Starting phenix.real_space_refine on Fri Feb 14 18:48:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xwy_6777/02_2025/5xwy_6777.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xwy_6777/02_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_6777/02_2025/5xwy_6777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xwy_6777/02_2025/5xwy_6777.map" model { file = "/net/cci-nas-00/data/ceres_data/5xwy_6777/02_2025/5xwy_6777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xwy_6777/02_2025/5xwy_6777.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.92, per 1000 atoms: 0.66 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 3.33 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: 3.52 Time building geometry restraints manager: 2.74 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: 0.450 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.890 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.750 ------------------------------------------------------------------------------- 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= 0.489 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 : 3.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.004 TRP A 971 HIS 0.016 0.003 HIS A 228 PHE 0.042 0.004 PHE A 608 TYR 0.043 0.003 TYR A 677 ARG 0.013 0.001 ARG A 224 *********************** 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 : 1.129 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: 0.3246 time to fit residues: 123.4069 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 : 1.155 ------------------------------------------------------------------------------- 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 97 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 369 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.168051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.134429 restraints weight = 11402.083| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.93 r_work: 0.3028 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10777 Z= 0.197 Angle : 0.722 12.446 14670 Z= 0.386 Chirality : 0.042 0.273 1615 Planarity : 0.004 0.034 1682 Dihedral : 16.224 159.303 1980 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.21 % Favored : 92.61 % Rotamer: Outliers : 2.99 % Allowed : 9.84 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.21), residues: 1109 helix: -2.00 (0.16), residues: 714 sheet: -1.76 (1.00), residues: 25 loop : -2.74 (0.28), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 971 HIS 0.010 0.002 HIS A 228 PHE 0.033 0.002 PHE A 478 TYR 0.021 0.002 TYR A 677 ARG 0.005 0.001 ARG A 322 *********************** 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 237 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8251 (tppt) cc_final: 0.8006 (mmtm) REVERT: A 150 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8497 (mmmm) REVERT: A 178 TYR cc_start: 0.8851 (t80) cc_final: 0.8443 (t80) REVERT: A 202 GLU cc_start: 0.7615 (tp30) cc_final: 0.7382 (tt0) REVERT: A 207 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8380 (mttp) REVERT: A 208 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8505 (tp) REVERT: A 254 MET cc_start: 0.8297 (tpt) cc_final: 0.7136 (tpt) REVERT: A 378 ASN cc_start: 0.8283 (t160) cc_final: 0.8060 (m110) REVERT: A 406 MET cc_start: 0.8164 (mtp) cc_final: 0.7948 (mtp) REVERT: A 424 GLU cc_start: 0.6997 (mp0) cc_final: 0.6694 (mm-30) REVERT: A 542 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7651 (ttm-80) REVERT: A 590 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8358 (m-30) REVERT: A 726 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7823 (ttpp) REVERT: A 773 GLU cc_start: 0.7590 (tp30) cc_final: 0.7317 (tp30) REVERT: A 1008 ILE cc_start: 0.8706 (mt) cc_final: 0.8296 (mp) REVERT: A 1017 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8184 (mtmt) REVERT: A 1034 ASN cc_start: 0.7698 (t0) cc_final: 0.7401 (m110) REVERT: A 1094 LYS cc_start: 0.8594 (ttpt) cc_final: 0.8336 (ttmm) REVERT: A 1142 LYS cc_start: 0.8503 (mttt) cc_final: 0.8270 (mttp) outliers start: 31 outliers final: 9 residues processed: 227 average time/residue: 0.3113 time to fit residues: 92.8358 Evaluate side-chains 174 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 71 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN A 731 ASN A 828 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.161077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.126056 restraints weight = 11506.173| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.89 r_work: 0.2919 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10777 Z= 0.313 Angle : 0.744 13.025 14670 Z= 0.390 Chirality : 0.045 0.378 1615 Planarity : 0.004 0.031 1682 Dihedral : 16.136 162.701 1975 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.85 % Favored : 92.97 % Rotamer: Outliers : 3.76 % Allowed : 11.48 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.23), residues: 1109 helix: -0.89 (0.18), residues: 725 sheet: -1.43 (0.90), residues: 30 loop : -2.61 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 971 HIS 0.009 0.002 HIS A 228 PHE 0.025 0.002 PHE A 478 TYR 0.029 0.002 TYR A 677 ARG 0.005 0.001 ARG A 472 *********************** 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 215 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8525 (mmmm) REVERT: A 154 ASN cc_start: 0.8288 (m-40) cc_final: 0.7902 (t0) REVERT: A 178 TYR cc_start: 0.8952 (t80) cc_final: 0.8717 (t80) REVERT: A 207 LYS cc_start: 0.8680 (mtmm) cc_final: 0.8407 (mttp) REVERT: A 208 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8517 (tp) REVERT: A 247 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: A 254 MET cc_start: 0.8586 (tpt) cc_final: 0.7656 (tpt) REVERT: A 267 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8806 (tp) REVERT: A 378 ASN cc_start: 0.8366 (t160) cc_final: 0.7915 (m110) REVERT: A 406 MET cc_start: 0.8239 (mtp) cc_final: 0.7915 (mtp) REVERT: A 424 GLU cc_start: 0.7251 (mp0) cc_final: 0.6956 (mm-30) REVERT: A 501 LYS cc_start: 0.8562 (tppt) cc_final: 0.8220 (mmtp) REVERT: A 542 ARG cc_start: 0.8096 (ttm-80) cc_final: 0.7542 (ttt90) REVERT: A 590 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: A 726 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7882 (ttpp) REVERT: A 735 LYS cc_start: 0.6911 (tptp) cc_final: 0.6707 (ttpt) REVERT: A 773 GLU cc_start: 0.7618 (tp30) cc_final: 0.7232 (tp30) REVERT: A 952 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 1008 ILE cc_start: 0.8837 (mt) cc_final: 0.8470 (mp) REVERT: A 1010 GLU cc_start: 0.8114 (tt0) cc_final: 0.7743 (mm-30) REVERT: A 1017 LYS cc_start: 0.8526 (mtmt) cc_final: 0.8102 (mtmt) REVERT: A 1034 ASN cc_start: 0.7769 (t0) cc_final: 0.7559 (m110) REVERT: A 1094 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8407 (ttmm) REVERT: A 1142 LYS cc_start: 0.8650 (mttt) cc_final: 0.8398 (mttp) outliers start: 39 outliers final: 16 residues processed: 208 average time/residue: 0.3122 time to fit residues: 86.2578 Evaluate side-chains 187 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 267 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 535 LEU Chi-restraints excluded: chain A residue 544 GLU 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 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 1045 LEU Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN A 432 ASN A 463 ASN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 788 ASN A 940 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 = 0.3704 r_free = 0.3704 target = 0.159455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.125176 restraints weight = 11457.531| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.87 r_work: 0.2899 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10777 Z= 0.370 Angle : 0.754 12.944 14670 Z= 0.394 Chirality : 0.046 0.403 1615 Planarity : 0.004 0.035 1682 Dihedral : 16.079 162.199 1975 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.76 % Favored : 93.06 % Rotamer: Outliers : 3.76 % Allowed : 12.54 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.24), residues: 1109 helix: -0.53 (0.19), residues: 728 sheet: -1.25 (0.93), residues: 30 loop : -2.55 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 971 HIS 0.008 0.001 HIS A 228 PHE 0.024 0.002 PHE A 478 TYR 0.024 0.002 TYR A 677 ARG 0.004 0.001 ARG A 472 *********************** 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 214 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 1.174 Fit side-chains REVERT: A 150 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8524 (mmmm) REVERT: A 202 GLU cc_start: 0.7747 (tp30) cc_final: 0.7190 (tt0) REVERT: A 208 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8513 (tp) REVERT: A 247 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: A 254 MET cc_start: 0.8805 (tpt) cc_final: 0.7908 (tpt) REVERT: A 260 LYS cc_start: 0.8806 (ptmt) cc_final: 0.8381 (ptmt) REVERT: A 267 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8806 (tp) REVERT: A 286 LYS cc_start: 0.8829 (mppt) cc_final: 0.8566 (mmtt) REVERT: A 406 MET cc_start: 0.8102 (mtp) cc_final: 0.7785 (mtp) REVERT: A 424 GLU cc_start: 0.7415 (mp0) cc_final: 0.7085 (mm-30) REVERT: A 501 LYS cc_start: 0.8656 (tppt) cc_final: 0.8345 (mmtp) REVERT: A 542 ARG cc_start: 0.8108 (ttm-80) cc_final: 0.7462 (ttt90) REVERT: A 590 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: A 726 LYS cc_start: 0.8317 (mtpp) cc_final: 0.8012 (ttpp) REVERT: A 773 GLU cc_start: 0.7689 (tp30) cc_final: 0.7248 (tp30) REVERT: A 845 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8217 (mmmt) REVERT: A 952 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8358 (tt) REVERT: A 1008 ILE