Starting phenix.real_space_refine on Tue May 20 04:10:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n1y_48824/05_2025/9n1y_48824.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n1y_48824/05_2025/9n1y_48824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n1y_48824/05_2025/9n1y_48824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n1y_48824/05_2025/9n1y_48824.map" model { file = "/net/cci-nas-00/data/ceres_data/9n1y_48824/05_2025/9n1y_48824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n1y_48824/05_2025/9n1y_48824.cif" } resolution = 3.23 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= 0.010 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 6126 2.51 5 N 1627 2.21 5 O 1764 1.98 5 H 9645 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19216 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 19216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1230, 19216 Classifications: {'peptide': 1230} Link IDs: {'PTRANS': 36, 'TRANS': 1193} Chain breaks: 2 Time building chain proxies: 8.76, per 1000 atoms: 0.46 Number of scatterers: 19216 At special positions: 0 Unit cell: (71.94, 109.872, 162.192, 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 1764 8.00 N 1627 7.00 C 6126 6.00 H 9645 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: 5.85 Conformation dependent library (CDL) restraints added in 1.6 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: 2270 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 70.6% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.919A pdb=" N GLN A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Proline residue: A 77 - end of helix Processing helix chain 'A' and resid 79 through 100 removed outlier: 3.528A pdb=" N THR A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 133 through 183 Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.678A pdb=" N PHE A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 214 removed outlier: 3.877A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE A 206 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 236 removed outlier: 4.148A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 248 removed outlier: 3.581A pdb=" N THR A 242 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 287 removed outlier: 3.956A pdb=" N ILE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.603A pdb=" N VAL A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 346 removed outlier: 3.520A pdb=" N ASN A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N PHE A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 375 Processing helix chain 'A' and resid 376 through 399 removed outlier: 3.549A pdb=" N LEU A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N SER A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.694A pdb=" N GLN A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 497 removed outlier: 3.634A pdb=" N ASP A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 497 " --> pdb=" O TRP A 493 " (cutoff:3.500A) 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 543 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 560 through 575 removed outlier: 4.146A pdb=" N ARG A 575 " --> pdb=" O ARG A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 589 removed outlier: 4.149A pdb=" N ALA A 588 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 601 Processing helix chain 'A' and resid 616 through 623 removed outlier: 3.890A pdb=" N ARG A 621 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 4.414A 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 659 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: 3.619A pdb=" N ILE A 744 " --> pdb=" O PRO A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 783 removed outlier: 3.613A pdb=" N MET A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 769 " --> pdb=" O ASN A 765 " (cutoff:3.500A) Proline residue: A 770 - end of helix removed outlier: 3.963A 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: 3.791A pdb=" N PHE A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 849 " --> pdb=" O ALA A 845 " (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 863 Processing helix chain 'A' and resid 863 through 868 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 removed outlier: 3.835A pdb=" N ILE A 876 " --> pdb=" O ALA A 872 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 877 " --> pdb=" O GLY A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 906 removed outlier: 3.646A pdb=" N VAL A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 946 removed outlier: 4.711A pdb=" N GLY A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA A 916 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N MET A 935 " --> pdb=" O GLN A 931 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) removed outlier: 4.124A 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: 