Starting phenix.real_space_refine on Sat Aug 23 07:20:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xwy_6777/08_2025/5xwy_6777.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xwy_6777/08_2025/5xwy_6777.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/5xwy_6777/08_2025/5xwy_6777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xwy_6777/08_2025/5xwy_6777.map" model { file = "/net/cci-nas-00/data/ceres_data/5xwy_6777/08_2025/5xwy_6777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xwy_6777/08_2025/5xwy_6777.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= 0.007 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 51 5.49 5 S 24 5.16 5 C 6528 2.51 5 N 1784 2.21 5 O 2106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10493 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 9407 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 13, 'PTRANS': 10, 'TRANS': 1093} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1086 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 22, 'rna3p_pyr': 12} Link IDs: {'rna2p': 17, 'rna3p': 33} Chain breaks: 1 Time building chain proxies: 2.56, per 1000 atoms: 0.24 Number of scatterers: 10493 At special positions: 0 Unit cell: (113.16, 111.52, 107.42, 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 24 16.00 P 51 15.00 O 2106 8.00 N 1784 7.00 C 6528 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: 0.67 Conformation dependent library (CDL) restraints added in 339.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 5 sheets defined 63.7% alpha, 2.9% beta 6 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 59 through 69 removed outlier: 4.058A pdb=" N LYS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.524A pdb=" N TYR A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 129 removed outlier: 3.911A pdb=" N VAL A 129 " --> pdb=" O GLU A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 130 through 150 removed outlier: 3.945A pdb=" N LYS A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.746A pdb=" N ILE A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.707A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.993A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.838A pdb=" N GLU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.551A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 247 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.590A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 278 removed outlier: 3.522A pdb=" N TYR A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.767A pdb=" N LYS A 289 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 290 " --> pdb=" O ASN A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 291 through 308 Processing helix chain 'A' and resid 317 through 325 removed outlier: 3.907A pdb=" N LYS A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 354 removed outlier: 3.663A pdb=" N GLU A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A 352 " --> pdb=" O CYS A 348 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 393 removed outlier: 3.651A pdb=" N PHE A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.761A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.515A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.511A pdb=" N ALA A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.555A pdb=" N LYS A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.904A pdb=" N TYR A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 539 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 583 through 602 removed outlier: 3.679A pdb=" N GLU A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 598 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.670A pdb=" N ILE A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 removed outlier: 4.128A pdb=" N LYS A 642 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 665 removed outlier: 3.549A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.571A pdb=" N ILE A 681 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 714 removed outlier: 3.957A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 