cc_start: 0.8825 (mt) cc_final: 0.8464 (mp) REVERT: A 1094 LYS cc_start: 0.8628 (ttpt) cc_final: 0.8403 (ttmm) REVERT: A 1142 LYS cc_start: 0.8695 (mttt) cc_final: 0.8417 (mttp) outliers start: 39 outliers final: 22 residues processed: 201 average time/residue: 0.3079 time to fit residues: 81.4229 Evaluate side-chains 193 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE 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 267 LEU Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 350 LYS 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 535 LEU Chi-restraints excluded: chain A residue 544 GLU 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 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 843 THR Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1095 GLU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 99 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 432 ASN A 463 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 = 0.3744 r_free = 0.3744 target = 0.163347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.128036 restraints weight = 11488.452| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.88 r_work: 0.3002 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10777 Z= 0.211 Angle : 0.660 12.686 14670 Z= 0.348 Chirality : 0.042 0.371 1615 Planarity : 0.003 0.023 1682 Dihedral : 15.816 160.771 1975 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.49 % Favored : 93.42 % Rotamer: Outliers : 3.47 % Allowed : 14.56 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.25), residues: 1109 helix: 0.01 (0.20), residues: 725 sheet: -1.12 (0.96), residues: 30 loop : -2.45 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 971 HIS 0.005 0.001 HIS A 228 PHE 0.020 0.002 PHE A 478 TYR 0.015 0.001 TYR A 677 ARG 0.003 0.000 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 5 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 216 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7983 (pp20) cc_final: 0.7297 (pp20) REVERT: A 150 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8452 (mmmm) REVERT: A 208 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8515 (tp) REVERT: A 220 LYS cc_start: 0.7435 (mmtp) cc_final: 0.6960 (mmpt) REVERT: A 247 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7376 (mt-10) REVERT: A 254 MET cc_start: 0.8755 (tpt) cc_final: 0.7752 (tpt) REVERT: A 334 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8012 (tt0) REVERT: A 378 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.7842 (m110) REVERT: A 424 GLU cc_start: 0.7398 (mp0) cc_final: 0.7020 (mm-30) REVERT: A 439 GLU cc_start: 0.8221 (tp30) cc_final: 0.8007 (tp30) REVERT: A 501 LYS cc_start: 0.8549 (tppt) cc_final: 0.8274 (mmtp) REVERT: A 542 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7331 (ttt90) REVERT: A 590 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8246 (m-30) REVERT: A 726 LYS cc_start: 0.8335 (mtpp) cc_final: 0.8025 (ttpp) REVERT: A 773 GLU cc_start: 0.7622 (tp30) cc_final: 0.7276 (tp30) REVERT: A 845 LYS cc_start: 0.8468 (mmmt) cc_final: 0.8190 (mmmt) REVERT: A 952 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8376 (tt) REVERT: A 1008 ILE cc_start: 0.8819 (mt) cc_final: 0.8446 (mp) REVERT: A 1010 GLU cc_start: 0.7907 (tt0) cc_final: 0.7488 (mm-30) REVERT: A 1094 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8362 (ttmm) REVERT: A 1142 LYS cc_start: 0.8622 (mttt) cc_final: 0.8373 (mttp) outliers start: 36 outliers final: 21 residues processed: 205 average time/residue: 0.2937 time to fit residues: 79.9273 Evaluate side-chains 200 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 334 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 485 LYS Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 579 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 703 TYR Chi-restraints excluded: chain A residue 749 LEU 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 816 LEU 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 1095 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 99 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 432 ASN A 930 GLN A 934 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.165602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.130558 restraints weight = 11452.100| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.74 r_work: 0.3036 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10777 Z= 0.188 Angle : 0.636 12.540 14670 Z= 0.337 Chirality : 0.041 0.362 1615 Planarity : 0.003 0.022 1682 Dihedral : 15.643 161.624 1975 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.76 % Allowed : 15.04 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.26), residues: 1109 helix: 0.32 (0.20), residues: 725 sheet: -1.10 (0.98), residues: 30 loop : -2.36 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 971 HIS 0.004 0.001 