Starting phenix.real_space_refine on Sun Jul 27 17:52:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vrc_21367/07_2025/6vrc_21367.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrc_21367/07_2025/6vrc_21367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vrc_21367/07_2025/6vrc_21367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrc_21367/07_2025/6vrc_21367.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrc_21367/07_2025/6vrc_21367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrc_21367/07_2025/6vrc_21367.cif" } resolution = 3.2 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 50 5.49 5 S 28 5.16 5 C 5822 2.51 5 N 1603 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9429 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 8359 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 983} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1070 Classifications: {'RNA': 51} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna2p': 18, 'rna3p': 32} Time building chain proxies: 6.43, per 1000 atoms: 0.68 Number of scatterers: 9429 At special positions: 0 Unit cell: (102.6, 92.88, 122.04, 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 28 16.00 P 50 15.00 O 1926 8.00 N 1603 7.00 C 5822 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 3 sheets defined 58.1% alpha, 0.8% beta 4 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 67 through 75 removed outlier: 3.795A pdb=" N MET A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 85 removed outlier: 3.611A pdb=" N ASN A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 105 removed outlier: 3.681A pdb=" N LEU A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.946A pdb=" N SER A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 163 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 179 through 203 removed outlier: 3.613A pdb=" N ASN A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.573A pdb=" N LYS A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 225 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.719A pdb=" N LYS A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.587A pdb=" N LYS A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 278 " --> pdb=" O HIS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 287 through 303 removed outlier: 3.605A pdb=" N LEU A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A 302 " --> pdb=" O HIS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 332 removed outlier: 3.764A pdb=" N LYS A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 348 removed outlier: 3.756A pdb=" N GLU A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 388 removed outlier: 3.582A pdb=" N ILE A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 367 " --> pdb=" O LYS A 363 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.854A pdb=" N ILE A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A 419 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 420 " --> pdb=" O GLN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 4.085A pdb=" N ARG A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 439 " --> pdb=" O TRP A 435 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.242A pdb=" N ASP A 493 " --> pdb=" O THR A 489 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 removed outlier: 4.047A pdb=" N ILE A 507 " --> pdb=" O PRO A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.733A pdb=" N ASP A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 596 removed outlier: 3.525A pdb=" N SER A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 removed outlier: 4.478A pdb=" N GLN A 603 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 606 " --> pdb=" O PRO A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 623 removed outlier: 3.574A pdb=" N PHE A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 620 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 658 removed outlier: 4.187A pdb=" N SER A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 removed outlier: 4.007A pdb=" N LYS A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 690 removed outlier: 3.535A pdb=" N ILE A 675 " --> pdb=" O PHE A 671 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 679 " --> pdb=" O ILE A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 697 removed outlier: 3.864A pdb=" N CYS A 696 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 729 Processing helix chain 'A' and resid 733 through 748 removed outlier: 3.727A pdb=" N SER A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 739 " --> pdb=" O GLN A 735 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 763 removed outlier: 3.816A pdb=" N PHE A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 761 " --> pdb=" O SER A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 773 removed outlier: 3.532A pdb=" N LEU A 771 " --> pdb=" O GLY A 767 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN A 772 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 773 " --> pdb=" O ALA A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 819 through 828 removed outlier: 3.686A pdb=" N LEU A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 826 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 828 " --> pdb=" O LEU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 838 Processing helix chain 'A' and resid 847 through 854 removed outlier: 3.935A pdb=" N ILE A 851 " --> pdb=" O SER A 847 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 854 " --> pdb=" O ASP A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 876 removed outlier: 3.857A pdb=" N GLN A 865 " --> pdb=" O GLU A 861 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 874 " --> pdb=" O HIS A 870 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A 875 " --> pdb=" O LYS A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 881 removed outlier: 3.598A pdb=" N ARG A 881 " --> pdb=" O GLY A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 907 removed outlier: 3.697A pdb=" N LYS A 888 " --> pdb=" O ALA A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 944 removed outlier: 3.813A pdb=" N SER A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE A 931 " --> pdb=" O GLY A 927 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 942 " --> pdb=" O PHE A 938 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1003 Processing helix chain 'A' and resid 1011 through 1021 removed outlier: 3.954A pdb=" N LYS A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A1019 " --> pdb=" O LYS A1015 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A1020 " --> pdb=" O ARG A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1026 removed outlier: 4.006A pdb=" N ASN A1026 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1044 removed outlier: 3.738A pdb=" N ARG A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A1042 " --> pdb=" O ASP A1038 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A1043 " --> pdb=" O ASP A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1052 Processing helix chain 'A' and resid 1055 through 1065 removed outlier: 3.713A pdb=" N LYS A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A1060 " --> pdb=" O LYS A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 3.592A pdb=" N CYS A1110 " --> pdb=" O SER A1106 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A1111 " --> pdb=" O ASN A1107 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A1112 " --> pdb=" O GLU A1108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 465 297 hydrogen bonds defined for protein. 858 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1961 1.33 - 1.45: 2434 1.45 - 1.57: 5169 1.57 - 1.69: 100 1.69 - 1.81: 48 Bond restraints: 9712 Sorted by residual: bond pdb=" N ILE A 112 " pdb=" CA ILE A 112 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.11e-02 8.12e+03 1.27e+01 bond pdb=" N ILE A 515 " pdb=" CA ILE A 515 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.22e+01 bond pdb=" N ILE A 263 " pdb=" CA ILE A 263 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.48e+00 bond pdb=" N ILE A 320 " pdb=" CA ILE A 320 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.22e-02 6.72e+03 9.40e+00 bond pdb=" N LEU A 601 " pdb=" CA LEU A 601 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.04e-02 9.25e+03 9.26e+00 ... (remaining 9707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 12032 2.07 - 4.15: 1088 4.15 - 6.22: 127 6.22 - 8.29: 36 8.29 - 10.37: 12 Bond angle restraints: 13295 Sorted by residual: angle pdb=" C3' A B 34 " pdb=" C2' A B 34 " pdb=" O2' A B 34 " ideal model delta sigma weight residual 114.60 124.79 -10.19 1.50e+00 4.44e-01 4.62e+01 angle pdb=" N GLU A 287 " pdb=" CA GLU A 287 " pdb=" C GLU A 287 " ideal model delta sigma weight residual 113.88 105.87 8.01 1.23e+00 6.61e-01 4.24e+01 angle pdb=" O3' A B 34 " pdb=" C3' A B 34 " pdb=" C2' A B 34 " ideal model delta sigma weight residual 109.50 118.71 -9.21 1.50e+00 4.44e-01 3.77e+01 angle pdb=" C CYS A 89 " pdb=" N ARG A 90 " pdb=" CA ARG A 90 " ideal model delta sigma weight residual 120.09 127.70 -7.61 1.25e+00 6.40e-01 3.70e+01 angle pdb=" N SER A 247 " pdb=" CA SER A 247 " pdb=" C SER A 247 " ideal model delta sigma weight residual 113.41 106.22 7.19 1.22e+00 6.72e-01 3.48e+01 ... (remaining 13290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 5769 35.61 - 71.22: 199 71.22 - 106.82: 20 106.82 - 142.43: 2 142.43 - 178.04: 4 Dihedral angle restraints: 5994 sinusoidal: 2982 harmonic: 3012 Sorted by residual: dihedral pdb=" O4' U B 37 " pdb=" C1' U B 37 " pdb=" N1 U B 37 " pdb=" C2 U B 37 " ideal model delta sinusoidal sigma weight residual -128.00 49.68 -177.68 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual -128.00 46.87 -174.87 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U B 33 " pdb=" C1' U B 33 " pdb=" N1 U B 33 " pdb=" C2 U B 33 " ideal model delta sinusoidal sigma weight residual -160.00 -44.75 -115.25 1 1.50e+01 4.44e-03 6.09e+01 ... (remaining 5991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1310 0.112 - 0.224: 174 0.224 - 0.335: 10 0.335 - 0.447: 3 0.447 - 0.559: 3 Chirality restraints: 1500 Sorted by residual: chirality pdb=" C3' G B 1 " pdb=" C4' G B 1 " pdb=" O3' G B 1 " pdb=" C2' G B 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.19 -0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" C3' A B 34 " pdb=" C4' A B 34 " pdb=" O3' A B 34 " pdb=" C2' A B 34 " both_signs ideal model delta sigma weight residual False -2.74 -2.20 -0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" C2' A B 34 " pdb=" C3' A B 34 " pdb=" O2' A B 34 " pdb=" C1' A B 34 " both_signs ideal model delta sigma weight residual False -2.52 -2.04 -0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 1497 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 103 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C LEU A 103 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU A 103 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU A 104 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 822 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ILE A 822 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE A 822 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP A 823 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 607 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00 pdb=" C ASN A 607 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN A 607 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN A 608 " 0.018 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 605 2.72 - 3.26: 8559 3.26 - 3.81: 14041 3.81 - 4.35: 18699 4.35 - 4.90: 30108 Nonbonded interactions: 72012 Sorted by model distance: nonbonded pdb=" O2' C B 7 " pdb=" O5' U B 8 " model vdw 2.170 3.040 nonbonded pdb=" OE2 GLU A 498 " pdb=" ND2 ASN A 772 " model vdw 2.209 3.120 nonbonded pdb=" OE2 GLU A 139 " pdb=" NZ LYS A 195 " model vdw 2.247 3.120 nonbonded pdb=" O ASN A 309 " pdb=" O6 G B 1 " model vdw 2.265 3.040 nonbonded pdb=" O GLN A 523 " pdb=" OH TYR A 694 " model vdw 2.274 3.040 ... (remaining 72007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.790 Find NCS groups from input model: 0.140 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.010 0.097 9712 Z= 0.542 Angle : 1.272 10.365 13295 Z= 0.794 Chirality : 0.079 0.559 1500 Planarity : 0.007 0.065 1503 Dihedral : 17.403 178.042 4028 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 3.70 % Allowed : 8.99 % Favored : 87.30 % Cbeta Deviations : 0.20 % 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: -4.83 (0.21), residues: 997 helix: -3.25 (0.17), residues: 550 sheet: -3.36 (0.60), residues: 38 loop : -2.92 (0.25), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP A 417 HIS 0.013 0.002 HIS A1093 PHE 0.034 0.003 PHE A1071 TYR 0.025 0.003 TYR A 486 ARG 0.024 0.002 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.35762 ( 307) hydrogen bonds : angle 9.52308 ( 878) covalent geometry : bond 0.00994 ( 9712) covalent geometry : angle 1.27191 (13295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 128 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.7242 (m-70) REVERT: A 218 ASP cc_start: 0.7939 (t70) cc_final: 0.7592 (t0) REVERT: A 250 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7939 (mtmm) REVERT: A 338 ARG cc_start: 0.8151 (tpt-90) cc_final: 0.7937 (mtp85) REVERT: A 586 GLN cc_start: 0.7422 (tt0) cc_final: 0.7202 (mt0) outliers start: 35 outliers final: 9 residues processed: 266 average time/residue: 0.2882 time to fit residues: 102.4837 Evaluate side-chains 133 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 938 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 109 GLN A 121 ASN A 124 ASN A 165 GLN A 259 ASN A 285 ASN A 289 ASN A 292 ASN A 328 ASN A 333 ASN A 360 GLN A 508 ASN A 532 ASN A 576 ASN A 598 GLN A 607 ASN A 654 GLN A 659 GLN A 772 ASN A 894 ASN A 915 HIS A1023 ASN A1052 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117202 restraints weight = 13268.463| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.93 r_work: 0.3060 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9712 Z= 0.158 Angle : 0.684 9.992 13295 Z= 0.361 Chirality : 0.043 0.253 1500 Planarity : 0.005 0.058 1503 Dihedral : 17.508 175.697 1853 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.60 % Allowed : 13.54 % Favored : 82.86 % 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: -3.33 (0.23), residues: 997 helix: -1.78 (0.20), residues: 569 sheet: -2.76 (0.83), residues: 27 loop : -2.69 (0.26), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 185 HIS 0.003 0.001 HIS A 73 PHE 0.026 0.002 PHE A 459 TYR 0.015 0.002 TYR A 889 ARG 0.005 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.06937 ( 307) hydrogen