Starting phenix.real_space_refine on Fri Sep 11 13:27:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vrc_21367/09_2026/6vrc_21367.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vrc_21367/09_2026/6vrc_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_21367/09_2026/6vrc_21367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vrc_21367/09_2026/6vrc_21367.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vrc_21367/09_2026/6vrc_21367.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vrc_21367/09_2026/6vrc_21367.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vrc_21367/09_2026/6vrc_21367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vrc_21367/09_2026/6vrc_21367.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1070 Classifications: {'RNAv2': 51} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna2p': 18, 'rna3p': 32} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.00, per 1000 atoms: 0.21 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: 0.90 Conformation dependent library (CDL) restraints added in 293.4 milliseconds 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: 0.99 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: 1.53 Time building geometry restraints manager: 1.16 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 - 3.00: 12730 3.00 - 6.00: 506 6.00 - 8.99: 50 8.99 - 11.99: 8 11.99 - 14.99: 1 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 109.80 124.79 -14.99 2.00e+00 2.50e-01 5.62e+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=" 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 angle pdb=" N LYS A 734 " pdb=" CA LYS A 734 " pdb=" C LYS A 734 " ideal model delta sigma weight residual 113.41 107.63 5.78 1.22e+00 6.72e-01 2.25e+01 ... (remaining 13290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 5620 35.61 - 71.22: 227 71.22 - 106.82: 9 106.82 - 142.43: 0 142.43 - 178.04: 2 Dihedral angle restraints: 5858 sinusoidal: 2846 harmonic: 3012 Sorted by residual: dihedral pdb=" C4' U B 25 " pdb=" C3' U B 25 " pdb=" C2' U B 25 " pdb=" C1' U B 25 " ideal model delta sinusoidal sigma weight residual 36.35 -40.37 76.72 1 3.10e+00 1.04e-01 7.69e+02 dihedral pdb=" C4' G B 15 " pdb=" C3' G B 15 " pdb=" C2' G B 15 " pdb=" C1' G B 15 " ideal model delta sinusoidal sigma weight residual 36.35 -38.11 74.46 1 3.10e+00 1.04e-01 7.31e+02 dihedral pdb=" C4' U B 36 " pdb=" C3' U B 36 " pdb=" C2' U B 36 " pdb=" C1' U B 36 " ideal model delta sinusoidal sigma weight residual 36.34 -37.01 73.35 1 3.10e+00 1.04e-01 7.13e+02 ... (remaining 5855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1330 0.149 - 0.299: 149 0.299 - 0.448: 20 0.448 - 0.597: 0 0.597 - 0.746: 1 Chirality restraints: 1500 Sorted by residual: 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 -2.79 -2.04 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C2' G B 1 " pdb=" C3' G B 1 " pdb=" O2' G B 1 " pdb=" C1' G B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.39 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C2' C B 7 " pdb=" C3' C B 7 " pdb=" O2' C B 7 " pdb=" C1' C B 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.41 -0.38 2.00e-01 2.50e+01 3.68e+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: 0.670 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.620 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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= 0.540 Angle : 1.338 14.991 13295 Z= 0.774 Chirality : 0.097 0.746 1500 Planarity : 0.007 0.065 1503 Dihedral : 16.945 178.042 3892 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.024 0.002 ARG A 36 TYR 0.025 0.003 TYR A 486 PHE 0.034 0.003 PHE A1071 TRP 0.029 0.004 TRP A 417 HIS 0.013 0.002 HIS A1093 Details of bonding type rmsd/Z covalent geometry : bond 0.00998 / 0.54 ( 9712) covalent geometry : angle 1.33751 / 0.77 (13295) hydrogen bonds : bond 0.35762 / 23.94 ( 307) hydrogen bonds : angle 9.52308 / 6.64 ( 878) *********************** 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 : 0.222 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: 0.7201 (mt0) outliers start: 35 outliers final: 9 residues processed: 266 average time/residue: 0.1034 time to fit residues: 36.8481 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 : 0.330 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3808 r_free = 0.3808 target = 0.153996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122942 restraints weight = 13163.661| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.79 r_work: 0.3152 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9712 Z= 0.156 Angle : 0.919 13.792 13295 Z= 0.416 Chirality : 0.073 0.747 1500 Planarity : 0.005 0.056 1503 Dihedral : 15.708 164.291 1717 