Starting phenix.real_space_refine on Tue Jun 17 04:33:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ege_47987/06_2025/9ege_47987.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ege_47987/06_2025/9ege_47987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ege_47987/06_2025/9ege_47987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ege_47987/06_2025/9ege_47987.map" model { file = "/net/cci-nas-00/data/ceres_data/9ege_47987/06_2025/9ege_47987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ege_47987/06_2025/9ege_47987.cif" } resolution = 2.8 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= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 54 5.16 5 C 6129 2.51 5 N 1627 2.21 5 O 1766 1.98 5 H 9648 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19224 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 19224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 19224 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 2 Time building chain proxies: 9.40, per 1000 atoms: 0.49 Number of scatterers: 19224 At special positions: 0 Unit cell: (70.6112, 110.731, 162.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 O 1766 8.00 N 1627 7.00 C 6129 6.00 H 9648 1.00 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: 5.03 Conformation dependent library (CDL) restraints added in 1.5 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 69.9% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 55 through 101 removed outlier: 3.828A pdb=" N GLN A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Proline residue: A 77 - end of helix removed outlier: 4.361A pdb=" N LEU A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A 81 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 4.115A pdb=" N VAL A 108 " --> pdb=" O LYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 133 through 183 removed outlier: 3.546A pdb=" N TRP A 163 " --> pdb=" O GLN A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.564A pdb=" N PHE A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 214 removed outlier: 3.689A pdb=" N ASP A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 236 removed outlier: 4.054A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 248 through 287 removed outlier: 3.610A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 296 through 346 removed outlier: 3.652A pdb=" N ASN A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 376 Processing helix chain 'A' and resid 376 through 399 removed outlier: 3.548A pdb=" N LEU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.624A pdb=" N GLN A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 537 through 544 removed outlier: 3.617A pdb=" N LEU A 544 " --> pdb=" O PHE A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 560 through 575 removed outlier: 4.117A pdb=" N ARG A 575 " --> pdb=" O ARG A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 4.101A pdb=" N ALA A 588 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 601 removed outlier: 3.885A pdb=" N MET A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 3.758A pdb=" N ALA A 622 " --> pdb=" O THR A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 687 through 703 Processing helix chain 'A' and resid 704 through 707 Processing helix chain 'A' and resid 740 through 748 removed outlier: 3.569A pdb=" N ILE A 744 " --> pdb=" O PRO A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 783 removed outlier: 4.125A pdb=" N THR A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) Proline residue: A 770 - end of helix removed outlier: 3.858A pdb=" N PHE A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 840 Processing helix chain 'A' and resid 843 through 849 removed outlier: 3.678A pdb=" N PHE A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 853 through 868 removed outlier: 4.492A pdb=" N ALA A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 871 No H-bonds generated for 'chain 'A' and resid 869 through 871' Processing helix chain 'A' and resid 872 through 897 Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.566A pdb=" N VAL A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE A 907 " --> pdb=" O VAL A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 946 removed outlier: 4.917A pdb=" N GLY A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA A 916 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N MET A 935 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 946 " --> pdb=" O GLU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 953 Processing helix chain 'A' and resid 955 through 967 removed outlier: 4.374A pdb=" N PHE A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 960 " --> pdb=" O GLU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1009 removed outlier: 3.769A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N PHE A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1035 removed outlier: 3.741A pdb=" N VAL A1017 " --> pdb=" O HIS