bonds : angle 4.60432 ( 878) covalent geometry : bond 0.00326 ( 9712) covalent geometry : angle 0.68378 (13295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7649 (t0) REVERT: A 218 ASP cc_start: 0.8107 (t70) cc_final: 0.7829 (t0) REVERT: A 383 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8947 (tp) REVERT: A 514 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7252 (mmtm) REVERT: A 820 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7754 (ttp80) REVERT: A 1013 LYS cc_start: 0.7798 (tttt) cc_final: 0.7433 (tptt) REVERT: A 1079 HIS cc_start: 0.8024 (m-70) cc_final: 0.7744 (m90) REVERT: A 1086 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8784 (tt) outliers start: 34 outliers final: 12 residues processed: 174 average time/residue: 0.3551 time to fit residues: 81.1412 Evaluate side-chains 115 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 43 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 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 165 GLN A 207 GLN A 416 GLN A 461 ASN A 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115305 restraints weight = 13355.752| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.97 r_work: 0.3023 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9712 Z= 0.151 Angle : 0.609 8.787 13295 Z= 0.320 Chirality : 0.041 0.182 1500 Planarity : 0.004 0.049 1503 Dihedral : 16.723 177.963 1832 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.49 % Allowed : 15.13 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.25), residues: 997 helix: -1.00 (0.21), residues: 575 sheet: -2.75 (0.81), residues: 31 loop : -2.53 (0.26), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 185 HIS 0.004 0.001 HIS A 913 PHE 0.027 0.002 PHE A 459 TYR 0.013 0.001 TYR A 889 ARG 0.006 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.06141 ( 307) hydrogen bonds : angle 4.03354 ( 878) covalent geometry : bond 0.00332 ( 9712) covalent geometry : angle 0.60947 (13295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8223 (t70) cc_final: 0.7923 (t0) REVERT: A 254 LYS cc_start: 0.8324 (mtpp) cc_final: 0.8113 (mtpp) REVERT: A 415 ARG cc_start: 0.8816 (mtm-85) cc_final: 0.8475 (ttp-110) REVERT: A 484 PHE cc_start: 0.7996 (m-80) cc_final: 0.7793 (m-80) REVERT: A 514 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7431 (mmtm) REVERT: A 621 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9050 (tp) REVERT: A 820 ARG cc_start: 0.8116 (ttp-110) cc_final: 0.7806 (ttp80) REVERT: A 1013 LYS cc_start: 0.7878 (tttt) cc_final: 0.7533 (tptt) REVERT: A 1086 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8877 (tt) outliers start: 33 outliers final: 17 residues processed: 148 average time/residue: 0.2788 time to fit residues: 54.4188 Evaluate side-chains 124 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 410 HIS Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 76 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 124 ASN A 165 GLN A 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.143200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111001 restraints weight = 13165.610| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.95 r_work: 0.2964 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9712 Z= 0.191 Angle : 0.627 10.277 13295 Z= 0.327 Chirality : 0.042 0.166 1500 Planarity : 0.004 0.051 1503 Dihedral : 16.584 178.046 1832 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.66 % Allowed : 15.56 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.25), residues: 997 helix: -0.60 (0.21), residues: 581 sheet: -2.53 (0.81), residues: 31 loop : -2.29 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 417 HIS 0.005 0.001 HIS A 913 PHE 0.028 0.002 PHE A 459 TYR 0.014 0.002 TYR A1004 ARG 0.008 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.06516 ( 307) hydrogen bonds : angle 3.99919 ( 878) covalent geometry : bond 0.00438 ( 9712) covalent geometry : angle 0.62700 (13295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 108 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8219 (t70) cc_final: 0.7941 (t0) REVERT: A 415 ARG cc_start: 0.8792 (mtm-85) cc_final: 0.8463 (ttp-110) REVERT: A 459 PHE cc_start: 0.7451 (t80) cc_final: 0.7237 (t80) REVERT: A 507 ILE cc_start: 0.9092 (tp) cc_final: 0.8697 (mt) REVERT: A 514 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7480 (mmtm) REVERT: A 605 THR cc_start: 0.9255 (m) cc_final: 0.7762 (t) REVERT: A 794 MET cc_start: 0.8878 (tpp) cc_final: 0.8498 (ttm) REVERT: A 876 LYS cc_start: 0.7687 (mmtm) cc_final: 0.7192 (tptm) REVERT: A 1013 LYS cc_start: 0.7966 (tttt) cc_final: 0.7489 (tptt) outliers start: 44 outliers final: 21 residues processed: 138 average time/residue: 0.2422 time to fit residues: 45.0643 Evaluate side-chains 124 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1046 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 3 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 