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.70 % Allowed : 13.23 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.23), residues: 997 helix: -1.78 (0.20), residues: 563 sheet: -3.56 (0.62), residues: 19 loop : -2.64 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 90 TYR 0.015 0.001 TYR A 889 PHE 0.025 0.002 PHE A 459 TRP 0.017 0.002 TRP A 185 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 ( 9712) covalent geometry : angle 0.91899 / 0.42 (13295) hydrogen bonds : bond 0.06430 / 4.33 ( 307) hydrogen bonds : angle 4.54115 / 3.11 ( 878) *********************** 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 180 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.7992 (OUTLIER) cc_final: 0.7667 (t0) REVERT: A 153 ASN cc_start: 0.7592 (t0) cc_final: 0.7329 (t0) REVERT: A 202 ARG cc_start: 0.8595 (mtt90) cc_final: 0.8356 (mtt180) REVERT: A 218 ASP cc_start: 0.8047 (t70) cc_final: 0.7788 (t0) REVERT: A 383 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8923 (tp) REVERT: A 514 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7333 (mmtm) REVERT: A 605 THR cc_start: 0.9055 (m) cc_final: 0.7602 (t) REVERT: A 820 ARG cc_start: 0.8054 (ttp-110) cc_final: 0.7746 (ttp80) REVERT: A 1017 ASN cc_start: 0.7812 (m-40) cc_final: 0.7612 (m-40) REVERT: A 1079 HIS cc_start: 0.8132 (m-70) cc_final: 0.7865 (m90) REVERT: A 1086 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8770 (tt) outliers start: 35 outliers final: 9 residues processed: 174 average time/residue: 0.1151 time to fit residues: 26.2097 Evaluate side-chains 119 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 340 LEU Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 422 SER 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 798 VAL 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 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 25 optimal weight: 0.0270 chunk 75 optimal weight: 0.0370 chunk 85 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN A 207 GLN A 285 ASN A 416 GLN A 461 ASN A 586 GLN A 607 ASN A1065 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.153709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122358 restraints weight = 13196.890| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.90 r_work: 0.3136 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4259 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= 0.129 Angle : 0.753 8.547 13295 Z= 0.347 Chirality : 0.063 0.459 1500 Planarity : 0.004 0.049 1503 Dihedral : 15.101 160.975 1696 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.17 % Allowed : 15.24 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.25), residues: 997 helix: -0.88 (0.22), residues: 575 sheet: -2.91 (0.78), residues: 29 loop : -2.47 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 36 TYR 0.011 0.001 TYR A 889 PHE 0.027 0.001 PHE A 459 TRP 0.010 0.001 TRP A 185 HIS 0.003 0.001 HIS A 870 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 9712) covalent geometry : angle 0.75329 / 0.35 (13295) hydrogen bonds : bond 0.05365 / 3.68 ( 307) hydrogen bonds : angle 3.86100 / 2.62 ( 878) *********************** 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 159 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8160 (t70) cc_final: 0.7871 (t0) REVERT: A 342 GLU cc_start: 0.8416 (pp20) cc_final: 0.8175 (pp20) REVERT: A 415 ARG cc_start: 0.8782 (mtm-85) cc_final: 0.8453 (ttp-110) REVERT: A 459 PHE cc_start: 0.7366 (t80) cc_final: 0.7119 (t80) REVERT: A 514 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7357 (mmtm) REVERT: A 820 ARG cc_start: 0.8041 (ttp-110) cc_final: 0.7753 (ttp80) REVERT: A 920 ASP cc_start: 0.8255 (m-30) cc_final: 0.7819 (m-30) REVERT: A 1013 LYS cc_start: 0.7927 (tttt) cc_final: 0.7531 (tptt) REVERT: A 1086 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8779 (tt) outliers start: 30 outliers final: 9 residues processed: 152 average time/residue: 0.1109 time to fit residues: 22.0828 Evaluate side-chains 114 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 356 SER Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 514 LYS 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 818 ILE 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 33 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 15 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 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 = 0.3731 r_free = 0.3731 target = 0.147868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116428 restraints weight = 13226.722| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.84 r_work: 0.3056 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9712 Z= 0.168 Angle : 0.775 8.365 13295 Z= 0.357 Chirality : 