Starting phenix.real_space_refine on Wed Mar 12 21:52:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pd2_17598/03_2025/8pd2_17598.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pd2_17598/03_2025/8pd2_17598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pd2_17598/03_2025/8pd2_17598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pd2_17598/03_2025/8pd2_17598.map" model { file = "/net/cci-nas-00/data/ceres_data/8pd2_17598/03_2025/8pd2_17598.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pd2_17598/03_2025/8pd2_17598.cif" } resolution = 3.25 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 5402 2.51 5 N 1372 2.21 5 O 1452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8270 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8270 Classifications: {'peptide': 1047} Link IDs: {'PTRANS': 32, 'TRANS': 1014} Chain breaks: 4 Time building chain proxies: 6.39, per 1000 atoms: 0.77 Number of scatterers: 8270 At special positions: 0 Unit cell: (79.42, 120.384, 122.892, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1452 8.00 N 1372 7.00 C 5402 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 77.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.761A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 4.082A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.735A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 188 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.729A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 254 removed outlier: 4.196A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 318 removed outlier: 3.548A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 375 removed outlier: 3.785A pdb=" N THR A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 380 removed outlier: 3.722A pdb=" N VAL A 380 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 411 removed outlier: 3.710A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 446 Processing helix chain 'A' and resid 449 through 469 removed outlier: 3.995A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 removed outlier: 4.959A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.554A pdb=" N LEU A 518 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 515 through 519' Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.572A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 removed outlier: 3.596A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.757A pdb=" N LEU A 670 " --> pdb=" O LYS A 666 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N MET A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 691 removed outlier: 3.816A pdb=" N GLU A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 706 removed outlier: 3.873A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 732 Processing helix chain 'A' and resid 732 through 755 removed outlier: 3.597A pdb=" N ASN A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.805A pdb=" N ILE A 759 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 783 Processing helix chain 'A' and resid 795 through 810 removed outlier: 3.975A pdb=" N MET A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 852 Proline residue: A 819 - end of helix removed outlier: 3.746A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.792A pdb=" N GLN A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.670A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 941 removed outlier: 3.691A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 removed outlier: 3.655A pdb=" N LEU A 956 " --> pdb=" O PRO A 952 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 977 Processing helix chain 'A' and resid 1043 through 1050 removed outlier: 3.769A pdb=" N LEU A1048 " --> pdb=" O GLU A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1108 removed outlier: 3.519A pdb=" N ARG A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.374A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.966A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1126 removed outlier: 6.596A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136 601 hydrogen bonds defined for protein. 