Starting phenix.real_space_refine on Fri Aug 22 22:00:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pd3_17599/08_2025/8pd3_17599.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pd3_17599/08_2025/8pd3_17599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pd3_17599/08_2025/8pd3_17599.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pd3_17599/08_2025/8pd3_17599.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pd3_17599/08_2025/8pd3_17599.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pd3_17599/08_2025/8pd3_17599.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 41 5.16 5 C 5303 2.51 5 N 1346 2.21 5 O 1431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8121 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8121 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 30, 'TRANS': 997} Chain breaks: 5 Time building chain proxies: 2.13, per 1000 atoms: 0.26 Number of scatterers: 8121 At special positions: 0 Unit cell: (79.42, 113.696, 125.4, 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 41 16.00 O 1431 8.00 N 1346 7.00 C 5303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 519.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 76.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.945A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.971A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.582A pdb=" N GLU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 154 removed outlier: 4.412A pdb=" N GLN A 140 " --> pdb=" O HIS A 136 " (cutoff:3.500A) Proline residue: A 144 - end of helix removed outlier: 3.985A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.561A pdb=" N VAL A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 188 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.996A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 254 removed outlier: 3.742A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A 251 " --> pdb=" O VAL A 247 " (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: 3.594A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.591A 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 376 removed outlier: 3.632A pdb=" N PHE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 411 removed outlier: 3.885A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.836A 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: 4.224A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 removed outlier: 4.836A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 514 through 519 removed outlier: 6.265A pdb=" N PHE A 517 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) 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 620 Processing helix chain 'A' and resid 627 through 636 removed outlier: 4.438A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TRP A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 653 removed outlier: 3.504A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 706 removed outlier: 4.342A pdb=" N VAL A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix removed outlier: 4.405A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 755 removed outlier: 3.753A pdb=" N ASP A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.944A pdb=" N ILE A 759 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 784 removed outlier: 3.936A pdb=" N LYS A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 767 " --> pdb=" O TRP A 763 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 771 " --> pdb=" O ASP A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 797 Processing helix chain 'A' and resid 798 through 811 removed outlier: 3.911A pdb=" N ARG A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU A 811 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 852 Proline residue: A 819 - end of helix removed outlier: 3.600A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 857 Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.630A pdb=" N GLN A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 942 removed outlier: 3.526A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 941 " --> pdb=" O LYS A 937 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET A 942 " --> pdb=" O MET A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 removed outlier: 3.641A pdb=" N LEU A 956 " --> pdb=" O PRO A 952 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 958 " --> pdb=" O GLU A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 964 Processing helix chain 'A' and resid 966 through 977 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1107 removed outlier: 3.617A 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 removed outlier: 3.710A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.460A 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: 6.816A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.848A 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: 6.689A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.001A 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 570 hydrogen bonds defined for protein. 