Starting phenix.real_space_refine on Fri Sep 11 17:07:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5xwy_6777/09_2026/5xwy_6777.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xwy_6777/09_2026/5xwy_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5xwy_6777/09_2026/5xwy_6777.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5xwy_6777/09_2026/5xwy_6777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xwy_6777/09_2026/5xwy_6777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xwy_6777/09_2026/5xwy_6777.map" model { file = "/net/cci-nas-00/data/ceres_data/5xwy_6777/09_2026/5xwy_6777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xwy_6777/09_2026/5xwy_6777.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 51 5.49 5 S 24 5.16 5 C 6528 2.51 5 N 1784 2.21 5 O 2106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10493 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 9407 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 13, 'PTRANS': 10, 'TRANS': 1093} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1086 Classifications: {'RNAv2': 51} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 10, 'rna3p_pur': 22, 'rna3p_pyr': 12} Link IDs: {'rna2p': 17, 'rna3p': 33} Chain breaks: 1 Time building chain proxies: 2.33, per 1000 atoms: 0.22 Number of scatterers: 10493 At special positions: 0 Unit cell: (113.16, 111.52, 107.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 51 15.00 O 2106 8.00 N 1784 7.00 C 6528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 247.0 milliseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 5 sheets defined 63.7% alpha, 2.9% beta 6 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 59 through 69 removed outlier: 4.058A pdb=" N LYS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.524A pdb=" N TYR A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 129 removed outlier: 3.911A pdb=" N VAL A 129 " --> pdb=" O GLU A 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 129' Processing helix chain 'A' and resid 130 through 150 removed outlier: 3.945A pdb=" N LYS A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.746A pdb=" N ILE A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.707A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.993A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.838A pdb=" N GLU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.551A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 247 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN A 249 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.590A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 278 removed outlier: 3.522A pdb=" N TYR A 277 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.767A pdb=" N LYS A 289 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 290 " --> pdb=" O ASN A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 291 through 308 Processing helix chain 'A' and resid 317 through 325 removed outlier: 3.907A pdb=" N LYS A 321 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 354 removed outlier: 3.663A pdb=" N GLU A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A 352 " --> pdb=" O CYS A 348 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 393 removed outlier: 3.651A pdb=" N PHE A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.761A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.515A pdb=" N LYS A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 477 removed outlier: 3.511A pdb=" N ALA A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 508 through 523 removed outlier: 3.555A pdb=" N LYS A 513 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.904A pdb=" N TYR A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 539 Processing helix chain 'A' and resid 562 through 567 Processing helix chain 'A' and resid 583 through 602 removed outlier: 3.679A pdb=" N GLU A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 598 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.670A pdb=" N ILE A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 644 removed outlier: 4.128A pdb=" N LYS A 642 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 665 removed outlier: 3.549A pdb=" N LEU A 655 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 695 removed outlier: 3.571A pdb=" N ILE A 681 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 714 removed outlier: 3.957A pdb=" N SER A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 731 removed outlier: 3.639A pdb=" N GLN A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 745 removed outlier: 4.225A pdb=" N PHE A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 767 removed outlier: 3.835A pdb=" N ASN A 760 " --> pdb=" O THR A 756 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 761 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 764 " --> pdb=" O ASN A 760 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 765 " --> pdb=" O MET A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 789 Processing helix chain 'A' and resid 796 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 817 through 822 Processing helix chain 'A' and resid 834 through 842 removed outlier: 3.551A pdb=" N LYS A 839 " --> pdb=" O ASN A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 865 removed outlier: 4.419A pdb=" N ASN A 861 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 863 " --> pdb=" O PHE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 879 Processing helix chain 'A' and resid 883 through 895 removed outlier: 3.532A pdb=" N TYR A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 913 removed outlier: 3.530A pdb=" N LYS A 902 " --> pdb=" O GLU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 946 removed outlier: 3.608A pdb=" N SER A 927 " --> pdb=" O GLU A 923 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS A 944 " --> pdb=" O HIS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 983 removed outlier: 3.907A pdb=" N GLY A 966 " --> pdb=" O HIS A 962 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 970 " --> pdb=" O GLY A 966 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 990 Processing helix chain 'A' and resid 1007 through 1020 removed outlier: 4.233A pdb=" N LYS A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 4.246A pdb=" N VAL A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1053 removed outlier: 3.556A pdb=" N ALA A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 removed outlier: 3.527A pdb=" N GLU A1069 " --> pdb=" O LEU A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1083 Processing helix chain 'A' and resid 1083 through 1096 removed outlier: 3.815A pdb=" N LYS A1087 " --> pdb=" O ASN A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 3.750A pdb=" N LYS A1145 " --> pdb=" O CYS A1141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 156 through 160 removed outlier: 3.668A pdb=" N LYS A 165 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 160 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 163 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AA5, first strand: chain 'A' and resid 1099 through 1104 removed outlier: 3.554A pdb=" N THR A1114 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LYS A1103 " --> pdb=" O ILE A1112 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE A1112 " --> pdb=" O LYS A1103 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.91 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: 14428 4.00 - 8.00: 200 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: 6319 35.24 - 70.47: 185 70.47 - 105.71: 16 105.71 - 140.94: 2 140.94 - 176.18: 1 Dihedral angle restraints: 6523 sinusoidal: 3183 harmonic: 3340 Sorted by residual: dihedral pdb=" C4' C B 53 " pdb=" C3' C B 53 " pdb=" C2' C B 53 " pdb=" C1' C B 53 " ideal model delta sinusoidal sigma weight residual 36.35 -40.61 76.96 1 3.10e+00 1.04e-01 7.74e+02 dihedral pdb=" C4' A B 15 " pdb=" C3' A B 15 " pdb=" C2' A B 15 " pdb=" C1' A B 15 " ideal model delta sinusoidal sigma weight residual 36.34 -39.28 75.62 1 3.10e+00 1.04e-01 7.51e+02 dihedral pdb=" C4' U B 26 " pdb=" C3' U B 26 " pdb=" C2' U B 26 " pdb=" C1' U B 26 " ideal model delta sinusoidal sigma weight residual 36.34 -37.30 73.64 1 3.10e+00 1.04e-01 7.18e+02 ... (remaining 6520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 1463 0.124 - 0.247: 110 0.247 - 0.371: 40 0.371 - 0.494: 1 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=" P A B 35 " pdb=" OP1 A B 35 " pdb=" OP2 A B 35 " pdb=" O5' A B 35 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" C3' A B 15 " pdb=" C4' A B 15 " pdb=" O3' A B 15 " pdb=" C2' A B 15 " both_signs ideal model delta sigma weight residual False -2.50 -2.83 0.34 2.00e-01 2.50e+01 2.82e+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: 0.660 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: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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= 0.364 Angle : 1.241 20.001 14670 Z= 0.636 Chirality : 0.082 0.618 1615 Planarity : 0.005 0.037 1682 Dihedral : 15.163 176.181 4367 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer: Outliers : 0.87 % Allowed : 6.46 % Favored : 92.67 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.91 % Twisted Proline : 0.00 % Twisted General : 0.82 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.96 (0.15), residues: 1109 helix: -4.22 (0.08), residues: 