0.066 0.602 1500 Planarity : 0.004 0.052 1503 Dihedral : 15.203 161.029 1694 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.17 % Allowed : 16.40 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.25), residues: 997 helix: -0.46 (0.22), residues: 579 sheet: -2.81 (0.84), residues: 21 loop : -2.35 (0.27), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 36 TYR 0.012 0.001 TYR A 889 PHE 0.020 0.002 PHE A 459 TRP 0.010 0.001 TRP A 417 HIS 0.004 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 9712) covalent geometry : angle 0.77463 / 0.36 (13295) hydrogen bonds : bond 0.05902 / 4.02 ( 307) hydrogen bonds : angle 3.82182 / 2.61 ( 878) *********************** 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 143 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8515 (mttt) cc_final: 0.8079 (ttmt) REVERT: A 218 ASP cc_start: 0.8188 (t70) cc_final: 0.7909 (t0) REVERT: A 415 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8449 (ttp-110) REVERT: A 514 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7487 (mmtm) REVERT: A 820 ARG cc_start: 0.8087 (ttp-110) cc_final: 0.7766 (ttp80) REVERT: A 876 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7091 (tttm) REVERT: A 1013 LYS cc_start: 0.7921 (tttt) cc_final: 0.7521 (tptt) REVERT: A 1086 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8905 (tt) outliers start: 30 outliers final: 15 residues processed: 136 average time/residue: 0.1081 time to fit residues: 19.7850 Evaluate side-chains 119 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 356 SER Chi-restraints excluded: chain A residue 358 SER 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 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 1074 LEU 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 92 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 41 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN A 165 GLN A 285 ASN A 292 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116663 restraints weight = 13182.234| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.90 r_work: 0.3049 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9712 Z= 0.151 Angle : 0.721 8.299 13295 Z= 0.335 Chirality : 0.063 0.535 1500 Planarity : 0.004 0.047 1503 Dihedral : 15.340 160.959 1694 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.17 % Allowed : 16.40 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.26), residues: 997 helix: -0.09 (0.22), residues: 588 sheet: -2.72 (0.85), residues: 19 loop : -2.30 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 36 TYR 0.011 0.001 TYR A 496 PHE 0.013 0.001 PHE A 459 TRP 0.009 0.001 TRP A 417 HIS 0.003 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9712) covalent geometry : angle 0.72145 / 0.34 (13295) hydrogen bonds : bond 0.05391 / 3.70 ( 307) hydrogen bonds : angle 3.69243 / 2.51 ( 878) *********************** 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: 30 poor density : 114 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8616 (mttt) cc_final: 0.8229 (ttmt) REVERT: A 218 ASP cc_start: 0.8166 (t70) cc_final: 0.7895 (t0) REVERT: A 507 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8659 (mt) REVERT: A 514 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7451 (mmtm) REVERT: A 727 MET cc_start: 0.8488 (ttp) cc_final: 0.8241 (ttp) REVERT: A 768 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9025 (tp) REVERT: A 794 MET cc_start: 0.8935 (tpp) cc_final: 0.8516 (ttm) REVERT: A 820 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7767 (ttp80) REVERT: A 876 LYS cc_start: 0.7566 (mmtm) cc_final: 0.7112 (tttm) REVERT: A 920 ASP cc_start: 0.8297 (m-30) cc_final: 0.7915 (m-30) REVERT: A 1013 LYS cc_start: 0.7921 (tttt) cc_final: 0.7495 (tptt) REVERT: A 1086 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8915 (tt) outliers start: 30 outliers final: 19 residues processed: 134 average time/residue: 0.1040 time to fit residues: 18.9346 Evaluate side-chains 128 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 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 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 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 815 THR 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 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 64 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.151834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119670 restraints weight = 13171.890| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.86 r_work: 0.3109 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9712 Z= 0.116 Angle : 0.661 8.084 13295 Z= 0.309 Chirality : 0.056 0.372 1500 Planarity : 0.003 0.050 1503 Dihedral : 15.330 171.403 1694 