4.515A pdb=" N PHE A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 960 " --> pdb=" O GLU A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1009 removed outlier: 3.786A pdb=" N PHE A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 976 " --> pdb=" O LYS A 972 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET A 992 " --> pdb=" O ALA A 988 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N PHE A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A1005 " --> pdb=" O ARG A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1035 removed outlier: 4.048A pdb=" N VAL A1017 " --> pdb=" O HIS A1013 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A1035 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1056 removed outlier: 4.165A pdb=" N ALA A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS A1043 " --> pdb=" O PRO A1039 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1054 " --> pdb=" O ARG A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1127 removed outlier: 3.739A pdb=" N GLN A1124 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1147 No H-bonds generated for 'chain 'A' and resid 1145 through 1147' Processing helix chain 'A' and resid 1148 through 1154 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: 3.736A 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 Processing helix chain 'A' and resid 1212 through 1216 removed outlier: 3.508A pdb=" N GLN A1215 " --> pdb=" O VAL A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1235 removed outlier: 4.156A pdb=" N ARG A1226 " --> pdb=" O GLY A1222 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG A1235 " --> pdb=" O ARG A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1265 removed outlier: 3.882A pdb=" N VAL A1259 " --> pdb=" O LYS A1255 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A1260 " --> pdb=" O THR A1256 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1282 removed outlier: 4.391A pdb=" N GLN A1281 " --> pdb=" O LEU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1308 through 1315 Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 441 removed outlier: 5.703A pdb=" N ASN A 439 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.601A 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: 5.703A pdb=" N ASN A 439 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 427 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 425 " --> pdb=" O GLU A 476 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU A 476 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 501 removed outlier: 6.415A pdb=" N LEU A 580 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 613 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU A 582 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR A 451 " --> pdb=" O SER A 612 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N MET A 450 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE A 627 " --> pdb=" O MET A 450 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA A 452 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE A 629 " --> pdb=" O ALA A 452 " (cutoff:3.500A) removed outlier: 6.429A 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: 5.120A 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: 5.120A pdb=" N CYS A1083 " --> pdb=" O GLY A1098 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N PHE A1080 " --> pdb=" O MET A1138 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET A1138 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP A1082 " --> pdb=" O LYS A1136 " (cutoff:3.500A) removed outlier: 5.722A 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: 7.874A pdb=" N ALA A1287 " --> pdb=" O THR A1108 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA A1110 " --> pdb=" O ALA A1287 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1761 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: 7.52 Time building geometry restraints manager: 6.74 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: 9625 1.03 - 1.23: 21 1.23 - 1.42: 4073 1.42 - 1.62: 5594 1.62 - 1.81: 88 Bond restraints: 19401 Sorted by residual: bond pdb=" N VAL A 736 " pdb=" H VAL A 736 " ideal model delta sigma weight residual 0.860 0.961 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" N SER A 686 " pdb=" H SER A 686 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N VAL A 707 " pdb=" CA VAL A 707 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N HIS A 640 " pdb=" CA HIS A 640 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.16e-02 7.43e+03 6.95e+00 bond pdb=" N GLU A 709 " pdb=" CA GLU A 709 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.17e-02 7.31e+03 6.55e+00 ... (remaining 19396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 34275 1.46 - 2.92: 674 2.92 - 4.38: 60 4.38 - 5.84: 10 5.84 - 7.31: 5 Bond angle restraints: 35024 