692 sheet: -2.31 (0.91), residues: 30 loop : -3.12 (0.25), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 224 TYR 0.043 0.003 TYR A 677 PHE 0.042 0.004 PHE A 608 TRP 0.019 0.004 TRP A 971 HIS 0.016 0.003 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00796 / 0.36 (10777) covalent geometry : angle 1.24090 / 0.64 (14670) hydrogen bonds : bond 0.30612 / 19.95 ( 436) hydrogen bonds : angle 9.71855 / 6.45 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 289 time to evaluate : 0.235 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: 0.1234 time to fit residues: 47.8622 Evaluate side-chains 202 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 1126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 785 GLN A 808 ASN A 934 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1020 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.167120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135803 restraints weight = 11443.787| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.70 r_work: 0.3065 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10777 Z= 0.192 Angle : 1.019 19.334 14670 Z= 0.470 Chirality : 0.079 1.220 1615 Planarity : 0.004 0.032 1682 Dihedral : 14.923 159.245 1844 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.94 % Favored : 92.88 % Rotamer: Outliers : 3.09 % Allowed : 9.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.21), residues: 1109 helix: -2.03 (0.16), residues: 711 sheet: -1.75 (1.00), residues: 25 loop : -2.80 (0.27), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 224 TYR 0.022 0.002 TYR A 677 PHE 0.034 0.002 PHE A 478 TRP 0.014 0.002 TRP A 971 HIS 0.010 0.002 HIS A1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (10777) covalent geometry : angle 1.01935 / 0.47 (14670) hydrogen bonds : bond 0.05240 / 3.39 ( 436) hydrogen bonds : angle 4.59085 / 3.01 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.6924 (mmm) cc_final: 0.6279 (ptp) REVERT: A 150 LYS cc_start: 0.8793 (mmmt) cc_final: 0.8440 (mmmm) REVERT: A 177 ASP cc_start: 0.8508 (t70) cc_final: 0.8292 (t70) REVERT: A 178 TYR cc_start: 0.8804 (t80) cc_final: 0.8529 (t80) REVERT: A 207 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8393 (mttp) REVERT: A 208 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8547 (tp) REVERT: A 260 LYS cc_start: 0.8345 (tttt) cc_final: 0.8128 (tttm) REVERT: A 378 ASN cc_start: 0.8340 (t160) cc_final: 0.8066 (m110) REVERT: A 393 ILE cc_start: 0.8924 (tt) cc_final: 0.8709 (tt) REVERT: A 406 MET cc_start: 0.8135 (mtp) cc_final: 0.7834 (mtp) REVERT: A 424 GLU cc_start: 0.6968 (mp0) cc_final: 0.6667 (mm-30) REVERT: A 542 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7620 (ttm-80) REVERT: A 590 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: A 726 LYS cc_start: 0.8408 (mtpp) cc_final: 0.7853 (ttpp) REVERT: A 773 GLU cc_start: 0.7539 (tp30) cc_final: 0.7249 (tp30) REVERT: A 1008 ILE cc_start: 0.8690 (mt) cc_final: 0.8281 (mp) REVERT: A 1017 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8181 (mtmt) REVERT: A 1034 ASN cc_start: 0.7742 (t0) cc_final: 0.7442 (m110) REVERT: A 1049 ASN cc_start: 0.8600 (t0) cc_final: 0.8399 (t0) REVERT: A 1094 LYS cc_start: 0.8534 (ttpt) cc_final: 0.8298 (ttmm) REVERT: A 1142 LYS cc_start: 0.8496 (mttt) cc_final: 0.8246 (mttp) outliers start: 32 outliers final: 11 residues processed: 233 average time/residue: 0.1213 time to fit residues: 37.6401 Evaluate side-chains 178 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 576 THR 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 1114 THR Chi-restraints excluded: chain A residue 1146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS A 432 ASN A 463 ASN ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN A 719 GLN A 731 ASN A 788 ASN A 828 ASN A 908 HIS A 940 HIS A 986 ASN ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN A1122 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.162694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.128244 restraints weight = 11563.592| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.76 r_work: 0.2943 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10777 Z= 0.266 Angle : 0.942 13.182 14670 Z= 0.446 Chirality : 0.073 1.010 1615 Planarity : 0.004 0.040 1682 Dihedral : 15.302 166.379 1839 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.21 % Favored : 92.70 % Rotamer: Outliers : 4.24 % Allowed : 11.57 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.23), residues: 1109 helix: -1.01 (0.18), residues: 726 sheet: -1.45 (0.89), residues: 30 loop : -2.66 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 472 TYR 0.030 0.002 TYR A 677 PHE 0.026 0.003 PHE A 478 TRP 0.012 0.003 