731 removed outlier: 3.639A pdb=" N GLN A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 745 removed outlier: 4.225A pdb=" N PHE A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 767 removed outlier: 3.835A pdb=" N ASN A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 761 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 764 " --> pdb=" O ASN A 760 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 765 " --> pdb=" O MET A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 789 Processing helix chain 'A' and resid 796 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 834 through 842 removed outlier: 3.551A pdb=" N LYS A 839 " --> pdb=" O ASN A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 865 removed outlier: 4.419A pdb=" N ASN A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 879 Processing helix chain 'A' and resid 883 through 895 removed outlier: 3.532A pdb=" N TYR A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.530A pdb=" N LYS A 902 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 946 removed outlier: 3.608A pdb=" N SER A 927 " --> pdb=" O GLU A 923 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 944 " --> pdb=" O HIS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 983 removed outlier: 3.907A pdb=" N GLY A 966 " --> pdb=" O HIS A 962 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 990 Processing helix chain 'A' and resid 1007 through 1020 removed outlier: 4.233A pdb=" N LYS A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 4.246A pdb=" N VAL A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 removed outlier: 3.556A pdb=" N ALA A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 3.527A pdb=" N GLU A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1083 Processing helix chain 'A' and resid 1083 through 1096 removed outlier: 3.815A pdb=" N LYS A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 3.750A pdb=" N LYS A1145 " --> pdb=" O CYS A1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 removed outlier: 3.668A pdb=" N LYS A 165 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 160 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 163 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AA5, first strand: chain 'A' and resid 1099 through 1104 removed outlier: 3.554A pdb=" N THR A1114 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS A1103 " --> pdb=" O ILE A1112 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE A1112 " --> pdb=" O LYS A1103 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.58 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2337 1.33 - 1.45: 2437 1.45 - 1.57: 5856 1.57 - 1.68: 102 1.68 - 1.80: 45 Bond restraints: 10777 Sorted by residual: bond pdb=" CA ILE A 402 " pdb=" CB ILE A 402 " ideal model delta sigma weight residual 1.540 1.586 -0.046 1.36e-02 5.41e+03 1.16e+01 bond pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N PHE A 545 " pdb=" CA PHE A 545 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.77e+00 bond pdb=" CA THR A 403 " pdb=" C THR A 403 " ideal model delta sigma weight residual 1.525 1.554 -0.029 1.11e-02 8.12e+03 6.68e+00 bond pdb=" N ASN A 696 " pdb=" CA ASN A 696 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.40e+00 ... (remaining 10772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 14476 4.00 - 8.00: 152 8.00 - 12.00: 34 12.00 - 16.00: 4 16.00 - 20.00: 4 Bond angle restraints: 14670 Sorted by residual: angle pdb=" C GLU A 544 " pdb=" N PHE A 545 " pdb=" CA PHE A 545 " ideal model delta sigma weight residual 121.70 138.66 -16.96 1.80e+00 3.09e-01 8.88e+01 angle pdb=" C MET A 44 " pdb=" N TYR A 45 " pdb=" CA TYR A 45 " ideal model delta sigma weight residual 121.70 135.33 -13.63 1.80e+00 3.09e-01 5.73e+01 angle pdb=" C ASP A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta sigma weight residual 121.97 135.52 -13.55 1.80e+00 3.09e-01 5.67e+01 angle pdb=" CA THR A 403 " pdb=" C THR A 403 " pdb=" N GLY A 404 " ideal model delta sigma weight residual 116.35 126.09 -9.74 1.30e+00 5.92e-01 5.61e+01 angle pdb=" C GLY A 866 " pdb=" N MET