A1013 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A1035 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1057 removed outlier: 3.961A pdb=" N ALA A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS A1043 " --> pdb=" O PRO A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1127 removed outlier: 4.035A pdb=" N GLN A1124 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1155 Processing helix chain 'A' and resid 1169 through 1176 Processing helix chain 'A' and resid 1177 through 1179 No H-bonds generated for 'chain 'A' and resid 1177 through 1179' Processing helix chain 'A' and resid 1184 through 1195 removed outlier: 3.705A pdb=" N VAL A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1203 Processing helix chain 'A' and resid 1206 through 1210 removed outlier: 3.588A pdb=" N GLU A1209 " --> pdb=" O GLU A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1216 removed outlier: 3.785A pdb=" N GLN A1215 " --> pdb=" O VAL A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1235 removed outlier: 3.587A pdb=" N ARG A1226 " --> pdb=" O GLY A1222 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A1235 " --> pdb=" O ARG A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1266 removed outlier: 3.763A pdb=" N VAL A1259 " --> pdb=" O LYS A1255 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1260 " --> pdb=" O THR A1256 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A1266 " --> pdb=" O ASP A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1308 through 1315 removed outlier: 3.579A pdb=" N LEU A1313 " --> pdb=" O TYR A1310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 441 removed outlier: 5.855A pdb=" N ASN A 439 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE A 427 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 438 through 441 removed outlier: 5.855A pdb=" N ASN A 439 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE A 427 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N PHE A 422 " --> pdb=" O THR A 480 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR A 480 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASN A 424 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N MET A 478 " --> pdb=" O ASN A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 501 removed outlier: 6.490A pdb=" N LEU A 580 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 613 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU A 582 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A 450 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE A 627 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 452 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE A 629 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 454 " --> pdb=" O PHE A 629 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1096 through 1099 removed outlier: 5.354A pdb=" N CYS A1083 " --> pdb=" O GLY A1098 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1096 through 1099 removed outlier: 5.354A pdb=" N CYS A1083 " --> pdb=" O GLY A1098 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE A1080 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N MET A1138 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASP A1082 " --> pdb=" O LYS A1136 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYS A1136 " --> pdb=" O ASP A1082 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1159 removed outlier: 6.363A pdb=" N LEU A1240 " --> pdb=" O ILE A1271 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE A1273 " --> pdb=" O LEU A1240 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A1242 " --> pdb=" O ILE A1273 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU A1109 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA A1287 " --> pdb=" O THR A1108 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA A1110 " --> pdb=" O ALA A1287 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1779 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: 7.83 Time building geometry restraints manager: 6.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9628 1.03 - 1.23: 136 1.23 - 1.43: 3961 1.43 - 1.62: 5596 1.62 - 1.82: 88 Bond restraints: 19409 Sorted by residual: bond pdb=" N VAL A 736 " pdb=" H VAL A 736 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N SER A 686 " pdb=" H SER A 686 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N ARG A 44 " pdb=" CA ARG A 44 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" CB ARG A 621 " pdb=" CG ARG A 621 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" N ARG A 44 " pdb=" H ARG A 44 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.27e+00 ... (remaining 19404 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 33575 1.24 - 2.48: 1342 2.48 - 3.73: 92 3.73 - 4.97: 21 4.97 - 6.21: 9 Bond angle restraints: 35039 Sorted by residual: angle pdb=" C GLN A 547 " pdb=" CA GLN A 547 " pdb=" CB GLN A 547 " ideal model delta sigma weight residual 116.34 