TRP A 971 HIS 0.008 0.002 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.27 (10777) covalent geometry : angle 0.94205 / 0.45 (14670) hydrogen bonds : bond 0.04976 / 3.16 ( 436) hydrogen bonds : angle 4.24437 / 2.74 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.389 Fit side-chains REVERT: A 150 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8493 (mmmm) REVERT: A 163 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7551 (pt) REVERT: A 207 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8419 (mttp) REVERT: A 208 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8538 (tp) REVERT: A 254 MET cc_start: 0.8706 (tpt) cc_final: 0.7709 (tpt) REVERT: A 260 LYS cc_start: 0.8577 (tttt) cc_final: 0.8321 (tppt) REVERT: A 267 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8790 (tp) REVERT: A 393 ILE cc_start: 0.9160 (tt) cc_final: 0.8850 (tt) REVERT: A 406 MET cc_start: 0.8162 (mtp) cc_final: 0.7821 (mtp) REVERT: A 424 GLU cc_start: 0.7297 (mp0) cc_final: 0.6965 (mm-30) REVERT: A 501 LYS cc_start: 0.8586 (tppt) cc_final: 0.8238 (mmtp) REVERT: A 542 ARG cc_start: 0.8113 (ttm-80) cc_final: 0.7516 (ttt90) REVERT: A 590 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: A 625 LEU cc_start: 0.8659 (mt) cc_final: 0.8333 (mp) REVERT: A 726 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7870 (ttpp) REVERT: A 730 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7905 (mm-40) REVERT: A 773 GLU cc_start: 0.7665 (tp30) cc_final: 0.7266 (tp30) REVERT: A 896 GLU cc_start: 0.7542 (mp0) cc_final: 0.7322 (mp0) REVERT: A 952 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8429 (tt) REVERT: A 1008 ILE cc_start: 0.8814 (mt) cc_final: 0.8466 (mp) REVERT: A 1068 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8668 (mm) REVERT: A 1094 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8395 (ttmm) REVERT: A 1142 LYS cc_start: 0.8654 (mttt) cc_final: 0.8401 (mttp) outliers start: 44 outliers final: 21 residues processed: 212 average time/residue: 0.1183 time to fit residues: 33.6731 Evaluate side-chains 190 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 463 ASN 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 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 704 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 989 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1152 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 74 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 ASN A 378 ASN A 432 ASN A 463 ASN A 776 ASN ** 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 = 0.3794 r_free = 0.3794 target = 0.167910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135764 restraints weight = 11536.641| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.62 r_work: 0.3088 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10777 Z= 0.141 Angle : 0.775 12.927 14670 Z= 0.377 Chirality : 0.058 0.524 1615 Planarity : 0.003 0.026 1682 Dihedral : 15.086 172.661 1839 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.76 % Favored : 93.06 % Rotamer: Outliers : 3.38 % Allowed : 12.83 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.25), residues: 1109 helix: -0.22 (0.19), residues: 720 sheet: -1.08 (0.95), residues: 30 loop : -2.47 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 959 TYR 0.016 0.001 TYR A 245 PHE 0.021 0.002 PHE A 478 TRP 0.012 0.002 TRP A 971 HIS 0.004 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (10777) covalent geometry : angle 0.77481 / 0.38 (14670) hydrogen bonds : bond 0.04053 / 2.58 ( 436) hydrogen bonds : angle 3.79937 / 2.43 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.379 Fit side-chains REVERT: A 26 GLU cc_start: 0.7892 (pp20) cc_final: 0.7214 (pp20) REVERT: A 150 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8375 (mmmm) REVERT: A 163 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7354 (pt) REVERT: A 207 LYS cc_start: 0.8639 (mtmm) cc_final: 0.8386 (mttp) REVERT: A 208 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8500 (tp) REVERT: A 254 MET cc_start: 0.8720 (tpt) cc_final: 0.7681 (tpt) REVERT: A 312 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5003 (pt) REVERT: A 378 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7813 (m110) REVERT: A 387 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.8037 (t80) REVERT: A 393 ILE cc_start: 0.8954 (tt) cc_final: 0.8715 (tt) REVERT: A 406 MET cc_start: 0.7932 (mtp) cc_final: 0.7718 (mtp) REVERT: A 424 GLU cc_start: 0.7178 (mp0) cc_final: 0.6844 (mm-30) REVERT: A 483 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.5894 (mp0) REVERT: A 485 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8093 (pttm) REVERT: A 501 LYS cc_start: 