A 867 " pdb=" CA MET A 867 " ideal model delta sigma weight residual 121.70 133.48 -11.78 1.80e+00 3.09e-01 4.28e+01 ... (remaining 14665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 6478 35.24 - 70.47: 158 70.47 - 105.71: 19 105.71 - 140.94: 3 140.94 - 176.18: 1 Dihedral angle restraints: 6659 sinusoidal: 3319 harmonic: 3340 Sorted by residual: dihedral pdb=" CA ASP A 401 " pdb=" C ASP A 401 " pdb=" N ILE A 402 " pdb=" CA ILE A 402 " ideal model delta harmonic sigma weight residual -180.00 -54.57 -125.43 0 5.00e+00 4.00e-02 6.29e+02 dihedral pdb=" CA THR A 403 " pdb=" C THR A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta harmonic sigma weight residual 180.00 67.50 112.50 0 5.00e+00 4.00e-02 5.06e+02 dihedral pdb=" CA LEU A 312 " pdb=" C LEU A 312 " pdb=" N SER A 313 " pdb=" CA SER A 313 " ideal model delta harmonic sigma weight residual 0.00 -40.28 40.28 0 5.00e+00 4.00e-02 6.49e+01 ... (remaining 6656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1545 0.124 - 0.247: 62 0.247 - 0.371: 7 0.371 - 0.494: 0 0.494 - 0.618: 1 Chirality restraints: 1615 Sorted by residual: chirality pdb=" CB ILE A 704 " pdb=" CA ILE A 704 " pdb=" CG1 ILE A 704 " pdb=" CG2 ILE A 704 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA GLU A 671 " pdb=" N GLU A 671 " pdb=" C GLU A 671 " pdb=" CB GLU A 671 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1612 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 677 " -0.018 2.00e-02 2.50e+03 1.77e-02 6.30e+00 pdb=" CG TYR A 677 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 677 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR A 677 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 677 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 677 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 677 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 677 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 202 " 0.013 2.00e-02 2.50e+03 2.49e-02 6.22e+00 pdb=" C GLU A 202 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU A 202 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 203 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 608 " -0.023 2.00e-02 2.50e+03 1.87e-02 6.14e+00 pdb=" CG PHE A 608 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 608 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 608 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 608 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 608 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 608 " -0.002 2.00e-02 2.50e+03 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2743 2.79 - 3.32: 9358 3.32 - 3.85: 17183 3.85 - 4.37: 21345 4.37 - 4.90: 34501 Nonbonded interactions: 85130 Sorted by model distance: nonbonded pdb=" O ILE A1120 " pdb=" OG1 THR A1133 " model vdw 2.263 3.040 nonbonded pdb=" OH TYR A 178 " pdb=" OD1 ASP A 285 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 662 " pdb=" O2' A B 30 " model vdw 2.291 3.040 nonbonded pdb=" OD1 ASN A 378 " pdb=" OG SER A 780 " model vdw 2.306 3.040 nonbonded pdb=" NZ LYS A 5 " pdb=" OP2 G B 23 " model vdw 2.307 3.120 ... (remaining 85125 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: 0.510 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.060 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: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.008 0.080 10777 Z= 0.363 Angle : 1.175 20.001 14670 Z= 0.623 Chirality : 0.061 0.618 1615 Planarity : 0.005 0.037 1682 Dihedral : 14.685 176.181 4503 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer: Outliers : 0.87 % Allowed : 6.46 % Favored : 92.67 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.91 % Twisted Proline : 0.00 % Twisted General : 0.82 % 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 aren not related in a simple way. whole: -5.96 (0.15), residues: 1109 helix: -4.22 (0.08), residues: 692 sheet: -2.31 (0.91), residues: 30 loop : -3.12 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 224 TYR 0.043 0.003 TYR A 677 PHE 0.042 0.004 PHE A 608 TRP 0.019 0.004 TRP A 971 HIS 0.016 0.003 