Starting phenix.real_space_refine on Sun Dec 29 02:03:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vrc_21367/12_2024/6vrc_21367.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrc_21367/12_2024/6vrc_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_21367/12_2024/6vrc_21367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrc_21367/12_2024/6vrc_21367.map" model { file = "/net/cci-nas-00/data/ceres_data/6vrc_21367/12_2024/6vrc_21367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrc_21367/12_2024/6vrc_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-5532/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: 6.26, per 1000 atoms: 0.66 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: 2.38 Conformation dependent library (CDL) restraints added in 1.0 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: 2.74 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: 2.90 Time building geometry restraints manager: 2.77 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: 0.470 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.200 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- 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= 0.622 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 *********************** 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 : 1.067 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: 0.2544 time to fit residues: 89.7706 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 : 1.071 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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= 0.205 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 *********************** 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 : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7200 (mmtm) REVERT: A 820 ARG cc_start: 0.7487 (ttp-110) cc_final: 0.7217 (ttp80) REVERT: A 1086 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8623 (tt) outliers start: 34 outliers final: 12 residues processed: 174 average time/residue: 0.3022 time to fit residues: 68.4740 Evaluate side-chains 111 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU 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 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 52 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 94 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 165 GLN A 207 GLN A 416 GLN A 461 ASN A 607 ASN A1065 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9712 Z= 0.163 Angle : 0.578 8.495 13295 Z= 0.303 Chirality : 0.039 0.178 1500 Planarity : 0.004 0.049 1503 Dihedral : 16.681 178.515 1832 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.49 % Allowed : 14.60 % Favored : 81.90 % 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: -2.40 (0.25), residues: 997 helix: -0.88 (0.22), residues: 568 sheet: -2.71 (0.81), residues: 31 loop : -2.47 (0.26), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 185 HIS 0.003 0.001 HIS A 913 PHE 0.028 0.001 PHE A 459 TYR 0.012 0.001 TYR A 889 ARG 0.004 0.001 ARG A 36 *********************** 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 160 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7996 (pp20) cc_final: 0.7697 (pp20) REVERT: A 820 ARG cc_start: 0.7492 (ttp-110) cc_final: 0.7259 (ttp80) REVERT: A 920 ASP cc_start: 0.8086 (m-30) cc_final: 0.7613 (m-30) REVERT: A 1086 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8631 (tt) outliers start: 33 outliers final: 12 residues processed: 150 average time/residue: 0.2860 time to fit residues: 57.2951 Evaluate side-chains 111 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 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 539 THR 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 1086 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 0.0770 overall best weight: 1.2340 ------------------------------------------------------------------------------- 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 285 ASN A 385 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9712 Z= 0.189 Angle : 0.568 7.509 13295 Z= 0.297 Chirality : 0.040 0.158 1500 Planarity : 0.003 0.052 1503 Dihedral : 16.435 178.107 1826 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.39 % Allowed : 16.08 % Favored : 80.53 % 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: -0.43 (0.22), residues: 580 sheet: -2.78 (0.85), residues: 21 loop : -2.32 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 185 HIS 0.004 0.001 HIS A 913 PHE 0.029 0.002 PHE A 459 TYR 0.012 0.001 TYR A 889 ARG 0.005 0.000 ARG A 36 *********************** 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 150 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 727 MET cc_start: 0.8190 (ttp) cc_final: 0.7858 (ttp) REVERT: A 820 ARG cc_start: 0.7482 (ttp-110) cc_final: 0.7222 (ttp80) REVERT: A 1086 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8722 (tt) outliers start: 32 outliers final: 16 residues processed: 141 average time/residue: 0.2803 time to fit residues: 53.2409 Evaluate side-chains 120 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 529 THR 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 998 LEU Chi-restraints excluded: chain A residue 1046 