0.8478 (tppt) cc_final: 0.8213 (mmtp) REVERT: A 515 LYS cc_start: 0.8778 (mttm) cc_final: 0.8568 (mtmm) REVERT: A 542 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7361 (ttt90) REVERT: A 590 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8197 (m-30) REVERT: A 726 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7826 (ttpp) REVERT: A 730 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7881 (mm-40) REVERT: A 773 GLU cc_start: 0.7597 (tp30) cc_final: 0.7233 (tp30) REVERT: A 789 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8213 (mmmt) REVERT: A 845 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8157 (mmmt) REVERT: A 952 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8433 (tt) REVERT: A 1008 ILE cc_start: 0.8769 (mt) cc_final: 0.8388 (mp) REVERT: A 1094 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8321 (ttmm) REVERT: A 1142 LYS cc_start: 0.8544 (mttt) cc_final: 0.8321 (mttp) outliers start: 35 outliers final: 17 residues processed: 196 average time/residue: 0.1181 time to fit residues: 31.0449 Evaluate side-chains 189 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 578 LYS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 704 ILE 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 989 ILE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1152 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 13 optimal weight: 0.3980 chunk 89 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3835 r_free = 0.3835 target = 0.171662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.137980 restraints weight = 11413.104| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.52 r_work: 0.3131 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10777 Z= 0.134 Angle : 0.745 12.586 14670 Z= 0.364 Chirality : 0.055 0.465 1615 Planarity : 0.003 0.023 1682 Dihedral : 15.055 174.523 1839 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.47 % Allowed : 13.79 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.25), residues: 1109 helix: 0.21 (0.20), residues: 721 sheet: -1.36 (1.05), residues: 24 loop : -2.42 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 959 TYR 0.018 0.001 TYR A 245 PHE 0.017 0.002 PHE A 478 TRP 0.011 0.002 TRP A 971 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10777) covalent geometry : angle 0.74453 / 0.36 (14670) hydrogen bonds : bond 0.03813 / 2.41 ( 436) hydrogen bonds : angle 3.62412 / 2.31 ( 1242) *********************** 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 : 0.356 Fit side-chains revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7770 (pp20) cc_final: 0.7132 (pp20) REVERT: A 150 LYS cc_start: 0.8675 (mmmt) cc_final: 0.8378 (mmmm) REVERT: A 163 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7372 (pt) REVERT: A 186 ASP cc_start: 0.7882 (t0) cc_final: 0.7669 (m-30) REVERT: A 207 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8370 (mttp) REVERT: A 208 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8513 (tp) REVERT: A 254 MET cc_start: 0.8691 (tpt) cc_final: 0.7639 (tpt) REVERT: A 260 LYS cc_start: 0.8598 (ptmt) cc_final: 0.8301 (ptmt) REVERT: A 340 LYS cc_start: 0.8727 (mttt) cc_final: 0.8510 (mtpp) REVERT: A 378 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.7800 (m110) REVERT: A 393 ILE cc_start: 0.8973 (tt) cc_final: 0.8710 (tt) REVERT: A 424 GLU cc_start: 0.7207 (mp0) cc_final: 0.6937 (mm-30) REVERT: A 439 GLU cc_start: 0.8120 (tp30) cc_final: 0.7870 (tp30) REVERT: A 451 MET cc_start: 0.7778 (mmm) cc_final: 0.7337 (mmp) REVERT: A 483 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5971 (mp0) REVERT: A 485 LYS cc_start: 0.8446 (ptmm) cc_final: 0.8082 (pttm) REVERT: A 501 LYS cc_start: 0.8497 (tppt) cc_final: 0.8277 (mmtp) REVERT: A 542 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7378 (ttt90) REVERT: A 590 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8192 (m-30) REVERT: A 726 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7982 (ttpp) REVERT: A 773 GLU cc_start: 0.7585 (tp30) cc_final: 0.7210 (tp30) REVERT: A 845 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8148 (mmmt) REVERT: A 885 GLU cc_start: 0.8214 (pp20) cc_final: 0.7517 (pm20) REVERT: A 952 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 959 ARG cc_start: 0.8627 (tpt-90) cc_final: 0.8403 (ttt90) REVERT: A 1008 ILE cc_start: 0.8790 (mt) cc_final: 0.8409 (mp) REVERT: A 1017 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8113 (mtmt) REVERT: A 1094 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8298 (ttmm) REVERT: A 1142 LYS cc_start: 0.8631 (mttt) cc_final: 0.8391 (mttp) outliers start: 36 outliers final: 19 residues processed: 206 average time/residue: 0.1196 time