165 GLN A 292 ASN A1093 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110236 restraints weight = 13158.522| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.90 r_work: 0.2951 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9712 Z= 0.213 Angle : 0.629 6.770 13295 Z= 0.329 Chirality : 0.043 0.165 1500 Planarity : 0.004 0.047 1503 Dihedral : 16.444 177.620 1832 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.81 % Allowed : 17.25 % Favored : 78.94 % 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: -1.86 (0.25), residues: 997 helix: -0.41 (0.21), residues: 584 sheet: -3.23 (0.66), residues: 41 loop : -2.24 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 417 HIS 0.005 0.001 HIS A 73 PHE 0.023 0.002 PHE A 459 TYR 0.014 0.002 TYR A 496 ARG 0.008 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.06531 ( 307) hydrogen bonds : angle 3.99713 ( 878) covalent geometry : bond 0.00492 ( 9712) covalent geometry : angle 0.62897 (13295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8243 (t70) cc_final: 0.7961 (t0) REVERT: A 415 ARG cc_start: 0.8808 (mtm-85) cc_final: 0.8487 (ttp-110) REVERT: A 507 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8708 (mt) REVERT: A 514 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7436 (mmtm) REVERT: A 605 THR cc_start: 0.9243 (m) cc_final: 0.7773 (t) REVERT: A 753 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7948 (p) REVERT: A 768 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9065 (tp) REVERT: A 820 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7961 (ttp80) REVERT: A 876 LYS cc_start: 0.7641 (mmtm) cc_final: 0.7170 (tttm) REVERT: A 1013 LYS cc_start: 0.7983 (tttt) cc_final: 0.7490 (tptt) outliers start: 36 outliers final: 21 residues processed: 134 average time/residue: 0.3021 time to fit residues: 54.4699 Evaluate side-chains 123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1046 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 104 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 0.0170 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 165 GLN A 607 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.141923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110732 restraints weight = 13171.410| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.81 r_work: 0.2938 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9712 Z= 0.214 Angle : 0.623 6.625 13295 Z= 0.326 Chirality : 0.043 0.159 1500 Planarity : 0.004 0.050 1503 Dihedral : 16.384 177.680 1832 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.81 % Allowed : 17.67 % Favored : 78.52 % 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: -1.66 (0.26), residues: 997 helix: -0.24 (0.22), residues: 586 sheet: -2.60 (0.63), residues: 51 loop : -2.24 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 417 HIS 0.006 0.001 HIS A1093 PHE 0.023 0.002 PHE A 459 TYR 0.014 0.002 TYR A 496 ARG 0.008 0.001 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.06471 ( 307) hydrogen bonds : angle 3.99365 ( 878) covalent geometry : bond 0.00497 ( 9712) covalent geometry : angle 0.62283 (13295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 1.666 Fit side-chains revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8240 (t70) cc_final: 0.7949 (t0) REVERT: A 415 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8468 (ttp-110) REVERT: A 507 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8719 (mt) REVERT: A 514 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7460 (mmtm) REVERT: A 605 THR cc_start: 0.9251 (m) cc_final: 0.7804 (t) REVERT: A 727 MET cc_start: 0.8634 (ttp) cc_final: 0.8384 (ttp) REVERT: A 753 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.7995 (p) REVERT: A 768 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9091 (tp) REVERT: A 794 MET cc_start: 0.8794 (tpp) cc_final: 0.8539 (ttm) REVERT: A 820 ARG cc_start: 0.8267 (ttp-110) cc_final: 0.7942 (ttp80) REVERT: A 876 LYS cc_start: 0.7620 (mmtm) cc_final: 0.7140 (tttm) REVERT: A 1013 LYS cc_start: 0.7935 (tttt) cc_final: 0.7532 (tptt) outliers start: 36 outliers final: 18 residues processed: 135 average time/residue: 0.3248 time to fit residues: 59.2315 Evaluate side-chains 123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1046 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 70 optimal weight: 0.4980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 165 GLN A 607 ASN A 772 ASN A 793 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110419 restraints weight = 13174.738| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.93 r_work: 0.2957 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9712 Z= 0.176 Angle : 0.586 6.398 13295 Z= 0.309 Chirality : 0.042 0.154 1500 Planarity : 0.004 0.047 1503 Dihedral : 16.284 177.963 1832 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.02 % Allowed : 18.20 % Favored : 77.78 % 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: -1.43 (0.26), residues: 997 helix: -0.01 (0.22), residues: 587 sheet: -2.58 (0.63), residues: 51 loop : -2.22 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 456 HIS 0.004 0.001 HIS A1093 PHE 0.011 0.001 PHE A 548 TYR 0.011 0.001 TYR A 496 ARG 0.006 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 307) hydrogen bonds : angle 3.87014 ( 878) covalent geometry : bond 0.00406 ( 9712) covalent geometry : angle 0.58625 (13295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 149 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7902 (ptt90) REVERT: A 218 ASP cc_start: 0.8279 (t70) cc_final: 0.7983 (t0) REVERT: A 275 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7263 (tt0) REVERT: A 415 ARG cc_start: 0.8828 (mtm-85) cc_final: 0.8507 (ttp-110) REVERT: A 507 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8688 (mt) REVERT: A 514 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7476 (mmtm) REVERT: A 605 THR cc_start: 0.9231 (m) cc_final: 0.7818 (t) REVERT: A 727 MET cc_start: 0.8551 (ttp) cc_final: 0.8271 (ttp) REVERT: A 753 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8014 (p) REVERT: A 768 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9033 (tp) REVERT: A 794 MET cc_start: 0.8824 (tpp) cc_final: 0.8453 (ttm) REVERT: A 820 ARG cc_start: 0.8269 (ttp-110) cc_final: 0.7939 (ttp80) REVERT: A 876 LYS cc_start: 0.7558 (mmtm) cc_final: 0.7112 (tttm) REVERT: A 1013 LYS cc_start: 0.7947 (tttt) cc_final: 0.7527 (tptt) outliers start: 38 outliers final: 22 residues processed: 135 average time/residue: 0.3055 time to fit residues: 55.9202 Evaluate side-chains 131 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1046 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 8 optimal weight: 0.0470 chunk 79 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 124 ASN A 165 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.146896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.114923 restraints weight = 13303.525| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.97 r_work: 0.3034 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9712 Z= 0.106 Angle : 0.515 9.485 13295 Z= 0.271 Chirality : 0.038 0.136 1500 Planarity : 0.003 0.048 1503 Dihedral : 16.047 177.887 1832 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.07 % Allowed : 19.05 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.27), residues: 997 helix: 0.44 (0.23), residues: 588 sheet: -2.46 (0.86), residues: 29 loop : -2.12 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 456 HIS 0.003 0.001 HIS A 913 PHE 0.036 0.001 PHE A 459 TYR 0.009 0.001 TYR A1109 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 307) hydrogen bonds : angle 3.54728 ( 878) covalent geometry : bond 0.00226 ( 9712) covalent geometry : angle 0.51549 (13295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8148 (m-10) cc_final: 0.7743 (m-10) REVERT: A 165 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: A 218 ASP cc_start: 0.8261 (t70) cc_final: 0.7929 (t0) REVERT: A 275 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7297 (tt0) REVERT: A 484 PHE cc_start: 0.7986 (m-80) cc_final: 0.7533 (m-80) REVERT: A 507 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8637 (mt) REVERT: A 514 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7241 (mmtm) REVERT: A 727 MET cc_start: 0.8519 (ttp) cc_final: 0.8253 (ttp) REVERT: A 768 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8980 (tp) REVERT: A 820 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7865 (ttp80) REVERT: A 876 LYS cc_start: 0.7291 (mmtm) cc_final: 0.7031 (tptm) REVERT: A 920 ASP cc_start: 0.8236 (m-30) cc_final: 0.7770 (m-30) REVERT: A 1013 LYS cc_start: 0.7858 (tttt) cc_final: 0.7498 (tptt) outliers start: 29 outliers final: 9 residues processed: 146 average time/residue: 0.2845 time to fit residues: 55.4142 Evaluate side-chains 125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 1074 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 124 ASN A 165 GLN A 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.146713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114529 restraints weight = 13153.339| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.96 r_work: 0.3026 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9712 Z= 0.113 Angle : 0.533 9.309 13295 Z= 0.278 Chirality : 0.038 0.133 1500 Planarity : 0.003 0.048 1503 Dihedral : 15.999 177.950 1832 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.12 % Allowed : 20.42 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.27), residues: 997 helix: 0.62 (0.23), residues: 586 sheet: -2.23 (0.92), residues: 19 loop : -2.15 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 172 HIS 0.003 0.001 HIS A1093 PHE 0.040 0.001 PHE A 459 TYR 0.008 0.001 TYR A 496 ARG 0.003 0.000 ARG A 36 Details of bonding type rmsd hydrogen