1773 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2613 1.34 - 1.46: 1899 1.46 - 1.58: 3840 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 8433 Sorted by residual: bond pdb=" CA ILE A 488 " pdb=" CB ILE A 488 " ideal model delta sigma weight residual 1.534 1.525 0.009 6.80e-03 2.16e+04 1.88e+00 bond pdb=" CA PHE A1080 " pdb=" CB PHE A1080 " ideal model delta sigma weight residual 1.527 1.505 0.022 1.75e-02 3.27e+03 1.59e+00 bond pdb=" C HIS A 889 " pdb=" N PRO A 890 " ideal model delta sigma weight residual 1.335 1.323 0.013 1.30e-02 5.92e+03 9.43e-01 bond pdb=" CB MET A1107 " pdb=" CG MET A1107 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.15e-01 bond pdb=" CA ILE A 488 " pdb=" C ILE A 488 " ideal model delta sigma weight residual 1.520 1.528 -0.008 8.80e-03 1.29e+04 8.39e-01 ... (remaining 8428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 11253 1.59 - 3.18: 148 3.18 - 4.77: 27 4.77 - 6.36: 3 6.36 - 7.95: 3 Bond angle restraints: 11434 Sorted by residual: angle pdb=" OG1 THR A 260 " pdb=" CB THR A 260 " pdb=" CG2 THR A 260 " ideal model delta sigma weight residual 109.30 103.33 5.97 2.00e+00 2.50e-01 8.92e+00 angle pdb=" OG1 THR A 783 " pdb=" CB THR A 783 " pdb=" CG2 THR A 783 " ideal model delta sigma weight residual 109.30 103.37 5.93 2.00e+00 2.50e-01 8.80e+00 angle pdb=" CA MET A1107 " pdb=" CB MET A1107 " pdb=" CG MET A1107 " ideal model delta sigma weight residual 114.10 119.99 -5.89 2.00e+00 2.50e-01 8.67e+00 angle pdb=" CB MET A 925 " pdb=" CG MET A 925 " pdb=" SD MET A 925 " ideal model delta sigma weight residual 112.70 120.65 -7.95 3.00e+00 1.11e-01 7.02e+00 angle pdb=" CB MET A 810 " pdb=" CG MET A 810 " pdb=" SD MET A 810 " ideal model delta sigma weight residual 112.70 120.16 -7.46 3.00e+00 1.11e-01 6.18e+00 ... (remaining 11429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 4617 17.18 - 34.35: 344 34.35 - 51.53: 66 51.53 - 68.71: 12 68.71 - 85.88: 7 Dihedral angle restraints: 5046 sinusoidal: 1997 harmonic: 3049 Sorted by residual: dihedral pdb=" CA ASP A1144 " pdb=" CB ASP A1144 " pdb=" CG ASP A1144 " pdb=" OD1 ASP A1144 " ideal model delta sinusoidal sigma weight residual -30.00 -84.60 54.60 1 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CG ARG A1185 " pdb=" CD ARG A1185 " pdb=" NE ARG A1185 " pdb=" CZ ARG A1185 " ideal model delta sinusoidal sigma weight residual 180.00 -136.73 -43.27 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CA LEU A 808 " pdb=" C LEU A 808 " pdb=" N ARG A 809 " pdb=" CA ARG A 809 " ideal model delta harmonic sigma weight residual 180.00 -164.51 -15.49 0 5.00e+00 4.00e-02 9.59e+00 ... (remaining 5043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 947 0.034 - 0.068: 311 0.068 - 0.102: 85 0.102 - 0.136: 25 0.136 - 0.170: 2 Chirality restraints: 1370 Sorted by residual: chirality pdb=" CB THR A 260 " pdb=" CA THR A 260 " pdb=" OG1 THR A 260 " pdb=" CG2 THR A 260 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CB THR A 783 " pdb=" CA THR A 783 " pdb=" OG1 THR A 783 " pdb=" CG2 THR A 783 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.99e-01 chirality pdb=" CA ILE A 948 " pdb=" N ILE A 948 " pdb=" C ILE A 948 " pdb=" CB ILE A 948 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1367 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 209 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 210 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 276 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 818 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO A 819 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 819 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 819 " 0.020 5.00e-02 4.00e+02 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2682 2.84 - 3.35: 8689 3.35 - 3.87: 13035 3.87 - 4.38: 14883 4.38 - 4.90: 25829 Nonbonded interactions: 65118 Sorted by model distance: nonbonded pdb=" NZ LYS A 664 " pdb=" CE2 TYR A 665 " model vdw 2.322 3.420 nonbonded pdb=" OE1 GLN A 900 " pdb=" NH2 ARG A 903 " model vdw 2.339 3.120 nonbonded pdb=" N GLN A1110 " pdb=" OE1 GLN A1110 " model vdw 2.366 3.120 nonbonded pdb=" N GLU A 606 " pdb=" OE1 GLU A 606 " model vdw 2.412 3.120 nonbonded pdb=" OE2 GLU A 581 " pdb=" NH1 ARG A 585 " model vdw 2.419 3.120 ... (remaining 65113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.310 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.720 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 0.030 8433 Z= 0.279 Angle : 0.520 7.950 11434 Z= 0.286 Chirality : 0.038 0.170 1370 Planarity : 0.003 0.039 1407 Dihedral : 12.987 85.882 3070 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.26), residues: 1037 helix: 0.83 (0.19), residues: 732 sheet: -0.58 (0.77), residues: 39 loop : -0.04 (0.39), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1112 HIS 0.005 0.001 HIS A 914 PHE 0.013 0.001 PHE A 365 TYR 0.008 0.001 TYR A 309 ARG 0.004 0.001 ARG A 809 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 121 PRO cc_start: 0.7139 (Cg_endo) cc_final: 0.6794 (Cg_exo) REVERT: A 125 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7326 (mt-10) REVERT: A 154 MET cc_start: 0.8182 (mtp) cc_final: 0.7935 (mtp) REVERT: A 155 ASP cc_start: 0.7234 (t0) cc_final: 0.6984 (t0) REVERT: A 163 PHE cc_start: 0.7505 (t80) cc_final: 0.7142 (t80) REVERT: A 209 ASP cc_start: 0.7481 (t0) cc_final: 0.6998 (t0) REVERT: A 233 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7003 (tt0) REVERT: A 295 ASN cc_start: 0.7472 (t0) cc_final: 0.7226 (t0) REVERT: A 337 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7236 (mp0) REVERT: A 346 GLU cc_start: 0.7067 (tt0) cc_final: 0.6829 (tt0) REVERT: A 375 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7716 (mtpt) REVERT: A 381 ASP cc_start: 0.7206 (m-30) cc_final: 0.6936 (m-30) REVERT: A 383 MET cc_start: 0.7419 (mmm) cc_final: 0.6718 (mmm) REVERT: A 385 TRP cc_start: 0.7899 (m100) cc_final: 0.7652 (m100) REVERT: A 475 GLN cc_start: 0.8158 (tp40) cc_final: 0.7908 (tp40) REVERT: A 485 ASP cc_start: 0.7799 (m-30) cc_final: 0.7307 (p0) REVERT: A 486 ILE cc_start: 0.8089 (mp) cc_final: 0.7758 (mp) REVERT: A 609 ARG cc_start: 0.7395 (mtp-110) cc_final: 0.7120 (mtm-85) REVERT: A 621 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6549 (mt-10) REVERT: A 632 LYS cc_start: 0.7912 (mtmt) cc_final: 0.7679 (mtmm) REVERT: A 740 PHE cc_start: 0.7072 (t80) cc_final: 0.6246 (t80) REVERT: A 856 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6590 (ttp80) REVERT: A 865 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6987 (ttp80) REVERT: A 911 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6870 (mm-30) REVERT: A 926 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7063 (mm-30) REVERT: A 954 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7270 (mp0) REVERT: A 1003 SER cc_start: 0.8622 (t) cc_final: 0.8121 (p) REVERT: A 1066 TYR cc_start: 0.8509 (m-80) cc_final: 0.8127 (m-80) REVERT: A 1116 LYS cc_start: 0.7396 (tppp) cc_final: 0.7165 (tppp) REVERT: A 1138 ILE cc_start: 0.7408 (mt) cc_final: 0.7142 (mp) REVERT: A 1173 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6697 (tttt) REVERT: A 1182 GLU cc_start: 0.6266 (mm-30) cc_final: 0.5601 (mm-30) REVERT: A 1190 ARG cc_start: 0.7533 (mmm-85) cc_final: 0.7248 (mmt90) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3098 time to fit residues: 103.7181 Evaluate side-chains 214 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 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 597 GLN A 613 GLN A 685 ASN A 691 ASN A 764 ASN A 831 ASN A 832 GLN A 877 GLN A 886 GLN A1120 HIS ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.111220 restraints weight = 11301.446| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.70 r_work: 0.3171 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8433 Z= 0.237 Angle : 0.555 10.065 11434 Z= 0.293 Chirality : 0.041 0.142 1370 Planarity : 0.004 0.044 1407 Dihedral : 3.909 16.369 1119 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.22 % Allowed : 9.44 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.79 (0.26), residues: 1037 helix: 1.66 (0.19), residues: 759 sheet: -0.37 (0.68), residues: 54 loop : 0.14 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 278 HIS 0.005 0.001 HIS A1133 PHE 0.020 0.002 PHE A 769 TYR 0.010 0.001 TYR A1066 ARG 0.013 0.001 ARG A 809 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8289 (mt-10) cc_final: 0.8034 (mt-10) REVERT: A 154 MET cc_start: 0.8589 (mtp) cc_final: 0.8298 (mtp) REVERT: A 163 PHE cc_start: 0.8317 (t80) cc_final: 0.7983 (t80) REVERT: A 209 ASP cc_start: 0.7691 (t0) cc_final: 0.7323 (t0) REVERT: A 233 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7400 (tt0) REVERT: A 250 LYS cc_start: 0.8569 (mttt) cc_final: 0.8347 (mttp) REVERT: A 277 LEU cc_start: 0.8500 (mt) cc_final: 0.8285 (mp) REVERT: A 375 LYS cc_start: 0.8373 (mtpp) cc_final: 0.8163 (mtpt) REVERT: A 383 MET cc_start: 0.8240 (mmm) cc_final: 0.7804 (mmm) REVERT: A 397 ILE cc_start: 0.8172 (pt) cc_final: 0.7862 (mt) REVERT: A 410 LEU cc_start: 0.8293 (mp) cc_final: 0.8027 (mt) REVERT: A 486 ILE cc_start: 0.8461 (mp) cc_final: 0.8206 (mp) REVERT: A 671 MET cc_start: 0.7862 (mmp) cc_final: 0.7363 (mmp) REVERT: A 676 HIS cc_start: 0.7824 (m-70) cc_final: 0.7258 (m-70) REVERT: A 680 PHE cc_start: 0.8067 (t80) cc_final: 0.7847 (t80) REVERT: A 740 PHE cc_start: 0.7512 (t80) cc_final: 0.7049 (t80) REVERT: A 828 LYS cc_start: 0.8421 (mmmt) cc_final: 0.8219 (mmtp) REVERT: A 872 GLU cc_start: 0.7935 (tp30) cc_final: 0.7727 (tp30) REVERT: A 926 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6873 (mm-30) REVERT: A 942 MET cc_start: 0.8503 (mmt) cc_final: 0.8085 (mmt) REVERT: A 1003 SER cc_start: 0.8807 (t) cc_final: 0.8491 (p) REVERT: A 1066 TYR cc_start: 0.8612 (m-80) cc_final: 0.8303 (m-80) REVERT: A 1116 LYS cc_start: 0.7820 (tppp) cc_final: 0.7557 (tppp) REVERT: A 1122 GLU cc_start: 0.8264 (tp30) cc_final: 0.8049 (mm-30) REVERT: A 1173 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7723 (tttt) REVERT: A 1190 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7926 (mmt90) outliers start: 20 outliers final: 11 residues processed: 219 average time/residue: 0.2515 time to fit residues: 71.4332 Evaluate side-chains 204 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1045 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 98 optimal weight: 0.1980 chunk 67 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A1191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.110526 restraints weight = 11477.145| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.69 r_work: 0.3184 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8433 Z= 0.209 Angle : 0.508 10.604 11434 Z= 0.265 Chirality : 0.040 0.135 1370 Planarity : 0.004 0.045 1407 Dihedral : 3.749 17.226 1119 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.67 % Allowed : 12.00 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.05 (0.26), residues: 1037 helix: 1.81 (0.19), residues: 759 sheet: -0.18 (0.68), residues: 54 loop : 0.38 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 278 HIS 0.004 0.001 HIS A1120 PHE 0.021 0.001 PHE A 769 TYR 0.012 0.001 TYR A 758 ARG 0.009 0.001 ARG A 856 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8419 (tp) cc_final: 0.8206 (tp) REVERT: A 125 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 154 MET cc_start: 0.8615 (mtp) cc_final: 0.8347 (mtp) REVERT: A 163 PHE cc_start: 0.8306 (t80) cc_final: 0.7954 (t80) REVERT: A 233 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7327 (tt0) REVERT: A 250 LYS cc_start: 0.8532 (mttt) cc_final: 0.8313 (mttp) REVERT: A 277 LEU cc_start: 0.8418 (mt) cc_final: 0.8188 (mp) REVERT: A 375 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8139 (mtpt) REVERT: A 383 MET cc_start: 0.8254 (mmm) cc_final: 0.7746 (mmm) REVERT: A 397 ILE cc_start: 0.8112 (pt) cc_final: 0.7867 (mt) REVERT: A 486 ILE cc_start: 0.8455 (mp) cc_final: 0.8150 (mm) REVERT: A 621 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6863 (mt-10) REVERT: A 671 MET cc_start: 0.7863 (mmp) cc_final: 0.7308 (mmp) REVERT: A 676 HIS cc_start: 0.7674 (m-70) cc_final: 0.7173 (m-70) REVERT: A 680 PHE cc_start: 0.7959 (t80) cc_final: 0.7717 (t80) REVERT: A 740 PHE cc_start: 0.7466 (t80) cc_final: 0.7027 (t80) REVERT: A 809 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7948 (mtp85) REVERT: A 828 LYS cc_start: 0.8359 (mmmt) cc_final: 0.8145 (mmtp) REVERT: A 926 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6820 (mm-30) REVERT: A 931 GLU cc_start: 0.7899 (tt0) cc_final: 0.7526 (mt-10) REVERT: A 942 MET cc_start: 0.8458 (mmt) cc_final: 0.8047 (mmt) REVERT: A 990 ARG cc_start: 0.8140 (ptp-110) cc_final: 0.7823 (ptp-110) REVERT: A 1003 SER cc_start: 0.8785 (t) cc_final: 0.8318 (m) REVERT: A 1066 TYR cc_start: 0.8617 (m-80) cc_final: 0.8191 (m-80) REVERT: A 1116 LYS cc_start: 0.7750 (tppp) cc_final: 0.7514 (tppp) REVERT: A 1173 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7717 (tttt) REVERT: A 1190 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7849 (mmt90) outliers start: 15 outliers final: 10 residues processed: 214 average time/residue: 0.2194 time to fit residues: 61.9902 Evaluate side-chains 204 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1136 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 18 optimal weight: 0.0770 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS A1120 HIS A1191 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.131749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110956 restraints weight = 11323.136| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.68 r_work: 0.3202 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8433 Z= 0.177 Angle : 0.490 10.100 11434 Z= 0.252 Chirality : 0.039 0.134 1370 Planarity : 0.004 0.045 1407 Dihedral : 3.642 17.778 1119 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.00 % Allowed : 12.78 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.23 (0.26), residues: 1037 helix: 1.96 (0.19), residues: 759 sheet: -0.09 (0.68), residues: 54 loop : 0.37 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.004 0.001 HIS A1120 PHE 0.021 0.001 PHE A 769 TYR 0.022 0.001 TYR A 984 ARG 0.006 0.001 ARG A 856 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8401 (tp) cc_final: 0.8197 (tp) REVERT: A 125 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 154 MET cc_start: 0.8535 (mtp) cc_final: 