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.07 % Allowed : 17.67 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.26), residues: 997 helix: 0.31 (0.22), residues: 591 sheet: -2.64 (0.91), residues: 19 loop : -2.37 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 36 TYR 0.009 0.001 TYR A 889 PHE 0.012 0.001 PHE A 548 TRP 0.012 0.001 TRP A 456 HIS 0.003 0.001 HIS A 870 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 9712) covalent geometry : angle 0.66130 / 0.31 (13295) hydrogen bonds : bond 0.04441 / 3.05 ( 307) hydrogen bonds : angle 3.48899 / 2.35 ( 878) *********************** 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 147 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8142 (mmm) cc_final: 0.7874 (mmm) REVERT: A 98 LYS cc_start: 0.8589 (mttt) cc_final: 0.8234 (ttmt) REVERT: A 218 ASP cc_start: 0.8165 (t70) cc_final: 0.7884 (t0) REVERT: A 262 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7312 (pp20) REVERT: A 415 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8090 (mtm110) REVERT: A 507 ILE cc_start: 0.9039 (tp) cc_final: 0.8642 (mt) REVERT: A 514 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7453 (mmtm) REVERT: A 534 GLU cc_start: 0.7877 (tp30) cc_final: 0.7601 (tp30) REVERT: A 621 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9032 (tp) REVERT: A 727 MET cc_start: 0.8491 (ttp) cc_final: 0.8231 (ttp) REVERT: A 768 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8969 (tp) REVERT: A 820 ARG cc_start: 0.8067 (ttp-110) cc_final: 0.7694 (ttp80) REVERT: A 876 LYS cc_start: 0.7363 (mmtm) cc_final: 0.6962 (tttm) REVERT: A 920 ASP cc_start: 0.8217 (m-30) cc_final: 0.7783 (m-30) REVERT: A 1013 LYS cc_start: 0.7856 (tttt) cc_final: 0.7448 (tptt) REVERT: A 1086 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8852 (tt) outliers start: 29 outliers final: 13 residues processed: 137 average time/residue: 0.1079 time to fit residues: 20.0927 Evaluate side-chains 123 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 124 ASN Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 514 LYS Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 621 LEU 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 Chi-restraints excluded: chain A residue 1086 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 73 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 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 = 0.147433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114975 restraints weight = 13114.933| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.89 r_work: 0.3040 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.5063 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= 0.177 Angle : 0.746 9.305 13295 Z= 0.348 Chirality : 0.064 0.584 1500 Planarity : 0.004 0.048 1503 Dihedral : 15.278 174.679 1694 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.17 % Allowed : 17.78 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.26), residues: 997 helix: 0.29 (0.22), residues: 597 sheet: -2.48 (0.89), residues: 19 loop : -2.34 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 36 TYR 0.011 0.001 TYR A 496 PHE 0.012 0.001 PHE A 125 TRP 0.013 0.001 TRP A 172 HIS 0.004 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 9712) covalent geometry : angle 0.74558 / 0.35 (13295) hydrogen bonds : bond 0.05650 / 3.87 ( 307) hydrogen bonds : angle 3.67246 / 2.50 ( 878) *********************** 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 135 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 96 MET cc_start: 0.8241 (mmm) cc_final: 0.8002 (mmm) REVERT: A 98 LYS cc_start: 0.8622 (mttt) cc_final: 0.8315 (ttmt) REVERT: A 218 ASP cc_start: 0.8207 (t70) cc_final: 0.7923 (t0) REVERT: A 507 ILE cc_start: 0.9083 (tp) cc_final: 0.8703 (mt) REVERT: A 514 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7497 (mmtm) REVERT: A 534 GLU cc_start: 0.7994 (tp30) cc_final: 0.7692 (tp30) REVERT: A 621 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9119 (tp) REVERT: A 727 MET cc_start: 0.8535 (ttp) cc_final: 0.8289 (ttp) REVERT: A 753 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7848 (p) REVERT: A 768 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9040 (tp) REVERT: A 794 MET cc_start: 0.8752 (tpp) cc_final: 0.8455 (ttm) REVERT: A 820 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7931 (ttp80) REVERT: A 876 LYS cc_start: 0.7497 (mmtm) cc_final: 0.7052 (tttm) REVERT: A 920 ASP cc_start: 0.8325 (m-30) cc_final: 0.7954 (m-30) REVERT: A 1013 LYS cc_start: 0.7958 (tttt) cc_final: 0.7613 (tptt) outliers start: 30 outliers final: 18 residues processed: 127 average time/residue: 0.1062 time to fit residues: 18.2220 Evaluate side-chains 