TYR Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 91 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9712 Z= 0.210 Angle : 0.565 6.643 13295 Z= 0.296 Chirality : 0.040 0.153 1500 Planarity : 0.003 0.047 1503 Dihedral : 16.221 178.123 1826 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.60 % Allowed : 16.61 % 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: -1.55 (0.26), residues: 997 helix: -0.15 (0.22), residues: 582 sheet: -2.56 (0.88), residues: 19 loop : -2.27 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 417 HIS 0.004 0.001 HIS A 913 PHE 0.015 0.001 PHE A 459 TYR 0.010 0.001 TYR A 889 ARG 0.005 0.000 ARG A 36 *********************** 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 146 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 415 ARG cc_start: 0.7987 (ttp-110) cc_final: 0.7532 (mtt90) REVERT: A 507 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 727 MET cc_start: 0.8194 (ttp) cc_final: 0.7886 (ttp) REVERT: A 768 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9016 (tp) REVERT: A 794 MET cc_start: 0.8551 (tpp) cc_final: 0.8184 (mmm) REVERT: A 1086 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8747 (tt) outliers start: 34 outliers final: 20 residues processed: 135 average time/residue: 0.2570 time to fit residues: 47.0815 Evaluate side-chains 125 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN 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 295 ILE 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 507 ILE 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 606 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 Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN A 285 ASN A1023 ASN A1093 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9712 Z= 0.366 Angle : 0.661 7.158 13295 Z= 0.344 Chirality : 0.045 0.158 1500 Planarity : 0.004 0.051 1503 Dihedral : 16.339 177.486 1826 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.92 % Allowed : 17.35 % Favored : 78.73 % 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: -1.63 (0.26), residues: 997 helix: -0.18 (0.22), residues: 583 sheet: -2.04 (0.67), residues: 45 loop : -2.38 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 780 HIS 0.005 0.001 HIS A 73 PHE 0.013 0.002 PHE A 604 TYR 0.015 0.002 TYR A 496 ARG 0.010 0.001 ARG A 36 *********************** 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 142 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 507 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8881 (mt) REVERT: A 605 THR cc_start: 0.9131 (m) cc_final: 0.7887 (t) REVERT: A 753 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7471 (p) REVERT: A 768 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9029 (tp) REVERT: A 794 MET cc_start: 0.8582 (tpp) cc_final: 0.8370 (ttm) REVERT: A 820 ARG cc_start: 0.7663 (ttp-110) cc_final: 0.7380 (ttp80) outliers start: 37 outliers final: 20 residues processed: 132 average time/residue: 0.2842 time to fit residues: 51.1921 Evaluate side-chains 124 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 342 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 539 THR Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 693 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 Chi-restraints excluded: chain A residue 1074 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 124 ASN A 285 ASN A 607 ASN A1023 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9712 Z= 0.141 Angle : 0.515 6.359 13295 Z= 0.274 Chirality : 0.038 0.138 1500 Planarity : 0.003 0.046 1503 Dihedral : 16.049 177.935 1826 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.65 % Allowed : 19.37 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 997 helix: 0.32 (0.22), residues: 587 sheet: -2.43 (0.92), residues: 19 loop : -2.25 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 456 HIS 0.004 0.001 HIS A1093 PHE 0.014 0.001 PHE A 548 TYR 0.009 0.001 TYR A1109 ARG 0.004 0.000 ARG A 36 *********************** 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 137 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8748 (mt) REVERT: A 727 MET cc_start: 0.8148 (ttp) cc_final: 0.7812 (ttp) REVERT: A 768 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8958 (tp) REVERT: A 820 ARG cc_start: 0.7500 (ttp-110) cc_final: 0.7206 (ttp80) REVERT: A 907 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6665 (mt-10) REVERT: A 920 ASP cc_start: 0.7963 (m-30) cc_final: 0.7539 (m-30) outliers start: 25 outliers final: 14 residues processed: 129 average time/residue: 0.2586 time to fit residues: 45.3034 Evaluate side-chains 118 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 693 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 998 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 292 ASN A 607 ASN A 793 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9712 Z= 0.149 Angle : 0.530 8.279 13295 Z= 0.277 Chirality : 0.038 0.134 1500 Planarity : 0.003 0.049 1503 Dihedral : 15.952 177.942 1826 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.75 % Allowed : 19.26 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.27), residues: 997 helix: 0.58 (0.23), residues: 590 sheet: -2.27 (0.93), residues: 19 loop : -2.20 