110.60 5.74 1.40e+00 5.10e-01 1.68e+01 angle pdb=" N VAL A 552 " pdb=" CA VAL A 552 " pdb=" C VAL A 552 " ideal model delta sigma weight residual 111.88 108.64 3.24 1.06e+00 8.90e-01 9.33e+00 angle pdb=" N VAL A 113 " pdb=" CA VAL A 113 " pdb=" C VAL A 113 " ideal model delta sigma weight residual 109.34 114.66 -5.32 2.08e+00 2.31e-01 6.55e+00 angle pdb=" CA SER A1089 " pdb=" C SER A1089 " pdb=" N ARG A1090 " ideal model delta sigma weight residual 119.38 116.33 3.05 1.24e+00 6.50e-01 6.07e+00 angle pdb=" CG LYS A 930 " pdb=" CD LYS A 930 " pdb=" CE LYS A 930 " ideal model delta sigma weight residual 111.30 116.86 -5.56 2.30e+00 1.89e-01 5.85e+00 ... (remaining 35034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 8099 17.46 - 34.91: 627 34.91 - 52.37: 224 52.37 - 69.82: 99 69.82 - 87.28: 54 Dihedral angle restraints: 9103 sinusoidal: 4927 harmonic: 4176 Sorted by residual: dihedral pdb=" CA THR A 111 " pdb=" C THR A 111 " pdb=" N ILE A 112 " pdb=" CA ILE A 112 " ideal model delta harmonic sigma weight residual 180.00 -153.23 -26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ILE A 112 " pdb=" C ILE A 112 " pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta harmonic sigma weight residual 180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA SER A1089 " pdb=" C SER A1089 " pdb=" N ARG A1090 " pdb=" CA ARG A1090 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 9100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 901 0.028 - 0.056: 394 0.056 - 0.084: 128 0.084 - 0.112: 58 0.112 - 0.140: 21 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA ILE A 785 " pdb=" N ILE A 785 " pdb=" C ILE A 785 " pdb=" CB ILE A 785 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE A1061 " pdb=" N ILE A1061 " pdb=" C ILE A1061 " pdb=" CB ILE A1061 " 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 1499 not shown) Planarity restraints: 2880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1033 " 0.150 9.50e-02 1.11e+02 5.02e-02 3.03e+00 pdb=" NE ARG A1033 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A1033 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A1033 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A1033 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A1033 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG A1033 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A1033 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A1033 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 102 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO A 103 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 620 " 0.008 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" N ARG A 621 " -0.026 2.00e-02 2.50e+03 pdb=" CA ARG A 621 " 0.006 2.00e-02 2.50e+03 pdb=" H ARG A 621 " 0.012 2.00e-02 2.50e+03 ... (remaining 2877 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 756 2.17 - 2.77: 37820 2.77 - 3.38: 55889 3.38 - 3.99: 69217 3.99 - 4.60: 110025 Nonbonded interactions: 273707 Sorted by model distance: nonbonded pdb=" H SER A1220 " pdb=" OE1 GLU A1223 " model vdw 1.557 2.450 nonbonded pdb=" OD2 ASP A 409 " pdb=" H ILE A 491 " model vdw 1.582 2.450 nonbonded pdb=" OD2 ASP A 848 " pdb=" HH TYR A1130 " model vdw 1.602 2.450 nonbonded pdb=" OE1 GLN A1281 " pdb=" H GLN A1281 " model vdw 1.605 2.450 nonbonded pdb=" O LYS A 276 " pdb="HD22 ASN A 307 " model vdw 1.618 2.450 ... (remaining 273702 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: 1.760 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: 0.340 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.400 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:14.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 0.057 9761 Z= 0.199 Angle : 0.580 6.056 13199 Z= 0.337 Chirality : 0.039 0.140 1502 Planarity : 0.004 0.065 1689 Dihedral : 14.542 87.276 3551 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.88 % Allowed : 9.94 % Favored : 89.18 % 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: 1.04 (0.24), residues: 1224 helix: 1.44 (0.18), residues: 779 sheet: -0.18 (0.72), residues: 46 loop : -0.64 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 114 HIS 0.005 0.001 HIS A 640 PHE 0.012 0.001 PHE A 896 TYR 0.018 0.002 TYR A 772 ARG 0.010 0.001 ARG A1033 Details of bonding type rmsd hydrogen bonds : bond 0.14589 ( 615) hydrogen bonds : angle 5.44150 ( 1779) covalent geometry : bond 0.00426 ( 9761) covalent geometry : angle 0.57970 (13199) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1070 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8225 (mmt) cc_final: 0.7578 (mmp) REVERT: A 417 LYS cc_start: 0.9099 (mtmt) cc_final: 0.8885 (mmmt) REVERT: A 503 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7777 (tt0) REVERT: A 539 ASN cc_start: 0.8574 (m110) cc_final: 0.7980 (p0) REVERT: A 630 GLU cc_start: 0.7654 (tp30) cc_final: 0.6877 (tp30) REVERT: A 696 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.7099 (tpp-160) REVERT: A 709 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7584 (pm20) REVERT: A 790 GLU cc_start: 0.8010 (tp30) cc_final: 0.7560 (mm-30) REVERT: A 931 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 934 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7814 (mm-30) REVERT: A 935 MET cc_start: 0.8176 (mmp) cc_final: 0.7968 (tmm) REVERT: A 1171 MET cc_start: 0.7514 (tmm) cc_final: 0.7087 (tmm) outliers start: 9 outliers final: 2 residues processed: 141 average time/residue: 2.5905 time to fit residues: 393.5178 Evaluate side-chains 96 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 772 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.131139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.089690 restraints weight = 46220.500| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.71 r_work: 0.3098 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9761 Z= 0.173 Angle : 0.571 6.346 13199 Z= 0.313 Chirality : 0.040 0.146 1502 Planarity : 0.004 0.074 1689 Dihedral : 4.893 33.129 1331 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.88 % Allowed : 12.67 % Favored : 86.45 % 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: 1.16 (0.24), residues: 1224 helix: 1.54 (0.18), residues: 784 sheet: -0.36 (0.79), residues: 41 loop : -0.60 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 898 HIS 0.007 0.001 HIS A 631 PHE 0.014 0.001 PHE A 896 TYR 0.016 0.002 TYR A 772 ARG 0.005 0.000 ARG A1033 Details of bonding type rmsd hydrogen bonds : bond 0.05522 ( 615) hydrogen bonds : angle 4.34979 ( 1779) covalent geometry : bond 0.00378 ( 9761) covalent geometry : angle 0.57060 (13199) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1070 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8659 (mmt) cc_final: 0.7918 (mmp) REVERT: A 450 MET cc_start: 0.7958 (ttt) cc_final: 0.7638 (tmt) REVERT: A 503 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 696 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7334 (tpp-160) REVERT: A 709 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7889 (mp0) REVERT: A 790 GLU cc_start: 0.8044 (tp30) cc_final: 0.7713 (tm-30) REVERT: A 935 MET cc_start: 0.8187 (mmp) cc_final: 0.7971 (mpm) REVERT: A 1010 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8354 (mp0) REVERT: A 1171 MET cc_start: 0.7709 (tmm) cc_final: 0.7282 (tmm) outliers start: 9 outliers final: 3 residues processed: 105 average time/residue: 2.4589 time to fit residues: 279.3272 Evaluate side-chains 91 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 946 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 48 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.130537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089049 restraints weight = 46099.512| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.70 r_work: 0.3107 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9761 Z= 0.181 Angle : 0.536 6.181 13199 Z= 0.294 Chirality : 0.039 0.144 1502 Planarity : 0.004 0.087 1689 Dihedral : 4.717 32.570 1329 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.97 % Allowed : 12.67 % Favored : 86.35 % 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: 1.18 (0.24), residues: 1224 helix: 1.59 (0.18), residues: 791 sheet: -0.00 (0.83), residues: 35 loop : -0.74 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 898 HIS 0.008 0.001 HIS A 631 PHE 0.015 0.001 PHE A 896 TYR 0.017 0.001 TYR A 772 ARG 0.003 0.000 ARG A 621 Details of bonding type rmsd hydrogen bonds : bond 0.05188 ( 615) hydrogen bonds : angle 4.19037 ( 1779) covalent geometry : bond 0.00406 ( 9761) covalent geometry : angle 0.53618 (13199) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1070 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8654 (mmt) cc_final: 0.7889 (mmp) REVERT: A 503 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 630 GLU cc_start: 0.8093 (tp30) cc_final: 0.7120 (tp30) REVERT: A 696 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7372 (tpp-160) REVERT: A 697 GLN cc_start: 0.8314 (tm-30) cc_final: 0.8075 (tm-30) REVERT: A 790 GLU cc_start: 0.8097 (tp30) cc_final: 0.7873 (mm-30) REVERT: A 1171 MET cc_start: 0.7757 (tmm) cc_final: 0.7330 (tmm) outliers start: 10 outliers final: 4 residues processed: 94 average time/residue: 2.5032 time to fit residues: 254.9587 Evaluate side-chains 90 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 946 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 35 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.130419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.088872 restraints weight = 46132.347| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.70 r_work: 0.3098 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9761 Z= 0.176 Angle : 0.525 6.214 13199 Z= 0.285 Chirality : 0.039 0.143 1502 Planarity : 0.003 0.038 1689 Dihedral : 4.620 32.322 1329 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.17 % Allowed : 12.77 % Favored : 86.06 % 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: 1.20 (0.24), residues: 1224 helix: 1.62 (0.18), residues: 794 sheet: -0.08 (1.00), residues: 24 loop : -0.78 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.003 0.001 HIS A 428 PHE 0.015 0.001 PHE A 896 TYR 0.016 0.001 TYR A 772 ARG 0.008 0.000 ARG A 621 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 615) hydrogen bonds : angle 4.07415 ( 1779) covalent geometry : bond 0.00397 ( 9761) covalent geometry : angle 0.52483 (13199) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1070 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8664 (mmt) cc_final: 0.7863 (mmp) REVERT: A 503 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7964 (tm-30) REVERT: A 696 ARG cc_start: 0.7766 (ttm-80) cc_final: 0.7335 (tpp-160) REVERT: A 697 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8096 (tm-30) REVERT: A 790 GLU cc_start: 0.8124 (tp30) cc_final: 0.7870 (mm-30) REVERT: A 843 ASP cc_start: 0.8434 (p0) cc_final: 0.8210 (p0) REVERT: A 934 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7485 (pt0) REVERT: A 1171 MET cc_start: 0.7763 (tmm) cc_final: 0.7338 (tmm) REVERT: A 1304 MET cc_start: 0.8016 (tpp) cc_final: 0.7471 (mmp) outliers start: 12 outliers final: 7 residues processed: 102 average time/residue: 2.4297 time to fit residues: 269.4259 Evaluate side-chains 97 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 990 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 11 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.130779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089188 restraints weight = 46540.889| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.72 r_work: 0.3106 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9761 Z= 0.150 Angle : 0.510 6.082 13199 Z= 0.277 Chirality : 0.038 0.142 1502 Planarity : 0.004 0.052 1689 Dihedral : 4.558 28.668 1329 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.88 % Allowed : 13.55 % Favored : 85.58 % 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: 1.31 (0.24), residues: 1224 helix: 1.73 (0.18), residues: 797 sheet: -0.13 (1.01), residues: 24 loop : -0.79 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.007 0.001 HIS A 631 PHE 0.014 0.001 PHE A 896 TYR 0.016 0.001 TYR A 772 ARG 0.006 0.000 ARG A1033 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 615) hydrogen bonds : angle 4.00470 ( 1779) covalent geometry : bond 0.00334 ( 9761) covalent geometry : angle 0.50999 (13199) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1070 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8554 (m-40) cc_final: 0.8347 (t0) REVERT: A 185 MET cc_start: 0.8646 (mmt) cc_final: 0.7779 (mmp) REVERT: A 503 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 630 GLU cc_start: 0.8180 (tp30) cc_final: 0.7131 (tp30) REVERT: A 696 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7328 (tpp-160) REVERT: A 697 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 1010 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: A 1138 MET cc_start: 0.8082 (mmm) cc_final: 0.7225 (mmm) REVERT: A 1171 MET cc_start: 0.7764 (tmm) cc_final: 0.7337 (tmm) outliers start: 9 outliers final: 5 residues processed: 97 average time/residue: 2.4876 time to fit residues: 261.9651 Evaluate side-chains 94 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 946 ASN Chi-restraints excluded: chain A residue 1010 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.131195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.089429 restraints weight = 46499.987| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.76 r_work: 0.3161 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9761 Z= 0.141 Angle : 0.510 7.482 13199 Z= 0.275 Chirality : 0.038 0.142 1502 Planarity : 0.003 0.037 1689 Dihedral : 4.402 24.965 1327 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.27 % Allowed : 13.65 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.24), residues: 1224 helix: 1.80 (0.18), residues: 797 sheet: -0.24 (1.00), residues: 24 loop : -0.82 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.003 0.001 HIS A 631 PHE 0.014 0.001 PHE A 540 TYR 0.015 0.001 TYR A 772 ARG 0.003 0.000 ARG A1033 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 615) hydrogen bonds : angle 3.93887 ( 1779) covalent geometry : bond 0.00312 ( 9761) covalent geometry : angle 0.51046 (13199) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1070 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8606 (m-40) cc_final: 0.8370 (t0) REVERT: A 185 MET cc_start: 0.8553 (mmt) cc_final: 0.7658 (mmp) REVERT: A 417 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8517 (mmmt) REVERT: A 503 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 696 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7313 (tpp-160) REVERT: A 697 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 790 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: A 934 