0.8286 (mtp) REVERT: A 163 PHE cc_start: 0.8258 (t80) cc_final: 0.7909 (t80) REVERT: A 187 ASN cc_start: 0.8191 (m-40) cc_final: 0.7772 (m-40) REVERT: A 216 LEU cc_start: 0.7856 (mt) cc_final: 0.7385 (mp) REVERT: A 233 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7339 (tt0) REVERT: A 250 LYS cc_start: 0.8512 (mttt) cc_final: 0.8297 (mttp) REVERT: A 277 LEU cc_start: 0.8398 (mt) cc_final: 0.8172 (mp) REVERT: A 375 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8182 (mtpt) REVERT: A 383 MET cc_start: 0.8226 (mmm) cc_final: 0.7805 (mmm) REVERT: A 397 ILE cc_start: 0.8153 (pt) cc_final: 0.7845 (mt) REVERT: A 486 ILE cc_start: 0.8452 (mp) cc_final: 0.8177 (mm) REVERT: A 621 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6840 (mt-10) REVERT: A 671 MET cc_start: 0.7865 (mmp) cc_final: 0.7289 (mmp) REVERT: A 676 HIS cc_start: 0.7603 (m-70) cc_final: 0.7105 (m-70) REVERT: A 740 PHE cc_start: 0.7452 (t80) cc_final: 0.7031 (t80) REVERT: A 931 GLU cc_start: 0.7905 (tt0) cc_final: 0.7554 (mt-10) REVERT: A 942 MET cc_start: 0.8504 (mmt) cc_final: 0.8094 (mmt) REVERT: A 990 ARG cc_start: 0.8117 (ptp-110) cc_final: 0.7915 (ptp-110) REVERT: A 1003 SER cc_start: 0.8730 (t) cc_final: 0.8334 (m) REVERT: A 1054 ASN cc_start: 0.8093 (p0) cc_final: 0.7826 (p0) REVERT: A 1072 ASP cc_start: 0.7372 (m-30) cc_final: 0.7160 (m-30) REVERT: A 1116 LYS cc_start: 0.7784 (tppp) cc_final: 0.7561 (tppp) REVERT: A 1173 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7726 (tttt) REVERT: A 1190 ARG cc_start: 0.8193 (mmm-85) cc_final: 0.7924 (mmt90) outliers start: 18 outliers final: 13 residues processed: 210 average time/residue: 0.3370 time to fit residues: 93.6913 Evaluate side-chains 203 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1136 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 4 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 101 optimal weight: 0.0370 chunk 3 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 830 ASN A 981 HIS A1191 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111121 restraints weight = 11345.136| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.68 r_work: 0.3196 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8433 Z= 0.203 Angle : 0.490 9.061 11434 Z= 0.253 Chirality : 0.039 0.134 1370 Planarity : 0.004 0.046 1407 Dihedral : 3.590 17.966 1119 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.89 % Allowed : 14.11 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.26), residues: 1037 helix: 2.00 (0.19), residues: 759 sheet: 0.18 (0.67), residues: 54 loop : 0.44 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 278 HIS 0.004 0.001 HIS A 676 PHE 0.022 0.001 PHE A 769 TYR 0.016 0.001 TYR A 758 ARG 0.004 0.001 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 122 LEU cc_start: 0.8406 (tp) cc_final: 0.8199 (tp) REVERT: A 125 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 154 MET cc_start: 0.8529 (mtp) cc_final: 0.8280 (mtp) REVERT: A 163 PHE cc_start: 0.8285 (t80) cc_final: 0.7929 (t80) REVERT: A 187 ASN cc_start: 0.8196 (m-40) cc_final: 0.7766 (m-40) REVERT: A 209 ASP cc_start: 0.7721 (t0) cc_final: 0.7346 (t0) REVERT: A 233 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7317 (tt0) REVERT: A 250 LYS cc_start: 0.8499 (mttt) cc_final: 0.8285 (mttp) REVERT: A 346 GLU cc_start: 0.7251 (tt0) cc_final: 0.6985 (tt0) REVERT: A 383 MET cc_start: 0.8238 (mmm) cc_final: 0.7863 (mmm) REVERT: A 397 ILE cc_start: 0.8146 (pt) cc_final: 0.7831 (mt) REVERT: A 486 ILE cc_start: 0.8475 (mp) cc_final: 0.8140 (mm) REVERT: A 621 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6942 (mt-10) REVERT: A 671 MET cc_start: 0.7845 (mmp) cc_final: 0.7224 (mmp) REVERT: A 676 HIS cc_start: 0.7569 (m-70) cc_final: 0.7070 (m-70) REVERT: A 697 MET cc_start: 0.6115 (mmm) cc_final: 0.5725 (mmm) REVERT: A 740 PHE cc_start: 0.7524 (t80) cc_final: 0.7135 (t80) REVERT: A 777 ASP cc_start: 0.5471 (m-30) cc_final: 0.5028 (t0) REVERT: A 926 GLU cc_start: 0.7405 (mp0) cc_final: 0.6905 (mm-30) REVERT: A 1003 SER cc_start: 0.8741 (t) cc_final: 0.8339 (m) REVERT: A 1054 ASN cc_start: 0.8146 (p0) cc_final: 0.7867 (p0) REVERT: A 1072 ASP cc_start: 0.7359 (m-30) cc_final: 0.7142 (m-30) REVERT: A 1116 LYS cc_start: 0.7793 (tppp) cc_final: 0.7562 (tppp) REVERT: A 1173 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7714 (tttt) outliers start: 17 outliers final: 11 residues processed: 207 average time/residue: 0.2344 time to fit residues: 64.0728 Evaluate side-chains 208 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1136 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS A 757 HIS A 981 