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 172 HIS 0.004 0.001 HIS A1093 PHE 0.012 0.001 PHE A 548 TYR 0.009 0.001 TYR A 496 ARG 0.003 0.000 ARG A 36 *********************** 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 133 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 507 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8747 (mt) REVERT: A 727 MET cc_start: 0.8133 (ttp) cc_final: 0.7792 (ttp) REVERT: A 753 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7276 (p) REVERT: A 768 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8984 (tp) REVERT: A 794 MET cc_start: 0.8438 (tpp) cc_final: 0.8208 (ttm) REVERT: A 820 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7292 (ttp80) REVERT: A 907 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6692 (mt-10) REVERT: A 920 ASP cc_start: 0.8042 (m-30) cc_final: 0.7618 (m-30) outliers start: 26 outliers final: 14 residues processed: 124 average time/residue: 0.3132 time to fit residues: 53.5763 Evaluate side-chains 120 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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 309 ASN Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 693 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 41 optimal weight: 0.0670 chunk 74 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.1980 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.052 9712 Z= 0.141 Angle : 0.510 8.354 13295 Z= 0.268 Chirality : 0.037 0.134 1500 Planarity : 0.003 0.047 1503 Dihedral : 15.847 177.868 1826 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.80 % Allowed : 20.21 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.27), residues: 997 helix: 0.85 (0.23), residues: 586 sheet: -2.10 (0.92), residues: 19 loop : -2.11 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 456 HIS 0.002 0.000 HIS A1093 PHE 0.012 0.001 PHE A 548 TYR 0.008 0.001 TYR A1109 ARG 0.002 0.000 ARG A 36 *********************** 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 132 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.040 Fit side-chains REVERT: A 415 ARG cc_start: 0.7946 (ttp-110) cc_final: 0.7545 (mtt90) REVERT: A 507 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8688 (mt) REVERT: A 514 LYS cc_start: 0.7330 (mmtm) cc_final: 0.7082 (mmmt) REVERT: A 517 ASP cc_start: 0.7872 (t0) cc_final: 0.7426 (t0) REVERT: A 768 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8950 (tp) REVERT: A 794 MET cc_start: 0.8373 (tpp) cc_final: 0.8146 (ttm) REVERT: A 820 ARG cc_start: 0.7466 (ttp-110) cc_final: 0.7150 (ttp80) REVERT: A 920 ASP cc_start: 0.7963 (m-30) cc_final: 0.7522 (m-30) outliers start: 17 outliers final: 11 residues processed: 124 average time/residue: 0.2623 time to fit residues: 43.9395 Evaluate side-chains 118 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 342 GLU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 693 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 0.0370 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 285 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.5175 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= 0.249 Angle : 0.601 8.836 13295 Z= 0.311 Chirality : 0.041 0.137 1500 Planarity : 0.004 0.050 1503 Dihedral : 15.913 177.823 1826 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.22 % Allowed : 19.79 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 997 helix: 0.59 (0.22), residues: 594 sheet: -1.25 (0.83), residues: 29 loop : -2.16 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 172 HIS 0.005 0.001 HIS A1093 PHE 0.010 0.001 PHE A 604 TYR 0.021 0.002 TYR A1046 ARG 0.007 0.001 ARG A 36 ********************** 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 128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 768 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9017 (tp) REVERT: A 820 ARG cc_start: 0.7599 (ttp-110) cc_final: 0.7284 (ttp80) outliers start: 21 outliers final: 13 residues processed: 120 average time/residue: 0.2693 time to fit residues: 43.3485 Evaluate side-chains 118 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 315 ILE Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 693 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 8.9990 chunk 25 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 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 = 0.147430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115447 restraints weight = 13083.779| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.97 r_work: 0.3040 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9712 Z= 0.160 Angle : 0.557 8.641 13295 Z= 0.288 Chirality : 0.038 0.132 1500 Planarity : 0.003 0.047 1503 Dihedral : 15.863 178.139 1826 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.01 % Allowed : 20.11 % 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: -0.51 (0.27), residues: 997 helix: 0.80 (0.23), residues: 590 sheet: -1.11 (0.86), residues: 29 loop : -2.16 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 172 HIS 0.004 0.001 HIS A1093 PHE 0.012 0.001 PHE A 548 TYR 0.021 0.001 TYR A1046 ARG 0.003 0.000 ARG A 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2088.80 seconds wall clock time: 39 minutes 5.59 seconds (2345.59 seconds total)