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7422 (pt0) REVERT: A 1010 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: A 1138 MET cc_start: 0.7992 (mmm) cc_final: 0.7212 (mmm) REVERT: A 1171 MET cc_start: 0.7686 (tmm) cc_final: 0.7259 (tmm) outliers start: 13 outliers final: 6 residues processed: 101 average time/residue: 2.4001 time to fit residues: 263.1814 Evaluate side-chains 96 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain A residue 1010 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.089184 restraints weight = 46154.143| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.70 r_work: 0.3106 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9761 Z= 0.167 Angle : 0.515 6.128 13199 Z= 0.279 Chirality : 0.039 0.139 1502 Planarity : 0.004 0.085 1689 Dihedral : 4.381 24.824 1327 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.27 % Allowed : 13.74 % Favored : 84.99 % 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: 1.32 (0.24), residues: 1224 helix: 1.76 (0.18), residues: 797 sheet: -0.26 (1.00), residues: 24 loop : -0.86 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 114 HIS 0.011 0.001 HIS A 631 PHE 0.015 0.001 PHE A 540 TYR 0.014 0.001 TYR A 411 ARG 0.007 0.000 ARG A1033 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 615) hydrogen bonds : angle 3.95562 ( 1779) covalent geometry : bond 0.00377 ( 9761) covalent geometry : angle 0.51477 (13199) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1070 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8636 (mmt) cc_final: 0.7728 (mmp) REVERT: A 417 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8524 (mmmt) REVERT: A 503 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7908 (tm-30) REVERT: A 696 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7401 (tpp-160) REVERT: A 697 GLN cc_start: 0.8353 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 1010 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: A 1138 MET cc_start: 0.8089 (mmm) cc_final: 0.7309 (mmm) REVERT: A 1171 MET cc_start: 0.7787 (tmm) cc_final: 0.7352 (tmm) outliers start: 13 outliers final: 6 residues processed: 99 average time/residue: 2.4350 time to fit residues: 261.3464 Evaluate side-chains 94 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1275 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 92 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.131307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.089962 restraints weight = 46155.370| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.71 r_work: 0.3170 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9761 Z= 0.133 Angle : 0.503 6.005 13199 Z= 0.271 Chirality : 0.038 0.141 1502 Planarity : 0.003 0.062 1689 Dihedral : 4.296 24.830 1327 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.07 % Allowed : 14.33 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.24), residues: 1224 helix: 1.87 (0.18), residues: 799 sheet: -0.21 (1.00), residues: 24 loop : -0.89 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 114 HIS 0.002 0.000 HIS A 428 PHE 0.022 0.001 PHE A 540 TYR 0.012 0.001 TYR A 772 ARG 0.009 0.000 ARG A1033 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 615) hydrogen bonds : angle 3.87569 ( 1779) covalent geometry : bond 0.00294 ( 9761) covalent geometry : angle 0.50304 (13199) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1070 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8592 (mmt) cc_final: 0.7669 (mmp) REVERT: A 417 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8507 (mmmt) REVERT: A 503 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7846 (tm-30) REVERT: A 696 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7378 (tpp-160) REVERT: A 697 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 790 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: A 920 ARG cc_start: 0.7737 (mtt180) cc_final: 0.7106 (ppt170) REVERT: A 934 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7517 (pt0) REVERT: A 1010 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: A 1138 MET cc_start: 0.8100 (mmm) cc_final: 0.7434 (mmm) REVERT: A 1171 MET cc_start: 0.7770 (tmm) cc_final: 0.7340 (tmm) outliers start: 11 outliers final: 6 residues processed: 103 average time/residue: 2.5333 time to fit residues: 282.8176 Evaluate side-chains 99 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 990 CYS Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1275 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 0.0570 chunk 83 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.132212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.090808 restraints weight = 46064.208| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.72 r_work: 0.3185 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9761 Z= 0.110 Angle : 0.494 5.942 13199 Z= 0.264 Chirality : 0.038 0.141 1502 Planarity : 0.004 0.075 1689 Dihedral : 4.215 24.762 1327 