GLU cc_start: 0.9251 (pp20) cc_final: 0.8465 (pp20) REVERT: B 179 ILE cc_start: 0.9514 (mm) cc_final: 0.9101 (mp) REVERT: B 287 MET cc_start: 0.6073 (tpt) cc_final: 0.4945 (tpt) REVERT: B 296 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 314 GLN cc_start: 0.8584 (pp30) cc_final: 0.7984 (pp30) REVERT: B 336 MET cc_start: 0.7624 (ppp) cc_final: 0.7314 (ppp) REVERT: B 392 TYR cc_start: 0.8651 (t80) cc_final: 0.8398 (t80) REVERT: B 400 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8227 (mmmm) outliers start: 33 outliers final: 27 residues processed: 168 average time/residue: 0.2752 time to fit residues: 59.4211 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 : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS 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 208 ASP 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 281 LEU 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 0.0060 chunk 39 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 HIS ** 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 = 0.4201 r_free = 0.4201 target = 0.140333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.114343 restraints weight = 24421.542| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 5.31 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4060 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= 0.222 Angle : 0.779 13.623 12040 Z= 0.394 Chirality : 0.046 0.220 1319 Planarity : 0.005 0.050 1372 Dihedral : 19.318 168.947 1597 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.78 % Allowed : 33.54 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.28), residues: 909 helix: 0.43 (0.30), residues: 309 sheet: -1.40 (0.44), residues: 132 loop : -1.90 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 421 HIS 0.003 0.001 HIS B 9 PHE 0.016 0.001 PHE A 403 TYR 0.019 0.001 TYR B 330 ARG 0.011 0.001 ARG B 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.844 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: 0.7431 (pm20) cc_final: 0.7180 (pm20) REVERT: A 69 ASN cc_start: 0.7672 (p0) cc_final: 0.7087 (p0) REVERT: A 74 MET cc_start: 0.7416 (mpp) cc_final: 0.7044 (mpp) REVERT: A 95 GLU cc_start: 0.8173 (mp0) cc_final: 0.7657 (mp0) REVERT: A 203 ASP cc_start: 0.6039 (OUTLIER) cc_final: 0.5595 (t70) REVERT: A 267 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8494 (mtmt) REVERT: A 285 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7799 (t80) REVERT: A 286 LYS cc_start: 0.9222 (tppt) cc_final: 0.8896 (tppt) REVERT: A 329 HIS cc_start: 0.7992 (m-70) cc_final: 0.7654 (m-70) REVERT: A 336 LYS cc_start: 0.8464 (pttm) cc_final: 0.8027 (pttm) REVERT: A 355 LYS cc_start: 0.9009 (tppt) cc_final: 0.8595 (tppt) REVERT: A 380 ASN cc_start: 0.9281 (p0) cc_final: 0.8772 (p0) REVERT: A 397 TYR cc_start: 0.8219 (m-80) cc_final: 0.7751 (m-10) REVERT: A 415 GLU cc_start: 0.8991 (mp0) cc_final: 0.8645 (mp0) REVERT: B 55 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8868 (mm-30) REVERT: B 92 MET cc_start: 0.9046 (pmm) cc_final: 0.8724 (pmm) REVERT: B 111 GLU cc_start: 0.9133 (pp20) cc_final: 0.8342 (pp20) REVERT: B 296 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 314 GLN cc_start: 0.8520 (pp30) cc_final: 0.7890 (pp30) REVERT: B 336 MET cc_start: 0.7573 (ppp) cc_final: 0.7266 (ppp) REVERT: B 392 TYR cc_start: 0.8614 (t80) cc_final: 0.8197 (t80) REVERT: B 400 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8362 (mmtt) outliers start: 31 outliers final: 25 residues processed: 164 average time/residue: 0.2623 time to fit residues: 56.0561 Evaluate side-chains 163 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 208 ASP 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 281 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 288 ILE 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 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 332 SER Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 34 optimal weight: 0.0670 chunk 92 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS ** 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 = 0.4156 r_free = 0.4156 target = 0.137488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.111729 restraints weight = 24708.026| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 5.27 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 8758 Z= 0.277 Angle : 0.792 12.923 12040 Z= 0.401 Chirality : 0.046 0.203 1319 Planarity : 0.005 0.052 1372 Dihedral : 19.442 168.562 1597 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.27), residues: 909 helix: 0.37 (0.30), residues: 309 sheet: -1.40 (0.49), residues: 105 loop : -1.86 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 369 HIS 0.005 0.001 HIS B 9 PHE 0.018 0.001 PHE A 403 TYR 0.021 0.002 TYR A 280 ARG 0.028 0.001 ARG B 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3770.06 seconds wall clock time: 68 minutes 4.00 seconds (4084.00 seconds total)