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111184 restraints weight = 11186.332| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.72 r_work: 0.3202 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8433 Z= 0.287 Angle : 0.520 9.110 11434 Z= 0.268 Chirality : 0.040 0.153 1370 Planarity : 0.004 0.048 1407 Dihedral : 3.656 18.207 1119 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.67 % Allowed : 13.67 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.16 (0.26), residues: 1037 helix: 1.87 (0.19), residues: 760 sheet: 0.38 (0.67), residues: 54 loop : 0.34 (0.46), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.004 0.001 HIS A 676 PHE 0.024 0.001 PHE A 769 TYR 0.016 0.001 TYR A 758 ARG 0.005 0.000 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 121 PRO cc_start: 0.7799 (Cg_endo) cc_final: 0.7433 (Cg_exo) REVERT: A 122 LEU cc_start: 0.8402 (tp) cc_final: 0.8103 (tp) REVERT: A 125 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8098 (mt-10) REVERT: A 154 MET cc_start: 0.8591 (mtp) cc_final: 0.8256 (mtp) REVERT: A 163 PHE cc_start: 0.8344 (t80) cc_final: 0.8016 (t80) REVERT: A 187 ASN cc_start: 0.8214 (m-40) cc_final: 0.7804 (m-40) REVERT: A 209 ASP cc_start: 0.7750 (t0) cc_final: 0.7395 (t0) REVERT: A 233 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7319 (tt0) REVERT: A 344 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 383 MET cc_start: 0.8168 (mmm) cc_final: 0.7809 (mmm) REVERT: A 397 ILE cc_start: 0.8172 (pt) cc_final: 0.7856 (mt) REVERT: A 486 ILE cc_start: 0.8461 (mp) cc_final: 0.8178 (mm) REVERT: A 621 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7055 (mt-10) REVERT: A 671 MET cc_start: 0.7788 (mmp) cc_final: 0.7165 (mmp) REVERT: A 676 HIS cc_start: 0.7629 (m-70) cc_final: 0.7088 (m-70) REVERT: A 697 MET cc_start: 0.6196 (mmm) cc_final: 0.5788 (mmm) REVERT: A 740 PHE cc_start: 0.7598 (t80) cc_final: 0.7246 (t80) REVERT: A 810 MET cc_start: 0.7853 (mmp) cc_final: 0.7479 (mmt) REVERT: A 926 GLU cc_start: 0.7488 (mp0) cc_final: 0.6985 (mm-30) REVERT: A 1003 SER cc_start: 0.8748 (t) cc_final: 0.8339 (m) REVERT: A 1054 ASN cc_start: 0.8233 (p0) cc_final: 0.7973 (p0) REVERT: A 1066 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: A 1072 ASP cc_start: 0.7334 (m-30) cc_final: 0.7092 (m-30) REVERT: A 1116 LYS cc_start: 0.7868 (tppp) cc_final: 0.7628 (tppp) REVERT: A 1173 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7703 (tttt) outliers start: 24 outliers final: 16 residues processed: 212 average time/residue: 0.2400 time to fit residues: 66.6680 Evaluate side-chains 212 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1136 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 4 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.132830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111968 restraints weight = 11220.873| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.71 r_work: 0.3193 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8433 Z= 0.233 Angle : 0.495 8.134 11434 Z= 0.257 Chirality : 0.039 0.154 1370 Planarity : 0.004 0.047 1407 Dihedral : 3.640 18.807 1119 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.89 % Allowed : 13.56 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.25 (0.26), residues: 1037 helix: 1.94 (0.19), residues: 758 sheet: 0.45 (0.66), residues: 54 loop : 0.37 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 278 HIS 0.004 0.001 HIS A 676 PHE 0.024 0.001 PHE A 769 TYR 0.020 0.001 TYR A 758 ARG 0.006 0.001 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 121 PRO cc_start: 0.7769 (Cg_endo) cc_final: 0.7410 (Cg_exo) REVERT: A 122 LEU cc_start: 0.8379 (tp) cc_final: 0.8073 (tp) REVERT: A 125 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 154 MET cc_start: 0.8547 (mtp) cc_final: 0.8243 (mtp) REVERT: A 163 PHE cc_start: 0.8312 (t80) cc_final: 0.7980 (t80) REVERT: A 187 ASN cc_start: 0.8212 (m-40) cc_final: 0.7780 (m-40) REVERT: A 205 MET cc_start: 0.8132 (tpp) cc_final: 0.7883 (mmt) REVERT: A 209 ASP cc_start: 0.7718 (t0) cc_final: 0.7375 (t0) REVERT: A 233 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7360 (tt0) REVERT: A 375 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8229 (ttpt) REVERT: A 383 MET cc_start: 0.8148 (mmm) cc_final: 0.7798 (mmm) REVERT: A 397 ILE cc_start: 0.8185 (pt) cc_final: 0.7859 (mt) REVERT: A 486 ILE cc_start: 0.8459 (mp) cc_final: 0.8169 (mm) REVERT: A 579 MET cc_start: 0.7921 (tpt) cc_final: 0.7468 (tpt) REVERT: A 621 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6976 (mt-10) REVERT: A 671 MET cc_start: 0.7771 (mmp) cc_final: 0.7147 (mmp) REVERT: A 676 HIS cc_start: 