bonds : bond 0.04618 ( 307) hydrogen bonds : angle 3.53479 ( 878) covalent geometry : bond 0.00246 ( 9712) covalent geometry : angle 0.53310 (13295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 149 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7811 (ptt90) REVERT: A 165 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: A 218 ASP cc_start: 0.8261 (t70) cc_final: 0.7955 (t0) REVERT: A 507 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8637 (mt) REVERT: A 514 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7246 (mmtm) REVERT: A 534 GLU cc_start: 0.7642 (tp30) cc_final: 0.7417 (tp30) REVERT: A 727 MET cc_start: 0.8500 (ttp) cc_final: 0.8235 (ttp) REVERT: A 768 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8977 (tp) REVERT: A 820 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7853 (ttp80) REVERT: A 876 LYS cc_start: 0.7337 (mmtm) cc_final: 0.7079 (tptm) REVERT: A 920 ASP cc_start: 0.8257 (m-30) cc_final: 0.7833 (m-30) REVERT: A 1013 LYS cc_start: 0.7883 (tttt) cc_final: 0.7513 (tptt) outliers start: 20 outliers final: 10 residues processed: 128 average time/residue: 0.3728 time to fit residues: 64.2964 Evaluate side-chains 123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 818 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 165 GLN A 285 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113235 restraints weight = 13168.555| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.93 r_work: 0.3000 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9712 Z= 0.144 Angle : 0.578 9.100 13295 Z= 0.300 Chirality : 0.040 0.141 1500 Planarity : 0.004 0.050 1503 Dihedral : 15.996 177.902 1832 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.33 % Allowed : 20.42 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 997 helix: 0.55 (0.22), residues: 593 sheet: -1.44 (0.82), residues: 31 loop : -2.21 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 172 HIS 0.004 0.001 HIS A1093 PHE 0.042 0.001 PHE A 459 TYR 0.010 0.001 TYR A 496 ARG 0.006 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.05141 ( 307) hydrogen bonds : angle 3.61156 ( 878) covalent geometry : bond 0.00328 ( 9712) covalent geometry : angle 0.57782 (13295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1994 Ramachandran restraints generated. 997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 96 MET cc_start: 0.8265 (mmm) cc_final: 0.7960 (mmt) REVERT: A 149 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7782 (ptt90) REVERT: A 165 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: A 218 ASP cc_start: 0.8266 (t70) cc_final: 0.7964 (t0) REVERT: A 275 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7307 (tt0) REVERT: A 484 PHE cc_start: 0.7893 (m-80) cc_final: 0.7414 (m-80) REVERT: A 507 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8659 (mt) REVERT: A 514 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7448 (mmtm) REVERT: A 727 MET cc_start: 0.8535 (ttp) cc_final: 0.8283 (ttp) REVERT: A 768 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9008 (tp) REVERT: A 794 MET cc_start: 0.8819 (tpp) cc_final: 0.8530 (ttm) REVERT: A 820 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7920 (ttp80) REVERT: A 876 LYS cc_start: 0.7373 (mmtm) cc_final: 0.7098 (tptm) REVERT: A 920 ASP cc_start: 0.8299 (m-30) cc_final: 0.7889 (m-30) REVERT: A 1013 LYS cc_start: 0.7932 (tttt) cc_final: 0.7540 (tptt) outliers start: 22 outliers final: 10 residues processed: 124 average time/residue: 0.2671 time to fit residues: 44.0571 Evaluate side-chains 122 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 755 GLU Chi-restraints excluded: chain A residue 768 LEU Chi-restraints excluded: chain A residue 818 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 31 optimal weight: 0.0030 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 124 ASN A 165 GLN A 285 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115119 restraints weight = 13233.491| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.97 r_work: 0.3032 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9712 Z= 0.110 Angle : 0.541 9.103 13295 Z= 0.281 Chirality : 0.038 0.133 1500 Planarity : 0.004 0.052 1503 Dihedral : 15.953 178.085 1830 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.12 % Allowed : 20.63 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.27), residues: 997 helix: 0.76 (0.23), residues: 586 sheet: -2.13 (0.93), residues: 19 loop : -2.07 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 456 HIS 0.003 0.001 HIS A1093 PHE 0.042 0.001 PHE A 459 TYR 0.010 0.001 TYR A1046 ARG 0.006 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 307) hydrogen bonds : angle 3.49994 ( 878) covalent geometry : bond 0.00237 ( 9712) covalent geometry : angle 0.54137 (13295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5051.20 seconds wall clock time: 92 minutes 47.10 seconds (5567.10 seconds total)