HIS A 228 PHE 0.017 0.002 PHE A 478 TYR 0.014 0.001 TYR A 677 ARG 0.004 0.000 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 6 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 217 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 150 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8441 (mmmm) REVERT: A 164 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: A 208 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8519 (tp) REVERT: A 220 LYS cc_start: 0.7362 (mmtp) cc_final: 0.6901 (mmpt) REVERT: A 254 MET cc_start: 0.8741 (tpt) cc_final: 0.7714 (tpt) REVERT: A 378 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7713 (m110) REVERT: A 424 GLU cc_start: 0.7350 (mp0) cc_final: 0.7111 (mm-30) REVERT: A 439 GLU cc_start: 0.8222 (tp30) cc_final: 0.7904 (tp30) REVERT: A 483 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5930 (mp0) REVERT: A 485 LYS cc_start: 0.8449 (ptmm) cc_final: 0.8108 (pttm) REVERT: A 501 LYS cc_start: 0.8537 (tppt) cc_final: 0.8295 (mmtp) REVERT: A 590 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8133 (m-30) REVERT: A 714 LEU cc_start: 0.8234 (mt) cc_final: 0.8000 (mp) REVERT: A 726 LYS cc_start: 0.8258 (mtpp) cc_final: 0.7957 (ttpp) REVERT: A 773 GLU cc_start: 0.7584 (tp30) cc_final: 0.7171 (tp30) REVERT: A 845 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8148 (mmmt) REVERT: A 846 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7672 (pp) REVERT: A 952 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8378 (tt) REVERT: A 1008 ILE cc_start: 0.8791 (mt) cc_final: 0.8412 (mp) REVERT: A 1094 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8320 (ttmm) REVERT: A 1142 LYS cc_start: 0.8641 (mttt) cc_final: 0.8383 (mttp) outliers start: 39 outliers final: 22 residues processed: 205 average time/residue: 0.2937 time to fit residues: 79.9444 Evaluate side-chains 195 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 208 LEU 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 390 LEU 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 579 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 749 LEU 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 816 LEU Chi-restraints excluded: chain A residue 846 ILE 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 1146 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 432 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.160925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.125456 restraints weight = 11614.846| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.83 r_work: 0.3009 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10777 Z= 0.242 Angle : 0.659 12.715 14670 Z= 0.348 Chirality : 0.043 0.359 1615 Planarity : 0.003 0.028 1682 Dihedral : 15.601 162.195 1973 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.57 % Allowed : 15.33 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1109 helix: 0.31 (0.20), residues: 733 sheet: -0.86 (1.04), residues: 30 loop : -2.43 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 971 HIS 0.005 0.001 HIS A 228 PHE 0.017 0.002 PHE A 848 TYR 0.016 0.001 TYR A 677 ARG 0.004 0.000 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 7 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 210 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7848 (pp20) cc_final: 0.7212 (pp20) REVERT: A 44 MET cc_start: 0.6729 (mmp) cc_final: 0.6257 (tpp) REVERT: A 150 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8449 (mmmm) REVERT: A 164 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7798 (pm20) REVERT: A 208 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8514 (tp) REVERT: A 220 LYS cc_start: 0.7394 (mmtp) cc_final: 0.6935 (mmpt) REVERT: A 247 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: A 254 MET cc_start: 0.8740 (tpt) cc_final: 0.7681 (tpt) REVERT: A 286 LYS cc_start: 0.8778 (mppt) cc_final: 0.8515 (mmtt) REVERT: A 312 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5144 (pp) REVERT: A 424 GLU cc_start: 0.7106 (mp0) cc_final: 0.6855 (mm-30) REVERT: A 439 GLU cc_start: 0.8188 (tp30) cc_final: 0.7831 (tp30) REVERT: A 542 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7397 (ttt90) REVERT: A 590 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: A 714 LEU cc_start: 0.8268 (mt) cc_final: 0.8019 (mp) REVERT: A 726 LYS cc_start: 0.8319 (mtpp) cc_final: 0.8016 (ttpp) REVERT: A 773 GLU cc_start: 0.7578 (tp30) cc_final: 0.7124 (tp30) REVERT: A 845 LYS cc_start: 0.8542 (mmmt) cc_final: 0.8215 (mmmt) REVERT: A 846 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7635 (pp) REVERT: A 952 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8376 (tt) REVERT: A 1008 ILE cc_start: 0.8783 (mt) cc_final: 0.8399 (mp) REVERT: A 1094 LYS cc_start: 0.8577 (ttpt) cc_final: 0.8343 (ttmm) REVERT: A 1142 LYS cc_start: 0.8676 (mttt) cc_final: 0.8417 (mttp) outliers start: 37 outliers final: 26 residues processed: 197 average time/residue: 0.3004 time to fit residues: 77.8293 Evaluate side-chains 200 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 473 HIS 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 579 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 690 MET Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 749 LEU 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 816 LEU Chi-restraints excluded: chain A residue 846 ILE 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 1146 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 45 optimal weight: 0.0270 chunk 81 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.0670 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN A 378 ASN A 432 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.169806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.135143 restraints weight = 11504.018| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.64 r_work: 0.3131 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10777 Z= 0.146 Angle : 0.606 12.523 14670 Z= 0.321 Chirality : 0.040 0.335 1615 Planarity : 0.002 0.023 1682 Dihedral : 15.494 161.714 1973 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.70 % Allowed : 16.49 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1109 helix: 0.75 (0.20), residues: 725 sheet: -0.95 (1.13), residues: 24 loop : -2.21 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 971 HIS 0.005 0.001 HIS A 962 PHE 0.013 0.001 PHE A 478 TYR 0.013 0.001 TYR A 662 ARG 0.005 0.000 ARG A 959 *********************** REFINEMENT MACRO_CYCLE 8 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 203 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.6706 (mmp) cc_final: 0.6244 (tpp) REVERT: A 164 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7793 (pm20) REVERT: A 186 ASP cc_start: 0.7901 (t0) cc_final: 0.7634 (m-30) REVERT: A 208 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8513 (tp) REVERT: A 254 MET cc_start: 0.8642 (tpt) cc_final: 0.7468 (tpt) REVERT: A 286 LYS cc_start: 0.8685 (mppt) cc_final: 0.8466 (mmtt) REVERT: A 299 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 312 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.4944 (pp) REVERT: A 378 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7684 (m110) REVERT: A 439 GLU cc_start: 0.8150 (tp30) cc_final: 0.7781 (tp30) REVERT: A 485 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7837 (pttm) REVERT: A 542 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7563 (ttt90) REVERT: A 720 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 726 LYS cc_start: 0.8265 (mtpp) cc_final: 0.7968 (ttpp) REVERT: A 773 GLU cc_start: 0.7546 (tp30) cc_final: 0.7150 (tp30) REVERT: A 952 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8370 (tt) REVERT: A 1008 ILE cc_start: 0.8780 (mt) cc_final: 0.8377 (mp) REVERT: A 1094 LYS cc_start: 0.8510 (ttpt) cc_final: 0.8290 (ttmm) REVERT: A 1142 LYS cc_start: 0.8614 (mttt) cc_final: 0.8369 (mttp) outliers start: 28 outliers final: 16 residues processed: 194 average time/residue: 0.3063 time to fit residues: 78.1678 Evaluate side-chains 184 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU 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 579 THR 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 749 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 78 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 0.0980 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 59 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 432 ASN A 606 ASN A 612 ASN A 930 GLN ** 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 = 0.3786 r_free = 0.3786 target = 0.167260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.132327 restraints weight = 11529.860| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.69 r_work: 0.3066 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10777 Z= 0.194 Angle : 0.637 12.584 14670 Z= 0.335 Chirality : 0.041 0.329 1615 Planarity : 0.003 0.029 1682 Dihedral : 15.422 161.693 1973 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.41 % Allowed : 16.59 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1109 helix: 0.77 (0.20), residues: 723 sheet: -0.72 (1.14), residues: 24 loop : -2.21 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 971 HIS 0.004 0.001 HIS A 228 PHE 0.016 0.002 PHE A 848 TYR 0.013 0.001 TYR A 677 ARG 0.004 0.000 ARG A 978 *********************** REFINEMENT MACRO_CYCLE 9 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 189 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.6741 (mmp) cc_final: 0.6268 (tpp) REVERT: A 164 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: A 186 ASP cc_start: 0.7912 (t0) cc_final: 0.7647 (m-30) REVERT: A 208 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8558 (tp) REVERT: A 254 MET cc_start: 0.8685 (tpt) cc_final: 0.7587 (tpt) REVERT: A 286 LYS cc_start: 0.8713 (mppt) cc_final: 0.8477 (mmtt) REVERT: A 485 LYS cc_start: 0.8235 (ptmm) cc_final: 0.7945 (pttm) REVERT: A 486 ASP cc_start: 0.8176 (m-30) cc_final: 0.7973 (m-30) REVERT: A 542 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7326 (ttt90) REVERT: A 714 LEU cc_start: 0.8192 (mt) cc_final: 0.7951 (mp) REVERT: A 720 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7736 (tm-30) REVERT: A 726 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7979 (ttpp) REVERT: A 773 GLU cc_start: 0.7585 (tp30) cc_final: 0.7094 (tp30) REVERT: A 952 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8398 (tt) REVERT: A 1008 ILE cc_start: 0.8784 (mt) cc_final: 0.8562 (mt) REVERT: A 1094 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8308 (ttmm) REVERT: A 1142 LYS cc_start: 0.8635 (mttt) cc_final: 0.8381 (mttp) outliers start: 25 outliers final: 18 residues processed: 183 average time/residue: 0.3036 time to fit residues: 73.1499 Evaluate side-chains 182 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU 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 579 THR Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 816 LEU 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 1095 GLU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.169458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135719 restraints weight = 11518.501| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.67 r_work: 0.3063 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10777 Z= 0.168 Angle : 0.630 16.041 14670 Z= 0.328 Chirality : 0.040 0.327 1615 Planarity : 0.002 0.023 1682 Dihedral : 15.361 161.567 1973 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 2.22 % Allowed : 17.26 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.26), residues: 1109 helix: 0.96 (0.20), residues: 711 sheet: -0.68 (1.15), residues: 24 loop : -2.08 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 971 HIS 0.004 0.001 HIS A 962 PHE 0.014 0.001 PHE A 848 TYR 0.012 0.001 TYR A 179 ARG 0.004 0.000 ARG A 978 ********************** REFINEMENT MACRO_CYCLE 10 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 189 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.6724 (mmp) cc_final: 0.6351 (tpp) REVERT: A 164 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7812 (pm20) REVERT: A 186 ASP cc_start: 0.7799 (t0) cc_final: 0.7566 (m-30) REVERT: A 208 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8522 (tp) REVERT: A 254 MET cc_start: 0.8636 (tpt) cc_final: 0.7524 (tpt) REVERT: A 286 LYS cc_start: 0.8672 (mppt) cc_final: 0.8445 (mmtt) REVERT: A 485 LYS cc_start: 0.8222 (ptmm) cc_final: 0.7859 (pttm) REVERT: A 486 ASP cc_start: 0.8066 (m-30) cc_final: 0.7784 (m-30) REVERT: A 542 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7285 (ttt90) REVERT: A 714 LEU cc_start: 0.8121 (mt) cc_final: 0.7890 (mp) REVERT: A 720 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 726 LYS cc_start: 0.8286 (mtpp) cc_final: 0.7970 (ttpp) REVERT: A 773 GLU cc_start: 0.7582 (tp30) cc_final: 0.7159 (tp30) REVERT: A 952 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8387 (tt) REVERT: A 1008 ILE cc_start: 0.8713 (mt) cc_final: 0.8331 (mp) REVERT: A 1094 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8275 (ttmm) REVERT: A 1142 LYS cc_start: 0.8580 (mttt) cc_final: 0.8322 (mttp) outliers start: 23 outliers final: 19 residues processed: 182 average time/residue: 0.3035 time to fit residues: 73.0054 Evaluate side-chains 184 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU 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 579 THR 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 749 LEU Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 816 LEU 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 1095 GLU Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.0270 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.170327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.136874 restraints weight = 11400.129| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.57 r_work: 0.3077 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10777 Z= 0.160 Angle : 0.626 16.456 14670 Z= 0.326 Chirality : 0.040 0.298 1615 Planarity : 0.002 0.023 1682 Dihedral : 15.289 161.423 1973 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.12 % Allowed : 17.55 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1109 helix: 1.06 (0.20), residues: 711 sheet: -0.68 (1.14), residues: 24 loop : -2.12 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 971 HIS 0.004 0.001 HIS A 962 PHE 0.017 0.001 PHE A 478 TYR 0.011 0.001 TYR A 179 ARG 0.004 0.000 ARG A 978 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4975.57 seconds wall clock time: 89 minutes 41.81 seconds (5381.81 seconds total)