1668 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: 1.34 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2574 1.35 - 1.46: 1857 1.46 - 1.58: 3772 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 8279 Sorted by residual: bond pdb=" N LEU A 70 " pdb=" CA LEU A 70 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" CA ILE A 488 " pdb=" CB ILE A 488 " ideal model delta sigma weight residual 1.534 1.524 0.010 6.80e-03 2.16e+04 2.26e+00 bond pdb=" CB GLU A1071 " pdb=" CG GLU A1071 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.92e-01 bond pdb=" CB GLU A 994 " pdb=" CG GLU A 994 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.91e-01 bond pdb=" CB ARG A 733 " pdb=" CG ARG A 733 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.25e-01 ... (remaining 8274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 10993 1.58 - 3.16: 196 3.16 - 4.74: 32 4.74 - 6.32: 7 6.32 - 7.90: 1 Bond angle restraints: 11229 Sorted by residual: angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 112.12 109.15 2.97 8.40e-01 1.42e+00 1.25e+01 angle pdb=" C LEU A 817 " pdb=" N ILE A 818 " pdb=" CA ILE A 818 " ideal model delta sigma weight residual 120.24 122.24 -2.00 6.30e-01 2.52e+00 1.00e+01 angle pdb=" C ILE A 818 " pdb=" CA ILE A 818 " pdb=" CB ILE A 818 " ideal model delta sigma weight residual 114.35 111.02 3.33 1.06e+00 8.90e-01 9.90e+00 angle pdb=" CA ARG A 733 " pdb=" CB ARG A 733 " pdb=" CG ARG A 733 " ideal model delta sigma weight residual 114.10 119.90 -5.80 2.00e+00 2.50e-01 8.40e+00 angle pdb=" CB MET A 925 " pdb=" CG MET A 925 " pdb=" SD MET A 925 " ideal model delta sigma weight residual 112.70 120.60 -7.90 3.00e+00 1.11e-01 6.94e+00 ... (remaining 11224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 4439 16.71 - 33.43: 400 33.43 - 50.14: 83 50.14 - 66.85: 14 66.85 - 83.57: 7 Dihedral angle restraints: 4943 sinusoidal: 1952 harmonic: 2991 Sorted by residual: dihedral pdb=" CA ARG A1162 " pdb=" C ARG A1162 " pdb=" N SER A1163 " pdb=" CA SER A1163 " ideal model delta harmonic sigma weight residual -180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LEU A 805 " pdb=" C LEU A 805 " pdb=" N ARG A 806 " pdb=" CA ARG A 806 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN A 448 " pdb=" C ASN A 448 " pdb=" N ASP A 449 " pdb=" CA ASP A 449 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 873 0.032 - 0.063: 326 0.063 - 0.095: 110 0.095 - 0.127: 37 0.127 - 0.158: 4 Chirality restraints: 1350 Sorted by residual: 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 2.59 -0.16 2.00e-01 2.50e+01 6.25e-01 chirality pdb=" CA ILE A 742 " pdb=" N ILE A 742 " pdb=" C ILE A 742 " pdb=" CB ILE A 742 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ASN A 448 " pdb=" N ASN A 448 " pdb=" C ASN A 448 " pdb=" CB ASN A 448 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1347 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 120 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO A 121 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1163 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A1164 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1164 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1164 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 733 " 0.142 9.50e-02 1.11e+02 6.37e-02 2.57e+00 pdb=" NE ARG A 733 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 733 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 733 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 733 " 0.003 2.00e-02 2.50e+03 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1377 2.76 - 3.30: 8397 3.30 - 3.83: 12765 3.83 - 4.37: 15061 4.37 - 4.90: 26259 Nonbonded interactions: 63859 Sorted by model distance: nonbonded pdb=" N GLU A 954 " pdb=" OE1 GLU A 954 " model vdw 2.227 3.120 nonbonded pdb=" N GLU A 994 " pdb=" OE1 GLU A 994 " model vdw 2.228 3.120 nonbonded pdb=" O PHE A 254 " pdb=" NE2 GLN A 256 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASN A 237 " pdb=" N ASP A 238 " model vdw 2.270 3.120 nonbonded pdb=" N GLU A1071 " pdb=" OE1 GLU A1071 " model vdw 2.273 3.120 ... (remaining 63854 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.370 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 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 : 0.003 0.035 8279 Z= 0.125 Angle : 0.560 7.902 11229 Z= 0.307 Chirality : 0.039 0.158 1350 Planarity : 0.004 0.068 1383 Dihedral : 13.667 83.567 3003 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.26), residues: 1016 helix: 0.81 (0.19), residues: 725 sheet: 0.93 (0.84), residues: 38 loop : -0.35 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 573 TYR 0.010 0.001 TYR A1178 PHE 0.018 0.001 PHE A 740 TRP 0.013 0.001 TRP A 635 HIS 0.006 0.001 HIS A 132 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8279) covalent geometry : angle 0.55968 (11229) hydrogen bonds : bond 0.17928 ( 570) hydrogen bonds : angle 6.58670 ( 1668) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.206 Fit side-chains REVERT: A 113 LEU cc_start: 0.7467 (tt) cc_final: 0.7187 (tp) REVERT: A 128 ARG cc_start: 0.7103 (ttm170) cc_final: 0.6867 (ttm-80) REVERT: A 160 MET cc_start: 0.6836 (mmt) cc_final: 0.6409 (mmm) REVERT: A 176 VAL cc_start: 0.7544 (p) cc_final: 0.7255 (m) REVERT: A 346 GLU cc_start: 0.6953 (tt0) cc_final: 0.6704 (tt0) REVERT: A 375 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7340 (mtmm) REVERT: A 385 TRP cc_start: 0.7977 (m100) cc_final: 0.7460 (m100) REVERT: A 579 MET cc_start: 0.6806 (tpt) cc_final: 0.6169 (tpt) REVERT: A 624 GLN cc_start: 0.7425 (mm-40) cc_final: 0.6997 (mm-40) REVERT: A 684 ILE cc_start: 0.7616 (mm) cc_final: 0.7388 (mt) REVERT: A 697 MET cc_start: 0.6534 (mmm) cc_final: 0.5858 (mmm) REVERT: A 852 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7998 (mmmt) REVERT: A 972 PHE cc_start: 0.7776 (t80) cc_final: 0.7446 (t80) REVERT: A 1054 ASN cc_start: 0.8049 (t0) cc_final: 0.7819 (t0) REVERT: A 1133 HIS cc_start: 0.6011 (t70) cc_final: 0.5781 (t-90) REVERT: A 1173 LYS cc_start: 0.7030 (ttmt) cc_final: 0.6603 (ttmm) REVERT: A 1183 GLU cc_start: 0.7767 (tt0) cc_final: 0.7538 (tt0) REVERT: A 1185 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7465 (mmm160) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.0931 time to fit residues: 26.3421 Evaluate side-chains 205 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 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 335 ASN A 374 GLN A 636 GLN A 691 ASN A 886 GLN A 981 HIS A1114 GLN A1120 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.135411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.113061 restraints weight = 11064.830| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.87 r_work: 0.3207 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8279 Z= 0.145 Angle : 0.548 7.685 11229 Z= 0.293 Chirality : 0.041 0.168 1350 Planarity : 0.004 0.059 1383 Dihedral : 4.197 19.397 1097 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.58 % Allowed : 13.12 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.26), residues: 1016 helix: 1.53 (0.19), residues: 732 sheet: 1.19 (1.05), residues: 28 loop : 0.01 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 903 TYR 0.014 0.001 TYR A 267 PHE 0.016 0.002 PHE A1136 TRP 0.014 0.001 TRP A 278 HIS 0.003 0.001 HIS A1133 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8279) covalent geometry : angle 0.54755 (11229) hydrogen bonds : bond 0.04733 ( 570) hydrogen bonds : angle 4.42607 ( 1668) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 160 MET cc_start: 0.7345 (mmt) cc_final: 0.7003 (mmm) REVERT: A 176 VAL cc_start: 0.8463 (p) cc_final: 0.8063 (m) REVERT: A 186 MET cc_start: 0.7789 (mtp) cc_final: 0.7553 (mtp) REVERT: A 187 ASN cc_start: 0.8077 (m-40) cc_final: 0.7810 (m-40) REVERT: A 217 LEU cc_start: 0.8280 (mp) cc_final: 0.7925 (mp) REVERT: A 375 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7815 (mtmm) REVERT: A 385 TRP cc_start: 0.8384 (m100) cc_final: 0.8110 (m100) REVERT: A 579 MET cc_start: 0.7583 (tpt) cc_final: 0.7157 (tpt) REVERT: A 684 ILE cc_start: 0.8213 (mm) cc_final: 0.7894 (mt) REVERT: A 697 MET cc_start: 0.6186 (mmm) cc_final: 0.5522 (mmm) REVERT: A 736 ASN cc_start: 0.7597 (m-40) cc_final: 0.7005 (m-40) REVERT: A 958 LYS cc_start: 0.7959 (ttpp) cc_final: 0.7407 (ttpp) REVERT: A 990 ARG cc_start: 0.7864 (ttm110) cc_final: 0.7227 (ttm110) REVERT: A 1054 ASN cc_start: 0.8342 (t0) cc_final: 0.8045 (t0) REVERT: A 1058 THR cc_start: 0.8555 (m) cc_final: 0.8348 (p) REVERT: A 1142 LEU cc_start: 0.5681 (tt) cc_final: 0.5455 (tp) REVERT: A 1173 LYS cc_start: 