121 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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 514 LYS Chi-restraints excluded: chain A residue 577 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 621 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 793 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.113478 restraints weight = 13300.258| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.89 r_work: 0.3007 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9712 Z= 0.199 Angle : 0.779 10.112 13295 Z= 0.363 Chirality : 0.068 0.683 1500 Planarity : 0.004 0.050 1503 Dihedral : 15.392 178.575 1694 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.75 % Allowed : 18.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.26), residues: 997 helix: 0.21 (0.22), residues: 599 sheet: -1.83 (0.69), residues: 43 loop : -2.38 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 36 TYR 0.013 0.002 TYR A 496 PHE 0.012 0.002 PHE A 604 TRP 0.010 0.002 TRP A 417 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 9712) covalent geometry : angle 0.77943 / 0.36 (13295) hydrogen bonds : bond 0.06030 / 4.12 ( 307) hydrogen bonds : angle 3.81571 / 2.60 ( 878) *********************** 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 131 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7443 (tt0) REVERT: A 96 MET cc_start: 0.8185 (mmm) cc_final: 0.7883 (mmm) REVERT: A 98 LYS cc_start: 0.8682 (mttt) cc_final: 0.8391 (ttmt) REVERT: A 218 ASP cc_start: 0.8205 (t70) cc_final: 0.7908 (t0) REVERT: A 341 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 507 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8681 (mt) REVERT: A 514 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7436 (mmtm) REVERT: A 534 GLU cc_start: 0.7923 (tp30) cc_final: 0.7621 (tp30) REVERT: A 621 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9120 (tp) REVERT: A 727 MET cc_start: 0.8534 (ttp) cc_final: 0.8260 (ttp) REVERT: A 753 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7853 (p) REVERT: A 768 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9018 (tp) REVERT: A 794 MET cc_start: 0.8793 (tpp) cc_final: 0.8534 (ttm) REVERT: A 820 ARG cc_start: 0.8243 (ttp-110) cc_final: 0.7910 (ttp80) REVERT: A 876 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7186 (tttm) REVERT: A 1013 LYS cc_start: 0.7942 (tttt) cc_final: 0.7548 (tptt) outliers start: 26 outliers final: 17 residues processed: 124 average time/residue: 0.1091 time to fit residues: 18.1855 Evaluate side-chains 127 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 577 GLU Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 621 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 14 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112929 restraints weight = 13215.762| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.92 r_work: 0.3005 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9712 Z= 0.204 Angle : 0.786 10.623 13295 Z= 0.365 Chirality : 0.069 0.708 1500 Planarity : 0.004 0.048 1503 Dihedral : 15.298 177.721 1694 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.86 % Allowed : 19.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.26), residues: 997 helix: 0.18 (0.22), residues: 599 sheet: -1.94 (0.68), residues: 45 loop : -2.35 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 36 TYR 0.013 0.002 TYR A 496 PHE 0.011 0.001 PHE A 604 TRP 0.011 0.002 TRP A 417 HIS 0.004 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 9712) covalent geometry : angle 0.78573 / 0.36 (13295) hydrogen bonds : bond 0.06058 / 4.14 ( 307) hydrogen bonds : angle 3.84487 / 2.62 ( 878) *********************** 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 138 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7649 (tt0) REVERT: A 96 MET cc_start: 0.8261 (mmm) cc_final: 0.7968 (mmm) REVERT: A 98 LYS cc_start: 0.8733 (mttt) cc_final: 0.8447 (ttmt) REVERT: A 149 ARG cc_start: 0.8098 (ptt90) cc_final: 0.7857 (ptt90) REVERT: A 218 ASP cc_start: 0.8182 (t70) cc_final: 0.7858 (t0) REVERT: A 243 GLU cc_start: 0.7459 (mp0) cc_final: 0.7217 (mp0) REVERT: A 341 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7244 (tm-30) REVERT: A 507 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8688 (mt) REVERT: A 514 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7417 (mmtm) REVERT: A 534 GLU cc_start: 0.7994 (tp30) cc_final: 0.7715 (tp30) REVERT: A 605 THR cc_start: 0.9223 (m) cc_final: 0.7785 (t) REVERT: A 621 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9144 (tp) REVERT: A 727 MET cc_start: 0.8539 (ttp) cc_final: 0.8275 (ttp) REVERT: A 753 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7896 (p) REVERT: A 768 