Sorted by residual: angle pdb=" N LEU A 643 " pdb=" CA LEU A 643 " pdb=" C LEU A 643 " ideal model delta sigma weight residual 113.28 106.91 6.37 1.22e+00 6.72e-01 2.73e+01 angle pdb=" N LEU A 644 " pdb=" CA LEU A 644 " pdb=" C LEU A 644 " ideal model delta sigma weight residual 113.16 106.97 6.19 1.24e+00 6.50e-01 2.49e+01 angle pdb=" CA GLY A 638 " pdb=" C GLY A 638 " pdb=" O GLY A 638 " ideal model delta sigma weight residual 121.11 117.11 4.00 9.00e-01 1.23e+00 1.98e+01 angle pdb=" CA THR A 639 " pdb=" C THR A 639 " pdb=" O THR A 639 " ideal model delta sigma weight residual 122.01 117.68 4.33 1.05e+00 9.07e-01 1.70e+01 angle pdb=" CA PRO A 711 " pdb=" C PRO A 711 " pdb=" O PRO A 711 " ideal model delta sigma weight residual 121.86 117.43 4.43 1.22e+00 6.72e-01 1.32e+01 ... (remaining 35019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8159 17.97 - 35.94: 593 35.94 - 53.91: 219 53.91 - 71.88: 77 71.88 - 89.85: 51 Dihedral angle restraints: 9099 sinusoidal: 4925 harmonic: 4174 Sorted by residual: 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 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 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 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLY A 410 " pdb=" C GLY A 410 " pdb=" N TYR A 411 " pdb=" CA TYR A 411 " ideal model delta harmonic sigma weight residual -180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1075 0.034 - 0.068: 286 0.068 - 0.102: 98 0.102 - 0.136: 39 0.136 - 0.170: 3 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA VAL A 707 " pdb=" N VAL A 707 " pdb=" C VAL A 707 " pdb=" CB VAL A 707 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA LEU A 644 " pdb=" N LEU A 644 " pdb=" C LEU A 644 " pdb=" CB LEU A 644 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA GLU A 709 " pdb=" N GLU A 709 " pdb=" C GLU A 709 " pdb=" CB GLU A 709 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 1498 not shown) Planarity restraints: 2879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 637 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.91e+00 pdb=" C ARG A 637 " 0.029 2.00e-02 2.50e+03 pdb=" O ARG A 637 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY A 638 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 236 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C PHE A 236 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE A 236 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG A 237 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 709 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.09e+00 pdb=" C GLU A 709 " -0.025 2.00e-02 2.50e+03 pdb=" O GLU A 709 " 0.009 2.00e-02 2.50e+03 pdb=" N PRO A 710 " 0.009 2.00e-02 2.50e+03 ... (remaining 2876 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1545 2.22 - 2.82: 41152 2.82 - 3.41: 52837 3.41 - 4.01: 67045 4.01 - 4.60: 105263 Nonbonded interactions: 267842 Sorted by model distance: nonbonded pdb=" O TYR A 411 " pdb=" H ASN A 490 " model vdw 1.626 2.450 nonbonded pdb=" OE1 GLU A 186 " pdb=" H ILE A 402 " model vdw 1.646 2.450 nonbonded pdb=" HZ2 LYS A 446 " pdb=" OE1 GLU A 449 " model vdw 1.657 2.450 nonbonded pdb=" HZ3 LYS A1175 " pdb=" OE1 GLU A1182 " model vdw 1.658 2.450 nonbonded pdb=" OD1 ASP A 590 " pdb=" HG SER A 593 " model vdw 1.660 2.450 ... (remaining 267837 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: 1.190 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: 0.320 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.070 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 0.038 9756 Z= 0.176 Angle : 0.564 7.306 13192 Z= 0.349 Chirality : 0.039 0.170 1501 Planarity : 0.003 0.033 1688 Dihedral : 14.541 89.847 3548 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 1.17 % Allowed : 7.71 % Favored : 91.12 % 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: 1.41 (0.25), residues: 1224 helix: 1.92 (0.19), residues: 772 sheet: -0.59 (0.77), residues: 44 loop : -0.79 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 114 HIS 0.004 0.001 HIS A 640 PHE 0.021 0.001 PHE A 236 TYR 0.015 0.001 TYR A 772 ARG 0.002 0.000 ARG A 698 Details of bonding type rmsd hydrogen bonds : bond 0.14374 ( 613) hydrogen bonds : angle 5.29002 ( 1761) covalent geometry : bond 0.00302 ( 9756) covalent geometry : angle 0.56432 (13192) *********************** 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 77 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 1.488 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: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.8949 (mmp) cc_final: 0.8314 (mmm) REVERT: A 288 MET cc_start: 0.8896 (tpt) cc_final: 0.8676 (tpt) REVERT: A 696 ARG cc_start: 0.8533 (ttm-80) cc_final: 0.8263 (ttt-90) REVERT: A 921 MET cc_start: 0.8746 (ttp) cc_final: 0.8237 (tmm) REVERT: A 1304 MET cc_start: 0.8705 (mmm) cc_final: 0.8301 (mmt) outliers