0.7840 (ttmt) cc_final: 0.7549 (ttmm) REVERT: A 1191 ASN cc_start: 0.7520 (m-40) cc_final: 0.7298 (m-40) outliers start: 14 outliers final: 5 residues processed: 216 average time/residue: 0.0804 time to fit residues: 22.8657 Evaluate side-chains 202 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 430 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 600 HIS A 691 ASN A 832 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.134094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.111652 restraints weight = 11038.592| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.88 r_work: 0.3192 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8279 Z= 0.156 Angle : 0.510 6.917 11229 Z= 0.273 Chirality : 0.040 0.153 1350 Planarity : 0.004 0.053 1383 Dihedral : 4.023 18.868 1097 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.15 % Allowed : 14.25 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.26), residues: 1016 helix: 1.64 (0.19), residues: 732 sheet: 0.70 (0.82), residues: 38 loop : -0.08 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 856 TYR 0.009 0.001 TYR A 309 PHE 0.015 0.002 PHE A1136 TRP 0.016 0.001 TRP A 278 HIS 0.009 0.001 HIS A1133 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8279) covalent geometry : angle 0.51015 (11229) hydrogen bonds : bond 0.04381 ( 570) hydrogen bonds : angle 4.21417 ( 1668) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7466 (mmt) cc_final: 0.7145 (mmm) REVERT: A 176 VAL cc_start: 0.8413 (p) cc_final: 0.8036 (m) REVERT: A 186 MET cc_start: 0.7934 (mtp) cc_final: 0.7716 (mtp) REVERT: A 217 LEU cc_start: 0.8194 (mp) cc_final: 0.7817 (mp) REVERT: A 375 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7910 (mtmm) REVERT: A 383 MET cc_start: 0.7534 (mmp) cc_final: 0.7282 (mmp) REVERT: A 385 TRP cc_start: 0.8362 (m100) cc_final: 0.8121 (m100) REVERT: A 579 MET cc_start: 0.7491 (tpt) cc_final: 0.7167 (tpt) REVERT: A 584 LEU cc_start: 0.8535 (mt) cc_final: 0.8310 (mm) REVERT: A 684 ILE cc_start: 0.8191 (mm) cc_final: 0.7872 (mt) REVERT: A 697 MET cc_start: 0.6202 (mmm) cc_final: 0.5595 (mmm) REVERT: A 958 LYS cc_start: 0.8026 (ttpp) cc_final: 0.7462 (ttpp) REVERT: A 990 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7179 (ttm110) REVERT: A 1037 THR cc_start: 0.8463 (t) cc_final: 0.8094 (m) REVERT: A 1058 THR cc_start: 0.8513 (m) cc_final: 0.8277 (p) REVERT: A 1173 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7555 (ttmm) REVERT: A 1191 ASN cc_start: 0.7544 (m-40) cc_final: 0.7308 (m-40) outliers start: 19 outliers final: 10 residues processed: 217 average time/residue: 0.0883 time to fit residues: 25.3805 Evaluate side-chains 210 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 691 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 0.0970 chunk 82 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 374 GLN A 832 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.111776 restraints weight = 11300.352| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.92 r_work: 0.3201 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8279 Z= 0.136 Angle : 0.483 6.934 11229 Z= 0.257 Chirality : 0.039 0.149 1350 Planarity : 0.004 0.051 1383 Dihedral : 3.911 19.197 1097 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.15 % Allowed : 14.93 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.26), residues: 1016 helix: 1.80 (0.19), residues: 726 sheet: 0.54 (0.92), residues: 33 loop : -0.02 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 903 TYR 0.008 0.001 TYR A 309 PHE 0.013 0.001 PHE A1136 TRP 0.014 0.001 TRP A 278 HIS 0.005 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 8279) covalent geometry : angle 0.48323 (11229) hydrogen bonds : bond 0.04076 ( 570) hydrogen bonds : angle 4.05386 ( 1668) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 160 MET cc_start: 0.7503 (mmt) cc_final: 0.7177 (mmm) REVERT: A 176 VAL cc_start: 0.8383 (p) cc_final: 0.8021 (m) REVERT: A 186 MET cc_start: 0.7983 (mtp) cc_final: 0.7753 (mtp) REVERT: A 217 LEU cc_start: 0.8176 (mp) cc_final: 0.7778 (mp) REVERT: A 375 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7944 (mtmm) REVERT: A 383 MET cc_start: 0.7527 (mmp) cc_final: 0.7303 (mmp) REVERT: A 579 MET cc_start: 0.7463 (tpt) cc_final: 0.7150 (tpt) REVERT: A 624 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7559 (tt0) REVERT: A 684 ILE cc_start: 0.8191 (mm) cc_final: 0.7857 (mt) REVERT: A 697 MET cc_start: 0.6258 (mmm) cc_final: 0.5699 (mmm) REVERT: A 958 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7456 (ttpp) REVERT: A 990 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7370 (ttm110) REVERT: A 1037 THR cc_start: 0.8452 (t) cc_final: 0.8101 (m) REVERT: A 1054 ASN cc_start: 0.8328 (t0) cc_final: 0.8069 (t0) REVERT: A 1058 THR cc_start: 0.8522 (m) cc_final: 0.8239 (p) REVERT: A 1142 LEU cc_start: 0.5836 (tt) cc_final: 0.5594 (tp) REVERT: A 1173 LYS cc_start: 0.7848 (ttmt) cc_final: 0.7563 (ttmm) REVERT: A 1191 ASN cc_start: 0.7577 (m-40) cc_final: 0.7330 (m-40) outliers start: 19 outliers final: 14 residues processed: 218 average time/residue: 0.0949 time to fit residues: 27.2735 Evaluate side-chains 218 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.133434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110870 restraints weight = 11172.312| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.90 r_work: 0.3175 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8279 Z= 0.166 Angle : 0.502 8.017 11229 Z= 0.265 Chirality : 0.040 0.147 1350 Planarity : 0.004 0.049 1383 Dihedral : 3.898 18.351 1097 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.60 % Allowed : 14.71 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.26), residues: 1016 helix: 1.83 (0.19), residues: 726 sheet: 0.70 (0.83), residues: 38 loop : -0.17 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1092 TYR 0.011 0.001 TYR A 984 PHE 0.021 0.002 PHE A 972 TRP 0.015 0.001 TRP A 278 HIS 0.007 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8279) covalent geometry : angle 0.50152 (11229) hydrogen bonds : bond 0.04137 ( 570) hydrogen bonds : angle 4.00222 ( 1668) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7503 (mmt) cc_final: 0.7161 (mmm) REVERT: A 176 VAL cc_start: 0.8385 (p) cc_final: 0.8029 (m) REVERT: A 186 MET cc_start: 0.8091 (mtp) cc_final: 0.7853 (mtp) REVERT: A 190 ASN cc_start: 0.8526 (p0) cc_final: 0.8326 (p0) REVERT: A 217 LEU cc_start: 0.8172 (mp) cc_final: 0.7762 (mp) REVERT: A 375 LYS cc_start: 0.8208 (mtmt) cc_final: 0.8004 (mtmm) REVERT: A 383 MET cc_start: 0.7610 (mmp) cc_final: 0.7302 (mmp) REVERT: A 624 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7526 (tt0) REVERT: A 684 ILE cc_start: 0.8175 (mm) cc_final: 0.7819 (mt) REVERT: A 736 ASN cc_start: 0.7720 (m-40) cc_final: 0.7273 (m-40) REVERT: A 832 GLN cc_start: 0.8403 (tp40) cc_final: 0.8173 (tp40) REVERT: A 958 LYS cc_start: 0.8073 (ttpp) cc_final: 0.7480 (ttpp) REVERT: A 990 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7397 (ttm110) REVERT: A 1037 THR cc_start: 0.8474 (t) cc_final: 0.8127 (m) REVERT: A 1173 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7567 (ttmm) outliers start: 23 outliers final: 17 residues processed: 218 average time/residue: 0.1059 time to fit residues: 30.3310 Evaluate side-chains 219 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 809 ARG Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.134866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112377 restraints weight = 11106.668| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.90 r_work: 0.3204 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8279 Z= 0.123 Angle : 0.467 8.496 11229 Z= 0.247 Chirality : 0.039 0.144 1350 Planarity : 0.004 0.047 1383 Dihedral : 3.795 18.841 1097 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.60 % Allowed : 16.06 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.27), residues: 1016 helix: 2.04 (0.19), residues: 723 sheet: 0.70 (0.81), residues: 43 loop : 0.04 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1190 TYR 0.009 0.001 TYR A 984 PHE 0.013 0.001 PHE A 769 TRP 0.013 0.001 TRP A 278 HIS 0.004 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8279) covalent geometry : angle 0.46676 (11229) hydrogen bonds : bond 0.03793 ( 570) hydrogen bonds : angle 3.85362 ( 1668) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 128 ARG cc_start: 0.7850 (ttm110) cc_final: 0.7624 (ptp-110) REVERT: A 160 MET cc_start: 0.7457 (mmt) cc_final: 0.7145 (mmm) REVERT: A 176 VAL cc_start: 0.8353 (p) cc_final: 0.8018 (m) REVERT: A 186 MET cc_start: 0.8054 (mtp) cc_final: 0.7820 (mtp) REVERT: A 190 ASN cc_start: 0.8492 (p0) cc_final: 0.8280 (p0) REVERT: A 217 LEU cc_start: 0.8170 (mp) cc_final: 0.7755 (mp) REVERT: A 375 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7974 (mtmm) REVERT: A 383 MET cc_start: 0.7578 (mmp) cc_final: 0.7259 (mmp) REVERT: A 579 MET cc_start: 0.7494 (tpt) cc_final: 0.7128 (tpt) REVERT: A 584 LEU cc_start: 0.8544 (mm) cc_final: 0.8187 (mp) REVERT: A 624 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7485 (tt0) REVERT: A 684 ILE cc_start: 0.8155 (mm) cc_final: 0.7780 (mt) REVERT: A 685 ASN cc_start: 0.8316 (m-40) cc_final: 0.8043 (m-40) REVERT: A 697 MET cc_start: 0.6439 (mmm) cc_final: 0.6076 (mmm) REVERT: A 736 ASN cc_start: 0.7689 (m-40) cc_final: 0.7238 (m-40) REVERT: A 832 GLN cc_start: 0.8408 (tp40) cc_final: 0.8192 (tp40) REVERT: A 881 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8091 (mt-10) REVERT: A 958 LYS cc_start: 0.8113 (ttpp) cc_final: 0.7513 (ttpp) REVERT: A 990 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7387 (ttm110) REVERT: A 1037 THR cc_start: 0.8449 (t) cc_final: 0.8107 (m) REVERT: A 1173 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7567 (ttmm) outliers start: 23 outliers final: 18 residues processed: 215 average time/residue: 0.1103 time to fit residues: 31.0055 Evaluate side-chains 217 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111954 restraints weight = 11144.254| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.89 r_work: 0.3181 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8279 Z= 0.155 Angle : 0.489 7.709 11229 Z= 0.257 Chirality : 0.039 0.144 1350 Planarity : 0.004 0.049 1383 Dihedral : 3.788 18.427 1097 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.83 % Allowed : 16.29 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.26), residues: 1016 helix: 2.01 (0.19), residues: 723 sheet: 0.69 (0.96), residues: 28 loop : 0.03 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 161 TYR 0.017 0.001 TYR A 267 PHE 0.017 0.001 PHE A 254 TRP 0.014 0.001 TRP A 278 HIS 0.006 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8279) covalent geometry : angle 0.48884 (11229) hydrogen bonds : bond 0.03941 ( 570) hydrogen bonds : angle 3.85556 ( 1668) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.314 Fit side-chains REVERT: A 160 MET cc_start: 0.7446 (mmt) cc_final: 0.7126 (mmm) REVERT: A 176 VAL cc_start: 0.8397 (p) cc_final: 0.8054 (m) REVERT: A 186 MET cc_start: 0.8116 (mtp) cc_final: 0.7875 (mtp) REVERT: A 190 ASN cc_start: 0.8517 (p0) cc_final: 0.8304 (p0) REVERT: A 217 LEU cc_start: 0.8185 (mp) cc_final: 0.7785 (mp) REVERT: A 375 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7966 (mtmm) REVERT: A 383 MET cc_start: 0.7592 (mmp) cc_final: 0.7269 (mmp) REVERT: A 579 MET cc_start: 0.7536 (tpt) cc_final: 0.7202 (tpt) REVERT: A 609 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7718 (mtm-85) REVERT: A 624 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7560 (tt0) REVERT: A 684 ILE cc_start: 0.8181 (mm) cc_final: 0.7805 (mt) REVERT: A 685 ASN cc_start: 0.8337 (m-40) cc_final: 0.8058 (m-40) REVERT: A 697 MET cc_start: 0.6471 (mmm) cc_final: 0.6106 (mmm) REVERT: A 736 ASN cc_start: 0.7707 (m-40) cc_final: 0.7234 (m-40) REVERT: A 832 GLN cc_start: 0.8397 (tp40) cc_final: 0.8158 (tp40) REVERT: A 881 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8098 (mt-10) REVERT: A 958 LYS cc_start: 0.8114 (ttpp) cc_final: 0.7527 (ttpp) REVERT: A 990 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7430 (ttm110) REVERT: A 1037 THR cc_start: 0.8447 (t) cc_final: 0.8109 (m) REVERT: A 1173 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7587 (ttmm) outliers start: 25 outliers final: 20 residues processed: 213 average time/residue: 0.1091 time to fit residues: 30.4944 Evaluate side-chains 217 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 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 374 GLN A1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112213 restraints weight = 11111.991| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.89 r_work: 0.3201 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8279 Z= 0.134 Angle : 0.480 7.699 11229 Z= 0.253 Chirality : 0.039 0.142 1350 Planarity : 0.004 0.048 1383 Dihedral : 3.756 18.552 1097 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.49 % Allowed : 16.86 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.26), residues: 1016 helix: 2.02 (0.19), residues: 727 sheet: 0.73 (0.83), residues: 38 loop : -0.06 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 161 TYR 0.014 0.001 TYR A 267 PHE 0.022 0.001 PHE A1109 TRP 0.013 0.001 TRP A 278 HIS 0.005 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8279) covalent geometry : angle 0.48049 (11229) hydrogen bonds : bond 0.03786 ( 570) hydrogen bonds : angle 3.79210 ( 1668) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.311 Fit side-chains REVERT: A 160 MET cc_start: 0.7456 (mmt) cc_final: 0.7127 (mmm) REVERT: A 176 VAL cc_start: 0.8334 (p) cc_final: 0.8012 (m) REVERT: A 186 MET cc_start: 0.8068 (mtp) cc_final: 0.7843 (mtp) REVERT: A 190 ASN cc_start: 0.8499 (p0) cc_final: 0.8278 (p0) REVERT: A 217 LEU cc_start: 0.8186 (mp) cc_final: 0.7776 (mp) REVERT: A 375 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7968 (mtmm) REVERT: A 383 MET cc_start: 0.7564 (mmp) cc_final: 0.7237 (mmp) REVERT: A 579 MET cc_start: 0.7473 (tpt) cc_final: 0.7124 (tpt) REVERT: A 609 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7674 (mtm-85) REVERT: A 624 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7568 (tt0) REVERT: A 684 ILE cc_start: 0.8177 (mm) cc_final: 0.7804 (mt) REVERT: A 685 ASN cc_start: 0.8333 (m-40) cc_final: 0.8046 (m-40) REVERT: A 697 MET cc_start: 0.6547 (mmm) cc_final: 0.6185 (mmm) REVERT: A 736 ASN cc_start: 0.7686 (m-40) cc_final: 0.7217 (m-40) REVERT: A 832 GLN cc_start: 0.8396 (tp40) cc_final: 0.8154 (tp40) REVERT: A 857 MET cc_start: 0.8051 (tpp) cc_final: 0.7657 (tpp) REVERT: A 881 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8099 (mt-10) REVERT: A 958 LYS cc_start: 0.8105 (ttpp) cc_final: 0.7502 (ttpp) REVERT: A 990 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7431 (ttm110) REVERT: A 1037 THR cc_start: 0.8442 (t) cc_final: 0.8108 (m) REVERT: A 1173 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7567 (ttmm) REVERT: A 1182 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7475 (mm-30) outliers start: 22 outliers final: 21 residues processed: 213 average time/residue: 0.1088 time to fit residues: 30.2736 Evaluate side-chains 221 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.0060 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A1074 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.135186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112726 restraints weight = 11016.233| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.88 r_work: 0.3199 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8279 Z= 0.128 Angle : 0.486 7.584 11229 Z= 0.253 Chirality : 0.039 0.177 1350 Planarity : 0.004 0.048 1383 Dihedral : 3.732 19.241 1097 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.49 % Allowed : 16.86 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.27), residues: 1016 helix: 2.05 (0.19), residues: 727 sheet: 0.76 (0.99), residues: 28 loop : 0.10 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 161 TYR 0.013 0.001 TYR A 267 PHE 0.014 0.001 PHE A 254 TRP 0.013 0.001 TRP A 278 HIS 0.005 0.001 HIS A1133 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8279) covalent geometry : angle 0.48579 (11229) hydrogen bonds : bond 0.03721 ( 570) hydrogen bonds : angle 3.76244 ( 1668) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 160 MET cc_start: 0.7440 (mmt) cc_final: 0.7115 (mmm) REVERT: A 176 VAL cc_start: 0.8325 (p) cc_final: 0.8005 (m) REVERT: A 186 MET cc_start: 0.8068 (mtp) cc_final: 0.7839 (mtp) REVERT: A 190 ASN cc_start: 0.8494 (p0) cc_final: 0.8276 (p0) REVERT: A 217 LEU cc_start: 0.8184 (mp) cc_final: 0.7767 (mp) REVERT: A 375 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7981 (mtmm) REVERT: A 383 MET cc_start: 0.7538 (mmp) cc_final: 0.7208 (mmp) REVERT: A 579 MET cc_start: 0.7477 (tpt) cc_final: 0.7174 (tpt) REVERT: A 584 LEU cc_start: 0.8455 (mm) cc_final: 0.8091 (mp) REVERT: A 609 ARG cc_start: 0.7968 (mtp-110) cc_final: 0.7669 (mtm-85) REVERT: A 624 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7571 (tt0) REVERT: A 684 ILE cc_start: 0.8187 (mm) cc_final: 0.7813 (mt) REVERT: A 685 ASN cc_start: 0.8278 (m-40) cc_final: 0.8001 (m-40) REVERT: A 697 MET cc_start: 0.6519 (mmm) cc_final: 0.6169 (mmm) REVERT: A 736 ASN cc_start: 0.7701 (m-40) cc_final: 0.7240 (m-40) REVERT: A 769 PHE cc_start: 0.7488 (t80) cc_final: 0.7261 (t80) REVERT: A 832 GLN cc_start: 0.8409 (tp40) cc_final: 0.8169 (tp40) REVERT: A 857 MET cc_start: 0.8070 (tpp) cc_final: 0.7685 (tpp) REVERT: A 881 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8093 (mt-10) REVERT: A 958 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7503 (ttpp) REVERT: A 990 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7441 (ttm110) REVERT: A 1037 THR cc_start: 0.8427 (t) cc_final: 0.8096 (m) REVERT: A 1173 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7576 (ttmm) REVERT: A 1182 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7474 (mm-30) outliers start: 22 outliers final: 20 residues processed: 212 average time/residue: 0.1094 time to fit residues: 30.3609 Evaluate side-chains 215 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 0.0030 chunk 18 