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.68 % Allowed : 15.11 % Favored : 84.21 % 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: 1.55 (0.24), residues: 1224 helix: 1.99 (0.18), residues: 799 sheet: -0.22 (1.00), residues: 24 loop : -0.89 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.003 0.000 HIS A 631 PHE 0.027 0.001 PHE A 540 TYR 0.019 0.001 TYR A 411 ARG 0.011 0.000 ARG A1033 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 615) hydrogen bonds : angle 3.77560 ( 1779) covalent geometry : bond 0.00238 ( 9761) covalent geometry : angle 0.49407 (13199) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1070 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ASN cc_start: 0.8548 (m-40) cc_final: 0.8276 (t0) REVERT: A 417 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8526 (mmmt) REVERT: A 696 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7415 (tpp-160) REVERT: A 697 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8051 (tm-30) REVERT: A 920 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7096 (ppt170) REVERT: A 934 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7529 (pt0) REVERT: A 1010 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: A 1138 MET cc_start: 0.8083 (mmm) cc_final: 0.7420 (mmm) REVERT: A 1171 MET cc_start: 0.7753 (tmm) cc_final: 0.7323 (tmm) outliers start: 7 outliers final: 5 residues processed: 98 average time/residue: 2.5187 time to fit residues: 267.9224 Evaluate side-chains 95 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1275 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 114 optimal weight: 2.9990 chunk 97 optimal weight: 0.0020 chunk 92 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.132443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.090977 restraints weight = 45834.805| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.72 r_work: 0.3189 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9761 Z= 0.111 Angle : 0.498 6.343 13199 Z= 0.265 Chirality : 0.038 0.139 1502 Planarity : 0.004 0.074 1689 Dihedral : 4.146 24.587 1327 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.49 % Allowed : 15.40 % Favored : 84.11 % 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: 1.67 (0.24), residues: 1224 helix: 2.10 (0.18), residues: 799 sheet: -0.31 (1.01), residues: 24 loop : -0.87 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.004 0.000 HIS A 631 PHE 0.030 0.001 PHE A 540 TYR 0.021 0.001 TYR A 411 ARG 0.012 0.000 ARG A1033 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 615) hydrogen bonds : angle 3.74839 ( 1779) covalent geometry : bond 0.00244 ( 9761) covalent geometry : angle 0.49818 (13199) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 1070 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ASP cc_start: 0.8481 (m-30) cc_final: 0.8245 (m-30) REVERT: A 417 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8522 (mmmt) REVERT: A 696 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7412 (tpp-160) REVERT: A 697 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 920 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7096 (ppt170) REVERT: A 934 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7516 (pt0) REVERT: A 1010 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: A 1138 MET cc_start: 0.8067 (mmm) cc_final: 0.7401 (mmm) REVERT: A 1171 MET cc_start: 0.7756 (tmm) cc_final: 0.7327 (tmm) outliers start: 5 outliers final: 4 residues processed: 97 average time/residue: 2.5145 time to fit residues: 264.5424 Evaluate side-chains 94 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1275 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 53 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 100 optimal weight: 0.0470 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 90 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.132894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.091422 restraints weight = 46302.803| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.73 r_work: 0.3201 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9761 Z= 0.107 Angle : 0.498 8.953 13199 Z= 0.263 Chirality : 0.038 0.139 1502 Planarity : 0.003 0.036 1689 Dihedral : 4.066 24.410 1327 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.49 % Allowed : 15.69 % Favored : 83.82 % 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: 1.74 (0.25), residues: 1224 helix: 2.17 (0.18), residues: 799 sheet: -0.32 (1.00), residues: 24 loop : -0.87 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 114 HIS 0.004 0.000 HIS A 631 PHE 0.031 0.001 PHE A 540 TYR 0.012 0.001 TYR A 772 ARG 0.005 0.000 ARG A 692 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 615) hydrogen bonds : angle 3.69112 ( 1779) covalent geometry : bond 0.00233 ( 9761) covalent geometry : angle 0.49835 (13199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14367.85 seconds wall clock time: 243 minutes 18.47 seconds (14598.47 seconds total)