start: 12 outliers final: 9 residues processed: 72 average time/residue: 0.4959 time to fit residues: 51.0312 Evaluate side-chains 67 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 650 TYR Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 984 CYS Chi-restraints excluded: chain A residue 1312 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.090644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.068776 restraints weight = 71876.771| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.38 r_work: 0.3127 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9756 Z= 0.154 Angle : 0.508 5.449 13192 Z= 0.285 Chirality : 0.038 0.140 1501 Planarity : 0.004 0.030 1688 Dihedral : 5.608 55.182 1348 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.68 % Favored : 96.24 % Rotamer: Outliers : 0.98 % Allowed : 7.90 % Favored : 91.12 % 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: 1.43 (0.25), residues: 1224 helix: 2.02 (0.19), residues: 776 sheet: -0.43 (0.90), residues: 34 loop : -1.05 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 898 HIS 0.003 0.001 HIS A 72 PHE 0.013 0.001 PHE A 774 TYR 0.015 0.001 TYR A 772 ARG 0.003 0.000 ARG A 958 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 613) hydrogen bonds : angle 4.40739 ( 1761) covalent geometry : bond 0.00320 ( 9756) covalent geometry : angle 0.50844 (13192) *********************** 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 73 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 1.513 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: symmetry clash revert: symmetry clash REVERT: A 288 MET cc_start: 0.8740 (tpt) cc_final: 0.8488 (tpt) REVERT: A 688 GLN cc_start: 0.8123 (mt0) cc_final: 0.7721 (mp10) REVERT: A 696 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8286 (ttt-90) REVERT: A 921 MET cc_start: 0.8821 (ttp) cc_final: 0.8256 (tmm) REVERT: A 1010 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8289 (mm-30) REVERT: A 1304 MET cc_start: 0.8578 (mmm) cc_final: 0.8183 (mmt) outliers start: 10 outliers final: 7 residues processed: 70 average time/residue: 0.5089 time to fit residues: 50.2814 Evaluate side-chains 69 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1313 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 41 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.091301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068571 restraints weight = 73743.264| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 3.57 r_work: 0.3181 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9756 Z= 0.166 Angle : 0.486 5.712 13192 Z= 0.272 Chirality : 0.038 0.135 1501 Planarity : 0.003 0.029 1688 Dihedral : 4.944 40.270 1337 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.83 % Rotamer: Outliers : 0.88 % Allowed : 9.17 % Favored : 89.95 % 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: 1.40 (0.24), residues: 1224 helix: 2.01 (0.19), residues: 778 sheet: -0.74 (0.85), residues: 34 loop : -1.07 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 0.001 HIS A1275 PHE 0.011 0.001 PHE A 774 TYR 0.015 0.001 TYR A 772 ARG 0.002 0.000 ARG A 201 Details of bonding type rmsd hydrogen bonds : bond 0.05015 ( 613) hydrogen bonds : angle 4.22518 ( 1761) covalent geometry : bond 0.00352 ( 9756) covalent geometry : angle 0.48598 (13192) *********************** 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 71 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 1.820 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: symmetry clash REVERT: A 185 MET cc_start: 0.9093 (mmp) cc_final: 0.8720 (mmm) REVERT: A 288 MET cc_start: 0.8860 (tpt) cc_final: 0.8596 (tpt) REVERT: A 688 GLN cc_start: 0.8044 (mt0) cc_final: 0.7646 (mp10) REVERT: A 696 ARG cc_start: 0.8558 (ttm-80) cc_final: 0.8324 (ttt-90) REVERT: A 921 MET cc_start: 0.8831 (ttp) cc_final: 0.8205 (tmm) REVERT: A 1010 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8297 (mm-30) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.5138 time to fit residues: 50.1690 Evaluate side-chains 68 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1270 CYS Chi-restraints excluded: chain A residue 1312 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** 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 = 0.3717 r_free = 0.3717 target = 0.090897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067947 restraints weight = 74260.379| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.59 r_work: 0.3178 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9756 Z= 0.161 Angle : 0.479 6.136 13192 Z= 0.267 Chirality : 0.038 0.134 1501 Planarity : 0.003 0.034 1688 Dihedral : 4.810 40.351 1335 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 1.17 % Allowed : 9.17 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.45 (0.24), residues: 1224 helix: 2.06 (0.19), residues: 778 