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A1074 ASN A1120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.136463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114028 restraints weight = 11116.490| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.88 r_work: 0.3224 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8279 Z= 0.110 Angle : 0.496 11.059 11229 Z= 0.254 Chirality : 0.038 0.152 1350 Planarity : 0.004 0.048 1383 Dihedral : 3.655 19.044 1097 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.15 % Allowed : 17.08 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.27), residues: 1016 helix: 2.17 (0.19), residues: 725 sheet: 0.98 (0.98), residues: 28 loop : 0.26 (0.40), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.011 0.001 TYR A 267 PHE 0.013 0.001 PHE A 254 TRP 0.013 0.001 TRP A 353 HIS 0.005 0.001 HIS A1133 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8279) covalent geometry : angle 0.49562 (11229) hydrogen bonds : bond 0.03509 ( 570) hydrogen bonds : angle 3.66650 ( 1668) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.411 Fit side-chains REVERT: A 160 MET cc_start: 0.7447 (mmt) cc_final: 0.7111 (mmm) REVERT: A 176 VAL cc_start: 0.8302 (p) cc_final: 0.7990 (m) REVERT: A 186 MET cc_start: 0.8032 (mtp) cc_final: 0.7795 (mtp) REVERT: A 190 ASN cc_start: 0.8473 (p0) cc_final: 0.8250 (p0) REVERT: A 200 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7787 (ttm) REVERT: A 217 LEU cc_start: 0.8198 (mp) cc_final: 0.7779 (mp) REVERT: A 338 LYS cc_start: 0.8356 (mtmt) cc_final: 0.8051 (mtmm) REVERT: A 375 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7953 (mtmm) REVERT: A 383 MET cc_start: 0.7519 (mmp) cc_final: 0.7193 (mmp) REVERT: A 579 MET cc_start: 0.7477 (tpt) cc_final: 0.7190 (tpt) REVERT: A 584 LEU cc_start: 0.8423 (mm) cc_final: 0.8093 (mp) REVERT: A 609 ARG cc_start: 0.7916 (mtp-110) cc_final: 0.7620 (mtm-85) REVERT: A 624 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7567 (tt0) REVERT: A 684 ILE cc_start: 0.8179 (mm) cc_final: 0.7748 (mt) REVERT: A 685 ASN cc_start: 0.8359 (m-40) cc_final: 0.8095 (m-40) REVERT: A 697 MET cc_start: 0.6511 (mmm) cc_final: 0.6156 (mmm) REVERT: A 736 ASN cc_start: 0.7705 (m-40) cc_final: 0.7242 (m-40) REVERT: A 810 MET cc_start: 0.6968 (mmm) cc_final: 0.6736 (mmp) REVERT: A 812 ARG cc_start: 0.8356 (ptm-80) cc_final: 0.8006 (ttt180) REVERT: A 832 GLN cc_start: 0.8423 (tp40) cc_final: 0.8186 (tp40) REVERT: A 856 ARG cc_start: 0.7686 (ptt-90) cc_final: 0.7478 (ppt170) REVERT: A 857 MET cc_start: 0.8072 (tpp) cc_final: 0.7704 (tpp) REVERT: A 958 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7496 (ttpp) REVERT: A 990 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7058 (ttm110) REVERT: A 993 ASP cc_start: 0.7785 (m-30) cc_final: 0.7306 (m-30) REVERT: A 1037 THR cc_start: 0.8399 (t) cc_final: 0.8061 (m) REVERT: A 1173 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7546 (ttmm) REVERT: A 1182 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7449 (mm-30) outliers start: 19 outliers final: 15 residues processed: 209 average time/residue: 0.1110 time to fit residues: 30.3897 Evaluate side-chains 213 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 640 ILE Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 865 ARG Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain A residue 1188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 89 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A1074 ASN A1120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112444 restraints weight = 11165.094| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.89 r_work: 0.3202 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8279 Z= 0.131 Angle : 0.505 10.305 11229 Z= 0.259 Chirality : 0.039 0.145 1350 Planarity : 0.004 0.049 1383 Dihedral : 3.668 18.921 1097 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.15 % Allowed : 17.76 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.27), residues: 1016 helix: 2.14 (0.19), residues: 725 sheet: 0.99 (0.98), residues: 28 loop : 0.30 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 161 TYR 0.011 0.001 TYR A 267 PHE 0.014 0.001 PHE A 254 TRP 0.013 0.001 TRP A 278 HIS 0.005 0.001 HIS A1133 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8279) covalent geometry : angle 0.50492 (11229) hydrogen bonds : bond 0.03663 ( 570) hydrogen bonds : angle 3.69173 ( 1668) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2249.92 seconds wall clock time: 39 minutes 11.92 seconds (2351.92 seconds total)