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00790 (10777) covalent geometry : angle 1.17538 (14670) hydrogen bonds : bond 0.30612 ( 436) hydrogen bonds : angle 9.71855 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 289 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.8060 (m-30) cc_final: 0.7649 (p0) REVERT: A 202 GLU cc_start: 0.7796 (tp30) cc_final: 0.7459 (tt0) REVERT: A 207 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8220 (mttp) REVERT: A 247 GLU cc_start: 0.5238 (mm-30) cc_final: 0.4412 (mm-30) REVERT: A 393 ILE cc_start: 0.9108 (tt) cc_final: 0.8891 (tt) REVERT: A 424 GLU cc_start: 0.6787 (mp0) cc_final: 0.6501 (mm-30) REVERT: A 501 LYS cc_start: 0.8429 (tttm) cc_final: 0.8167 (tppt) REVERT: A 542 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7967 (ttm-80) REVERT: A 618 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7288 (mm) REVERT: A 629 ASP cc_start: 0.4729 (t70) cc_final: 0.4516 (t0) REVERT: A 631 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6084 (pmt100) REVERT: A 758 ARG cc_start: 0.8247 (ptt-90) cc_final: 0.7925 (ptp-170) REVERT: A 832 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7994 (p) REVERT: A 888 LYS cc_start: 0.8631 (ttpm) cc_final: 0.8414 (ttpp) REVERT: A 974 ASP cc_start: 0.8294 (m-30) cc_final: 0.8087 (m-30) REVERT: A 1008 ILE cc_start: 0.8741 (mt) cc_final: 0.8390 (mp) REVERT: A 1094 LYS cc_start: 0.8591 (ttpt) cc_final: 0.8344 (ttmm) REVERT: A 1118 GLU cc_start: 0.7869 (pp20) cc_final: 0.7646 (tp30) REVERT: A 1142 LYS cc_start: 0.8362 (mttt) cc_final: 0.8016 (mttp) outliers start: 9 outliers final: 2 residues processed: 295 average time/residue: 0.1271 time to fit residues: 48.9429 Evaluate side-chains 202 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 1126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 84 ASN A 151 ASN A 191 ASN A 294 HIS A 314 ASN A 400 ASN A 492 ASN A 547 ASN A 611 ASN A 626 ASN A 665 ASN A 771 HIS A 776 ASN A 785 GLN A 808 ASN A 908 HIS A 934 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.163532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.128887 restraints weight = 11440.283| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.86 r_work: 0.2973 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10777 Z= 0.204 Angle : 0.772 12.752 14670 Z= 0.409 Chirality : 0.044 0.285 1615 Planarity : 0.004 0.032 1682 Dihedral : 16.255 160.449 1980 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.30 % Favored : 92.52 % Rotamer: Outliers : 3.09 % Allowed : 9.64 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -3.65 (0.20), residues: 1109 helix: -2.11 (0.15), residues: 710 sheet: -1.71 (0.99), residues: 25 loop : -2.80 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 224 TYR 0.028 0.002 TYR A 677 PHE 0.031 0.002 PHE A 478 TRP 0.014 0.002 TRP A 971 HIS 0.010 0.002 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00455 (10777) covalent geometry : angle 0.77198 (14670) hydrogen bonds : bond 0.05367 ( 436) hydrogen bonds : angle 4.61849 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8534 (mmmm) REVERT: A 177 ASP cc_start: 0.8550 (t70) cc_final: 0.8314 (t70) REVERT: A 178 TYR cc_start: 0.8870 (t80) cc_final: 0.8599 (t80) REVERT: A 207 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8359 (mttp) REVERT: A 208 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8511 (tp) REVERT: A 246 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7001 (tm-30) REVERT: A 247 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7224 (mt-10) REVERT: A 254 MET cc_start: 0.8406 (tpt) cc_final: 0.7334 (tpt) REVERT: A 260 LYS cc_start: 0.8401 (tttt) cc_final: 0.8117 (tttm) REVERT: A 378 ASN cc_start: 0.8380 (t160) cc_final: 0.8072 (m110) REVERT: A 393 ILE cc_start: 0.8989 (tt) cc_final: 0.8740 (tt) REVERT: A 406 MET cc_start: 0.8176 (mtp) cc_final: 0.7867 (mtp) REVERT: A 424 GLU cc_start: 0.7183 (mp0) cc_final: 0.6902 (mm-30) REVERT: A 542 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7646 (ttm-80) REVERT: A 590 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8290 (m-30) REVERT: A 726 