0.7594 (m-70) cc_final: 0.7034 (m-70) REVERT: A 740 PHE cc_start: 0.7590 (t80) cc_final: 0.7273 (t80) REVERT: A 926 GLU cc_start: 0.7425 (mp0) cc_final: 0.6993 (mm-30) REVERT: A 976 ARG cc_start: 0.8776 (ttm-80) cc_final: 0.8410 (ttm-80) REVERT: A 1003 SER cc_start: 0.8748 (t) cc_final: 0.8326 (m) REVERT: A 1066 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8136 (m-80) REVERT: A 1116 LYS cc_start: 0.7850 (tppp) cc_final: 0.7609 (tppp) REVERT: A 1173 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7711 (tttt) outliers start: 26 outliers final: 18 residues processed: 208 average time/residue: 0.2420 time to fit residues: 66.2986 Evaluate side-chains 209 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1136 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 62 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.111946 restraints weight = 11380.572| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.67 r_work: 0.3180 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8433 Z= 0.200 Angle : 0.489 9.375 11434 Z= 0.253 Chirality : 0.039 0.143 1370 Planarity : 0.004 0.047 1407 Dihedral : 3.593 18.695 1119 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.78 % Allowed : 13.33 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.39 (0.26), residues: 1037 helix: 2.02 (0.19), residues: 761 sheet: 0.58 (0.66), residues: 54 loop : 0.48 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 635 HIS 0.003 0.001 HIS A 676 PHE 0.022 0.001 PHE A 769 TYR 0.022 0.001 TYR A 758 ARG 0.005 0.001 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 116 VAL cc_start: 0.8350 (p) cc_final: 0.8030 (t) REVERT: A 121 PRO cc_start: 0.7745 (Cg_endo) cc_final: 0.7398 (Cg_exo) REVERT: A 122 LEU cc_start: 0.8374 (tp) cc_final: 0.8101 (tp) REVERT: A 125 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 154 MET cc_start: 0.8547 (mtp) cc_final: 0.8272 (mtp) REVERT: A 163 PHE cc_start: 0.8291 (t80) cc_final: 0.7936 (t80) REVERT: A 187 ASN cc_start: 0.8187 (m-40) cc_final: 0.7758 (m-40) REVERT: A 205 MET cc_start: 0.8140 (tpp) cc_final: 0.7141 (mmt) REVERT: A 209 ASP cc_start: 0.7718 (t0) cc_final: 0.7359 (t0) REVERT: A 216 LEU cc_start: 0.7797 (mt) cc_final: 0.7488 (mp) REVERT: A 233 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7324 (tt0) REVERT: A 383 MET cc_start: 0.8152 (mmm) cc_final: 0.7778 (mmm) REVERT: A 397 ILE cc_start: 0.8135 (pt) cc_final: 0.7818 (mt) REVERT: A 486 ILE cc_start: 0.8433 (mp) cc_final: 0.8149 (mm) REVERT: A 579 MET cc_start: 0.7841 (tpt) cc_final: 0.7410 (tpt) REVERT: A 621 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6905 (mt-10) REVERT: A 671 MET cc_start: 0.7800 (mmp) cc_final: 0.7238 (mmt) REVERT: A 676 HIS cc_start: 0.7553 (m-70) cc_final: 0.7015 (m-70) REVERT: A 740 PHE cc_start: 0.7550 (t80) cc_final: 0.7251 (t80) REVERT: A 809 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7922 (mtp85) REVERT: A 926 GLU cc_start: 0.7530 (mp0) cc_final: 0.7200 (mm-30) REVERT: A 1003 SER cc_start: 0.8754 (t) cc_final: 0.8313 (m) REVERT: A 1066 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8121 (m-80) REVERT: A 1104 MET cc_start: 0.8092 (tpp) cc_final: 0.7799 (tpt) REVERT: A 1116 LYS cc_start: 0.7804 (tppp) cc_final: 0.7570 (tppp) REVERT: A 1173 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7668 (tttt) outliers start: 25 outliers final: 18 residues processed: 210 average time/residue: 0.2264 time to fit residues: 63.4934 Evaluate side-chains 213 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1136 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.132871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.111971 restraints weight = 11438.437| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.68 r_work: 0.3212 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8433 Z= 0.178 Angle : 0.485 8.846 11434 Z= 0.250 Chirality : 0.038 0.136 1370 Planarity : 0.003 0.046 1407 Dihedral : 3.523 18.535 1119 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.11 % Allowed : 14.00 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.54 (0.26), residues: 1037 helix: 2.13 (0.19), residues: 760 sheet: 0.61 (0.66), residues: 54 loop : 0.50 (0.46), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 278 HIS 0.003 0.001 HIS A 676 PHE 0.021 0.001 PHE A 769 TYR 0.011 0.001 TYR A 984 ARG 0.004 0.000 ARG A 940 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7934 (mt-10) REVERT: A 163 PHE cc_start: 0.8252 (t80) cc_final: 0.7909 (t80) REVERT: A 187 ASN cc_start: 0.8201 (m-40) cc_final: 0.7775 (m-40) REVERT: A 205 MET cc_start: 0.8093 (tpp) cc_final: 0.7118 (mmt) REVERT: A 209 ASP cc_start: 0.7692 (t0) cc_final: 0.7330 (t0) REVERT: A 216 LEU cc_start: 0.7814 (mt) cc_final: 0.7496 (mp) REVERT: A 233 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7325 (tt0) REVERT: A 383 MET cc_start: 0.8152 (mmm) cc_final: 0.7776 (mmm) REVERT: A 397 ILE cc_start: 0.8161 (pt) cc_final: 0.7833 (mt) REVERT: A 486 ILE cc_start: 0.8417 (mp) cc_final: 0.8138 (mm) REVERT: A 621 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6900 (mt-10) REVERT: A 671 MET cc_start: 0.7787 (mmp) cc_final: 0.7331 (mmp) REVERT: A 676 HIS cc_start: 0.7523 (m-70) cc_final: 0.6995 (m-70) REVERT: A 740 PHE cc_start: 0.7494 (t80) cc_final: 0.7267 (t80) REVERT: A 862 LYS cc_start: 0.8294 (ttmm) cc_final: 0.7993 (ttmm) REVERT: A 1003 SER cc_start: 0.8748 (t) cc_final: 0.8317 (m) REVERT: A 1066 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: A 1116 LYS cc_start: 0.7806 (tppp) cc_final: 0.7575 (tppp) REVERT: A 1173 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7669 (tttt) outliers start: 19 outliers final: 16 residues processed: 208 average time/residue: 0.2262 time to fit residues: 63.4134 Evaluate side-chains 207 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1136 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112030 restraints weight = 11365.769| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.67 r_work: 0.3205 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8433 Z= 0.213 Angle : 0.517 9.644 11434 Z= 0.264 Chirality : 0.039 0.137 1370 Planarity : 0.004 0.047 1407 Dihedral : 3.553 18.366 1119 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.00 % Allowed : 14.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.48 (0.26), residues: 1037 helix: 2.09 (0.19), residues: 760 sheet: 0.57 (0.65), residues: 54 loop : 0.49 (0.46), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 635 HIS 0.004 0.001 HIS A 676 PHE 0.021 0.001 PHE A 769 TYR 0.012 0.001 TYR A1009 ARG 0.005 0.000 ARG A 940 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7959 (mt-10) REVERT: A 163 PHE cc_start: 0.8278 (t80) cc_final: 0.7926 (t80) REVERT: A 187 ASN cc_start: 0.8199 (m-40) cc_final: 0.7779 (m-40) REVERT: A 205 MET cc_start: 0.8118 (tpp) cc_final: 0.7107 (mmt) REVERT: A 209 ASP cc_start: 0.7700 (t0) cc_final: 0.7328 (t0) REVERT: A 233 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7323 (tt0) REVERT: A 383 MET cc_start: 0.8151 (mmm) cc_final: 0.7783 (mmm) REVERT: A 397 ILE cc_start: 0.8138 (pt) cc_final: 0.7818 (mt) REVERT: A 486 ILE cc_start: 0.8429 (mp) cc_final: 0.8147 (mm) REVERT: A 621 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6886 (mt-10) REVERT: A 662 MET cc_start: 0.7310 (mmt) cc_final: 0.6949 (mmt) REVERT: A 671 MET cc_start: 0.7781 (mmp) cc_final: 0.7350 (mmp) REVERT: A 676 HIS cc_start: 0.7546 (m-70) cc_final: 0.7008 (m-70) REVERT: A 740 PHE cc_start: 0.7513 (t80) cc_final: 0.7284 (t80) REVERT: A 810 MET cc_start: 0.7647 (mmm) cc_final: 0.7446 (mmp) REVERT: A 862 LYS cc_start: 0.8379 (ttmm) cc_final: 0.8098 (ttmm) REVERT: A 926 GLU cc_start: 0.7587 (mp0) cc_final: 0.7278 (mm-30) REVERT: A 993 ASP cc_start: 0.7865 (m-30) cc_final: 0.7547 (m-30) REVERT: A 1066 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: A 1173 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7664 (tttt) outliers start: 18 outliers final: 17 residues processed: 204 average time/residue: 0.2875 time to fit residues: 80.7049 Evaluate side-chains 207 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 128 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 632 LYS Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1069 THR Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1136 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 81 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 103 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112242 restraints weight = 11456.518| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.69 r_work: 0.3218 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8433 Z= 0.177 Angle : 0.505 9.491 11434 Z= 0.258 Chirality : 0.038 0.133 1370 Planarity : 0.004 0.047 1407 Dihedral : 3.533 18.288 1119 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.11 % Allowed : 15.11 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.59 (0.26), residues: 1037 helix: 2.19 (0.19), residues: 758 sheet: 0.66 (0.65), residues: 54 loop : 0.47 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 635 HIS 0.004 0.001 HIS A 676 PHE 0.020 0.001 PHE A 769 TYR 0.012 0.001 TYR A 984 ARG 0.004 0.000 ARG A 940 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4764.03 seconds wall clock time: 85 minutes 42.07 seconds (5142.07 seconds total)