sheet: -1.06 (0.82), residues: 34 loop : -1.05 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 0.001 HIS A 423 PHE 0.012 0.001 PHE A 266 TYR 0.014 0.001 TYR A 772 ARG 0.002 0.000 ARG A 958 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 613) hydrogen bonds : angle 4.11297 ( 1761) covalent geometry : bond 0.00344 ( 9756) covalent geometry : angle 0.47899 (13192) *********************** 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 71 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 1.409 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: 0.9093 (mmp) cc_final: 0.8873 (mmt) REVERT: A 266 PHE cc_start: 0.8775 (m-80) cc_final: 0.8491 (m-80) REVERT: A 288 MET cc_start: 0.8834 (tpt) cc_final: 0.8567 (tpt) REVERT: A 688 GLN cc_start: 0.8132 (mt0) cc_final: 0.7790 (mp10) REVERT: A 696 ARG cc_start: 0.8579 (ttm-80) cc_final: 0.8319 (ttt-90) REVERT: A 921 MET cc_start: 0.8824 (ttp) cc_final: 0.8206 (tmm) REVERT: A 1010 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8283 (mm-30) outliers start: 12 outliers final: 10 residues processed: 68 average time/residue: 0.4925 time to fit residues: 47.6672 Evaluate side-chains 68 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1313 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 97 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** 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 = 0.3738 r_free = 0.3738 target = 0.091839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068988 restraints weight = 73916.450| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.59 r_work: 0.3205 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9756 Z= 0.113 Angle : 0.453 5.476 13192 Z= 0.249 Chirality : 0.037 0.135 1501 Planarity : 0.003 0.036 1688 Dihedral : 4.686 40.257 1335 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 0.98 % Allowed : 9.76 % Favored : 89.27 % 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: 1.69 (0.25), residues: 1224 helix: 2.23 (0.19), residues: 779 sheet: -0.91 (0.84), residues: 34 loop : -0.92 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 114 HIS 0.002 0.001 HIS A 423 PHE 0.011 0.001 PHE A 774 TYR 0.012 0.001 TYR A 772 ARG 0.002 0.000 ARG A 958 Details of bonding type rmsd hydrogen bonds : bond 0.04496 ( 613) hydrogen bonds : angle 3.95010 ( 1761) covalent geometry : bond 0.00235 ( 9756) covalent geometry : angle 0.45332 (13192) *********************** 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 70 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 1.442 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: symmetry clash REVERT: A 185 MET cc_start: 0.9112 (mmp) cc_final: 0.8897 (mmt) REVERT: A 266 PHE cc_start: 0.8735 (m-80) cc_final: 0.8407 (m-80) REVERT: A 288 MET cc_start: 0.8752 (tpt) cc_final: 0.8510 (tpt) REVERT: A 688 GLN cc_start: 0.8034 (mt0) cc_final: 0.7752 (mp10) REVERT: A 696 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8306 (ttt-90) REVERT: A 921 MET cc_start: 0.8812 (ttp) cc_final: 0.8173 (tmm) REVERT: A 1010 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8261 (mm-30) REVERT: A 1304 MET cc_start: 0.8516 (mmm) cc_final: 0.8179 (mmt) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.4417 time to fit residues: 43.5080 Evaluate side-chains 68 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1312 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 24 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** 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 = 0.3715 r_free = 0.3715 target = 0.090598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.067606 restraints weight = 74745.078| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.61 r_work: 0.3176 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9756 Z= 0.187 Angle : 0.484 5.363 13192 Z= 0.269 Chirality : 0.038 0.138 1501 Planarity : 0.003 0.036 1688 Dihedral : 4.729 39.985 1335 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 1.37 % Allowed : 9.56 % Favored : 89.07 % 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 (0.25), residues: 1224 helix: 2.12 (0.19), residues: 778 sheet: -1.44 (0.82), residues: 35 loop : -0.91 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 0.001 HIS A1275 PHE 0.011 0.001 PHE A 266 TYR 0.013 0.001 TYR A 772 ARG 0.002 0.000 ARG A 958 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 613) hydrogen bonds : angle 4.06031 ( 1761) covalent geometry : bond 0.00405 ( 9756) covalent geometry : angle 0.48375 (13192) *********************** 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 71 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.605 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: symmetry clash REVERT: A 185 MET cc_start: 0.9112 (mmp) cc_final: 0.8873 (mmt) REVERT: A 266 PHE cc_start: 0.8809 (m-80) cc_final: 0.8450 (m-80) REVERT: A 688 GLN cc_start: 0.7993 (mt0) cc_final: 0.7637 (mp10) REVERT: A 696 ARG cc_start: 0.8571 (ttm-80) cc_final: 0.8311 (ttt-90) REVERT: A 921 MET cc_start: 0.8838 (ttp) cc_final: 0.8224 (tmm) REVERT: A 1010 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8200 (mm-30) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.4695 time to fit residues: 48.5625 Evaluate side-chains 67 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1270 CYS Chi-restraints excluded: chain A residue 1312 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.091419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.068551 restraints weight = 74242.596| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.58 r_work: 0.3192 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9756 Z= 0.132 Angle : 0.458 5.460 13192 Z= 0.252 Chirality : 0.037 0.135 1501 Planarity : 0.003 0.037 1688 Dihedral : 4.650 40.196 1335 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 1.27 % Allowed : 9.95 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1224 helix: 2.23 (0.19), residues: 781 sheet: -1.11 (0.84), residues: 34 loop : -0.86 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 114 HIS 0.002 0.001 HIS A 423 PHE 0.011 0.001 PHE A 774 TYR 0.012 0.001 TYR A 772 ARG 0.002 0.000 ARG A 958 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 613) hydrogen bonds : angle 3.92441 ( 1761) covalent geometry : bond 0.00284 ( 9756) covalent geometry : angle 0.45778 (13192) *********************** 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 71 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 1.534 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: symmetry clash REVERT: A 185 MET cc_start: 0.9128 (mmp) cc_final: 0.8901 (mmt) REVERT: A 266 PHE cc_start: 0.8826 (m-80) cc_final: 0.8465 (m-80) REVERT: A 688 GLN cc_start: 0.8058 (mt0) cc_final: 0.7775 (mp10) REVERT: A 696 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8308 (ttt-90) REVERT: A 921 MET cc_start: 0.8815 (ttp) cc_final: 0.8197 (tmm) REVERT: A 1010 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8312 (mm-30) REVERT: A 1304 MET cc_start: 0.8503 (mmm) cc_final: 0.8114 (mmt) outliers start: 13 outliers final: 12 residues processed: 67 average time/residue: 0.4376 time to fit residues: 43.7199 Evaluate side-chains 70 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1312 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** 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 = 0.3729 r_free = 0.3729 target = 0.091437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.068748 restraints weight = 73956.655| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.56 r_work: 0.3200 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9756 Z= 0.131 Angle : 0.454 5.457 13192 Z= 0.249 Chirality : 0.037 0.135 1501 Planarity : 0.003 0.038 1688 Dihedral : 4.570 39.712 1335 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.84 % Favored : 96.08 % Rotamer: Outliers : 1.37 % Allowed : 10.24 % Favored : 88.39 % 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: 1.84 (0.25), residues: 1224 helix: 2.30 (0.19), residues: 783 sheet: -1.10 (0.84), residues: 34 loop : -0.77 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 163 HIS 0.002 0.001 HIS A1275 PHE 0.010 0.001 PHE A 774 TYR 0.012 0.001 TYR A 772 ARG 0.002 0.000 ARG A 958 Details of bonding type rmsd hydrogen bonds : bond 0.04315 ( 613) hydrogen bonds : angle 3.86181 ( 1761) covalent geometry : bond 0.00280 ( 9756) covalent geometry : angle 0.45427 (13192) *********************** 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 72 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 1.565 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: symmetry clash REVERT: A 185 MET cc_start: 0.9122 (mmp) cc_final: 0.8730 (mmm) REVERT: A 266 PHE cc_start: 0.8880 (m-80) cc_final: 0.8426 (m-80) REVERT: A 696 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8335 (ttt-90) REVERT: A 805 MET cc_start: 0.8603 (ttm) cc_final: 0.8126 (ttm) REVERT: A 921 MET cc_start: 0.8788 (ttp) cc_final: 0.8172 (tmm) REVERT: A 1010 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8276 (mm-30) REVERT: A 1304 MET cc_start: 0.8541 (mmm) cc_final: 0.8172 (mmt) outliers start: 14 outliers final: 12 residues processed: 68 average time/residue: 0.4388 time to fit residues: 44.6986 Evaluate side-chains 69 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 406 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1312 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** 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 = 0.3739 r_free = 0.3739 target = 0.091883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069032 restraints weight = 73507.122| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.57 r_work: 0.3201 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9756 Z= 0.136 Angle : 0.458 5.309 