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8043 (ttpp) REVERT: A 773 GLU cc_start: 0.7584 (tp30) cc_final: 0.7296 (tp30) REVERT: A 987 GLN cc_start: 0.7774 (mp10) cc_final: 0.7553 (mp10) REVERT: A 1008 ILE cc_start: 0.8717 (mt) cc_final: 0.8337 (mp) REVERT: A 1034 ASN cc_start: 0.7788 (t0) cc_final: 0.7506 (m110) REVERT: A 1094 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8349 (ttmm) REVERT: A 1142 LYS cc_start: 0.8587 (mttt) cc_final: 0.8342 (mttp) outliers start: 32 outliers final: 10 residues processed: 231 average time/residue: 0.1107 time to fit residues: 34.1052 Evaluate side-chains 176 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 100 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN A 463 ASN A 592 GLN A 731 ASN A 828 ASN A 986 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.126560 restraints weight = 11577.003| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.84 r_work: 0.2929 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10777 Z= 0.216 Angle : 0.739 13.117 14670 Z= 0.388 Chirality : 0.045 0.417 1615 Planarity : 0.004 0.033 1682 Dihedral : 16.139 162.334 1975 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.76 % Favored : 93.06 % Rotamer: Outliers : 3.76 % Allowed : 12.05 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 aren not related in a simple way. whole: -2.34 (0.23), residues: 1109 helix: -0.95 (0.18), residues: 725 sheet: -1.48 (0.90), residues: 30 loop : -2.63 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 472 TYR 0.026 0.002 TYR A 677 PHE 0.026 0.002 PHE A 478 TRP 0.012 0.002 TRP A 971 HIS 0.008 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00497 (10777) covalent geometry : angle 0.73874 (14670) hydrogen bonds : bond 0.04706 ( 436) hydrogen bonds : angle 4.15404 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 150 LYS cc_start: 0.8900 (mmmt) cc_final: 0.8535 (mmmm) REVERT: A 164 GLU cc_start: 0.7666 (pt0) cc_final: 0.7454 (pm20) REVERT: A 207 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8379 (mttp) REVERT: A 208 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8512 (tp) REVERT: A 254 MET cc_start: 0.8635 (tpt) cc_final: 0.7636 (tpt) REVERT: A 378 ASN cc_start: 0.8324 (t160) cc_final: 0.7866 (m110) REVERT: A 393 ILE cc_start: 0.9088 (tt) cc_final: 0.8809 (tt) REVERT: A 406 MET cc_start: 0.8200 (mtp) cc_final: 0.7871 (mtp) REVERT: A 424 GLU cc_start: 0.7253 (mp0) cc_final: 0.6929 (mm-30) REVERT: A 465 ASP cc_start: 0.8934 (t0) cc_final: 0.8722 (t0) REVERT: A 501 LYS cc_start: 0.8538 (tppt) cc_final: 0.8224 (mmtp) REVERT: A 542 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7505 (ttt90) REVERT: A 590 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8288 (m-30) REVERT: A 726 LYS cc_start: 0.8357 (mtpp) cc_final: 0.8045 (ttpp) REVERT: A 773 GLU cc_start: 0.7619 (tp30) cc_final: 0.7250 (tp30) REVERT: A 952 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8422 (tt) REVERT: A 1008 ILE cc_start: 0.8842 (mt) cc_final: 0.8474 (mp) REVERT: A 1010 GLU cc_start: 0.8029 (tt0) cc_final: 0.7792 (mm-30) REVERT: A 1017 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8106 (mtmt) REVERT: A 1068 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8611 (mm) REVERT: A 1094 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8371 (ttmm) REVERT: A 1142 LYS cc_start: 0.8617 (mttt) cc_final: 0.8360 (mttp) outliers start: 39 outliers final: 19 residues processed: 211 average time/residue: 0.1122 time to fit residues: 31.6097 Evaluate side-chains 193 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1152 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN A 463 ASN A 547 ASN A 719 GLN A 771 HIS ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.163673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.130262 restraints weight = 11564.503| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.80 r_work: 0.2961 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10777 Z= 0.153 Angle : 0.660 12.635 14670 Z= 0.351 Chirality : 0.042 0.356 1615 Planarity : 0.003 0.028 1682 Dihedral : 15.963 161.795 1975 