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9047 (tp) REVERT: A 794 MET cc_start: 0.8784 (tpp) cc_final: 0.8510 (ttm) REVERT: A 820 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7884 (ttp80) REVERT: A 876 LYS cc_start: 0.7644 (mmtm) cc_final: 0.7168 (tttm) REVERT: A 1013 LYS cc_start: 0.7932 (tttt) cc_final: 0.7532 (tptt) outliers start: 27 outliers final: 18 residues processed: 131 average time/residue: 0.1177 time to fit residues: 20.5998 Evaluate side-chains 126 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.241 ------------------------------------------------------------------------------- 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 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 485 LEU 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 606 THR Chi-restraints excluded: chain A residue 621 LEU 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 1046 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 38 optimal weight: 0.0040 chunk 14 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS A 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.152511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120637 restraints weight = 13228.458| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.82 r_work: 0.3136 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9712 Z= 0.110 Angle : 0.661 8.503 13295 Z= 0.311 Chirality : 0.055 0.348 1500 Planarity : 0.003 0.048 1503 Dihedral : 15.249 179.458 1694 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.22 % Allowed : 19.68 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.27), residues: 997 helix: 0.67 (0.23), residues: 602 sheet: -2.17 (0.91), residues: 19 loop : -2.21 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 550 TYR 0.008 0.001 TYR A1109 PHE 0.016 0.001 PHE A 548 TRP 0.010 0.001 TRP A 456 HIS 0.002 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 ( 9712) covalent geometry : angle 0.66148 / 0.31 (13295) hydrogen bonds : bond 0.04075 / 2.81 ( 307) hydrogen bonds : angle 3.46500 / 2.32 ( 878) ********************** 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 131 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8609 (mttt) cc_final: 0.8362 (ttmt) REVERT: A 218 ASP cc_start: 0.8146 (t70) cc_final: 0.7838 (t0) REVERT: A 341 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7040 (tm-30) REVERT: A 507 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8620 (mt) REVERT: A 514 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7188 (mmtm) REVERT: A 534 GLU cc_start: 0.7847 (tp30) cc_final: 0.7505 (tp30) REVERT: A 621 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8990 (tp) REVERT: A 727 MET cc_start: 0.8476 (ttp) cc_final: 0.8213 (ttp) REVERT: A 768 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9001 (tp) REVERT: A 794 MET cc_start: 0.8834 (tpp) cc_final: 0.8490 (ttm) REVERT: A 820 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7815 (ttp80) REVERT: A 876 LYS cc_start: 0.7414 (mmtm) cc_final: 0.7090 (tptm) REVERT: A 920 ASP cc_start: 0.8177 (m-30) cc_final: 0.7683 (m-30) REVERT: A 1013 LYS cc_start: 0.7871 (tttt) cc_final: 0.7565 (tptt) outliers start: 21 outliers final: 12 residues processed: 124 average time/residue: 0.1228 time to fit residues: 19.9274 Evaluate side-chains 120 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 342 GLU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 485 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 621 LEU 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 802 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 89 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.144625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112288 restraints weight = 13206.310| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.91 r_work: 0.2997 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9712 Z= 0.239 Angle : 0.823 11.299 13295 Z= 0.381 Chirality : 0.070 0.737 1500 Planarity : 0.004 0.050 1503 Dihedral : 15.188 176.586 1694 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.43 % Allowed : 19.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.27), residues: 997 helix: 0.31 (0.22), residues: 601 sheet: -1.75 (0.69), residues: 43 loop : -2.33 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 36 TYR 0.013 0.002 TYR A 496 PHE 0.016 0.002 PHE A 378 TRP 0.012 0.002 TRP A 417 HIS 0.005 0.001 HIS A 913 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 ( 9712) covalent geometry : angle 0.82340 / 0.38 (13295) hydrogen bonds : bond 0.06390 / 4.35 ( 307) hydrogen bonds : angle 3.85454 / 2.63 ( 878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1953.25 seconds wall clock time: 34 minutes 19.66 seconds (2059.66 seconds total)