13192 Z= 0.251 Chirality : 0.037 0.134 1501 Planarity : 0.003 0.039 1688 Dihedral : 4.552 39.368 1335 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.51 % Favored : 96.41 % Rotamer: Outliers : 1.37 % Allowed : 10.54 % Favored : 88.10 % 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: 1.82 (0.25), residues: 1224 helix: 2.30 (0.19), residues: 783 sheet: -1.30 (0.71), residues: 44 loop : -0.76 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 163 HIS 0.002 0.001 HIS A 423 PHE 0.010 0.001 PHE A 774 TYR 0.011 0.001 TYR A 772 ARG 0.002 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 613) hydrogen bonds : angle 3.86494 ( 1761) covalent geometry : bond 0.00293 ( 9756) covalent geometry : angle 0.45758 (13192) *********************** 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 71 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.658 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: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.9118 (mmp) cc_final: 0.8725 (mmm) REVERT: A 266 PHE cc_start: 0.8881 (m-80) cc_final: 0.8427 (m-80) REVERT: A 696 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8329 (ttt-90) REVERT: A 805 MET cc_start: 0.8611 (ttm) cc_final: 0.8129 (ttm) REVERT: A 1010 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8277 (mm-30) REVERT: A 1304 MET cc_start: 0.8517 (mmm) cc_final: 0.8165 (mmt) outliers start: 14 outliers final: 13 residues processed: 67 average time/residue: 0.4432 time to fit residues: 44.4968 Evaluate side-chains 69 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 901 SER Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1312 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** 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 = 0.3744 r_free = 0.3744 target = 0.092103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.069137 restraints weight = 73488.642| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.59 r_work: 0.3209 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9756 Z= 0.118 Angle : 0.446 5.477 13192 Z= 0.243 Chirality : 0.037 0.135 1501 Planarity : 0.003 0.037 1688 Dihedral : 4.465 39.008 1335 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 1.07 % Allowed : 10.83 % Favored : 88.10 % 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: 1.97 (0.25), residues: 1224 helix: 2.39 (0.19), residues: 783 sheet: -0.80 (0.66), residues: 55 loop : -0.68 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 898 HIS 0.002 0.001 HIS A1275 PHE 0.010 0.001 PHE A 774 TYR 0.011 0.001 TYR A 772 ARG 0.002 0.000 ARG A 958 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 613) hydrogen bonds : angle 3.79084 ( 1761) covalent geometry : bond 0.00251 ( 9756) covalent geometry : angle 0.44592 (13192) ********************** 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 68 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 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: symmetry clash revert: symmetry clash REVERT: A 185 MET cc_start: 0.9121 (mmp) cc_final: 0.8776 (mmm) REVERT: A 541 ILE cc_start: 0.8840 (mm) cc_final: 0.8634 (mt) REVERT: A 696 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8324 (ttt-90) REVERT: A 805 MET cc_start: 0.8596 (ttm) cc_final: 0.8102 (ttm) REVERT: A 921 MET cc_start: 0.8758 (ttp) cc_final: 0.8126 (tmm) REVERT: A 1010 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8249 (mm-30) REVERT: A 1304 MET cc_start: 0.8503 (mmm) cc_final: 0.8153 (mmt) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.4728 time to fit residues: 45.1719 Evaluate side-chains 66 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1312 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** 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 = 0.3738 r_free = 0.3738 target = 0.091767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.068814 restraints weight = 73971.673| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.60 r_work: 0.3199 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9756 Z= 0.152 Angle : 0.462 5.489 13192 Z= 0.254 Chirality : 0.037 0.134 1501 Planarity : 0.003 0.038 1688 Dihedral : 4.494 38.881 1335 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 1.07 % Allowed : 11.02 % Favored : 87.90 % 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: 1.89 (0.25), residues: 1224 helix: 2.34 (0.19), residues: 783 sheet: -1.31 (0.63), residues: 62 loop : -0.62 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 163 HIS 0.002 0.001 HIS A1275 PHE 0.010 0.001 PHE A 774 TYR 0.011 0.001 TYR A 772 ARG 0.002 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 613) hydrogen bonds : angle 3.85795 ( 1761) covalent geometry : bond 0.00329 ( 9756) covalent geometry : angle 0.46211 (13192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7038.29 seconds wall clock time: 121 minutes 34.69 seconds (7294.69 seconds total)