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.40 % Favored : 93.42 % Rotamer: Outliers : 3.47 % Allowed : 12.73 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -1.59 (0.25), residues: 1109 helix: -0.28 (0.19), residues: 724 sheet: -1.30 (0.94), residues: 30 loop : -2.54 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 959 TYR 0.017 0.001 TYR A 677 PHE 0.021 0.002 PHE A 478 TRP 0.011 0.002 TRP A 971 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00338 (10777) covalent geometry : angle 0.66039 (14670) hydrogen bonds : bond 0.04171 ( 436) hydrogen bonds : angle 3.85909 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8004 (pp20) cc_final: 0.7607 (pp20) REVERT: A 150 LYS cc_start: 0.8820 (mmmt) cc_final: 0.8504 (mmmm) REVERT: A 164 GLU cc_start: 0.7788 (pt0) cc_final: 0.7551 (pm20) REVERT: A 202 GLU cc_start: 0.7614 (tp30) cc_final: 0.7075 (tt0) REVERT: A 207 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8356 (mttp) REVERT: A 208 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8482 (tp) REVERT: A 247 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: A 254 MET cc_start: 0.8705 (tpt) cc_final: 0.7730 (tpt) REVERT: A 378 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.7914 (m110) REVERT: A 393 ILE cc_start: 0.9015 (tt) cc_final: 0.8783 (tt) REVERT: A 406 MET cc_start: 0.8078 (mtp) cc_final: 0.7847 (mtp) REVERT: A 424 GLU cc_start: 0.7259 (mp0) cc_final: 0.6953 (mm-30) REVERT: A 501 LYS cc_start: 0.8532 (tppt) cc_final: 0.8273 (mmtp) REVERT: A 542 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7493 (ttt90) REVERT: A 590 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8204 (m-30) REVERT: A 726 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7962 (ttpp) REVERT: A 773 GLU cc_start: 0.7684 (tp30) cc_final: 0.7277 (tp30) REVERT: A 845 LYS cc_start: 0.8382 (mmmt) cc_final: 0.8167 (mmmt) REVERT: A 952 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8358 (tt) REVERT: A 1008 ILE cc_start: 0.8804 (mt) cc_final: 0.8442 (mp) REVERT: A 1094 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8401 (ttmm) REVERT: A 1142 LYS cc_start: 0.8603 (mttt) cc_final: 0.8370 (mttp) outliers start: 36 outliers final: 23 residues processed: 195 average time/residue: 0.1031 time to fit residues: 26.9397 Evaluate side-chains 195 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1152 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6148 > 50: distance: 50 - 52: 35.877 distance: 52 - 53: 38.971 distance: 53 - 54: 56.852 distance: 53 - 56: 57.308 distance: 54 - 55: 41.190 distance: 54 - 58: 56.571 distance: 58 - 59: 39.737 distance: 59 - 60: 41.564 distance: 59 - 62: 39.112 distance: 60 - 61: 39.894 distance: 60 - 66: 33.082 distance: 61 - 91: 41.893 distance: 62 - 63: 39.529 distance: 63 - 64: 57.244 distance: 63 - 65: 39.164 distance: 66 - 67: 56.736 distance: 67 - 68: 57.795 distance: 68 - 69: 40.050 distance: 68 - 75: 38.937 distance: 69 - 99: 40.817 distance: 70 - 71: 68.444 distance: 71 - 72: 39.093 distance: 72 - 74: 46.320 distance: 75 - 76: 57.385 distance: 76 - 79: 56.720 distance: 77 - 78: 39.851 distance: 77 - 84: 40.061 distance: 81 - 83: 55.987 distance: 85 - 88: 39.913 distance: 86 - 87: 55.830 distance: 86 - 91: 40.250 distance: 87 - 112: 41.752 distance: 88 - 89: 39.188 distance: 88 - 90: 40.452 distance: 91 - 92: 29.657 distance: 92 - 93: 40.039 distance: 92 - 95: 48.864 distance: 93 - 99: 69.805 distance: 95 - 96: 30.710 distance: 96 - 97: 40.972 distance: 96 - 98: 50.519 distance: 99 - 100: 44.462 distance: 100 - 101: 20.894 distance: 100 - 103: 44.467 distance: 101 - 102: 38.888 distance: 103 - 104: 40.972 distance: 103 - 105: 39.943 distance: 106 - 107: 56.453 distance: 107 - 108: 55.657 distance: 108 - 109: 57.784 distance: 108 - 112: 56.054 distance: 112 - 113: 55.821 distance: 113 - 114: 64.670 distance: 113 - 116: 56.000 distance: 114 - 115: 42.745 distance: 114 - 120: 62.122 distance: 116 - 117: 39.505 distance: 117 - 118: 59.025 distance: 117 - 119: 69.565 distance: 120 - 121: 39.986 distance: 121 - 124: 39.951 distance: 122 - 123: 39.829 distance: 122 - 125: 35.038