to fit residues: 32.9175 Evaluate side-chains 190 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 578 LYS 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 704 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 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 1146 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3833 r_free = 0.3833 target = 0.171660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.135786 restraints weight = 11576.257| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.79 r_work: 0.3095 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10777 Z= 0.139 Angle : 0.739 12.594 14670 Z= 0.360 Chirality : 0.055 0.472 1615 Planarity : 0.003 0.022 1682 Dihedral : 15.015 173.597 1837 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.69 % Rotamer: Outliers : 2.89 % Allowed : 15.53 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.25), residues: 1109 helix: 0.44 (0.20), residues: 721 sheet: -1.35 (1.04), residues: 24 loop : -2.37 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 959 TYR 0.020 0.001 TYR A 245 PHE 0.015 0.002 PHE A 478 TRP 0.010 0.002 TRP A 971 HIS 0.004 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (10777) covalent geometry : angle 0.73863 / 0.36 (14670) hydrogen bonds : bond 0.03761 / 2.37 ( 436) hydrogen bonds : angle 3.56222 / 2.27 ( 1242) *********************** 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 197 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7437 (pp) REVERT: A 186 ASP cc_start: 0.7896 (t0) cc_final: 0.7660 (m-30) REVERT: A 208 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 247 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7646 (mt-10) REVERT: A 254 MET cc_start: 0.8697 (tpt) cc_final: 0.7584 (tpt) REVERT: A 378 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.7768 (m110) REVERT: A 393 ILE cc_start: 0.8988 (tt) cc_final: 0.8709 (tt) REVERT: A 424 GLU cc_start: 0.7207 (mp0) cc_final: 0.6968 (mm-30) REVERT: A 439 GLU cc_start: 0.8145 (tp30) cc_final: 0.7904 (tp30) REVERT: A 451 MET cc_start: 0.7735 (mmm) cc_final: 0.7289 (mmp) REVERT: A 485 LYS cc_start: 0.8384 (ptmm) cc_final: 0.8040 (pttm) REVERT: A 501 LYS cc_start: 0.8541 (tppt) cc_final: 0.8314 (mmtp) REVERT: A 531 LYS cc_start: 0.8584 (tttm) cc_final: 0.8372 (ttmm) REVERT: A 542 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7395 (ttt90) REVERT: A 631 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6952 (pmt100) REVERT: A 726 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7996 (ttpp) REVERT: A 773 GLU cc_start: 0.7622 (tp30) cc_final: 0.7232 (tp30) REVERT: A 845 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8138 (mmmt) REVERT: A 885 GLU cc_start: 0.8214 (pp20) cc_final: 0.7537 (pm20) REVERT: A 952 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8363 (tt) REVERT: A 1008 ILE cc_start: 0.8800 (mt) cc_final: 0.8404 (mp) REVERT: A 1010 GLU cc_start: 0.7986 (tt0) cc_final: 0.7450 (mm-30) REVERT: A 1017 LYS cc_start: 0.8539 (mtmt) cc_final: 0.8166 (mtmt) REVERT: A 1094 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8316 (ttmm) REVERT: A 1142 LYS cc_start: 0.8642 (mttt) cc_final: 0.8413 (mttp) outliers start: 30 outliers final: 20 residues processed: 188 average time/residue: 0.1213 time to fit residues: 30.3957 Evaluate side-chains 184 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 473 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 578 LYS 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 704 ILE 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 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 7 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN A 432 ASN A 606 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 = 0.3752 r_free = 0.3752 target = 0.164268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.129080 restraints weight = 11467.110| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.69 r_work: 0.2957 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 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 : 0.006 0.041 10777 Z= 0.239 Angle : 0.857 12.641 14670 Z= 0.411 Chirality : 0.066 0.709 1615 Planarity : 0.003 0.034 1682 Dihedral : 15.083 169.336 1837 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.47 % Allowed : 15.04 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.25), residues: 1109 helix: 0.19 (0.19), residues: 730 sheet: -0.96 (0.95), residues: 30 loop : -2.58 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 978 TYR 0.019 0.002 TYR A 677 PHE 0.020 0.002 PHE A 556 TRP 0.008 0.002 TRP A 971 HIS 0.006 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (10777) covalent geometry : angle 0.85651 / 0.41 (14670) hydrogen bonds : bond 0.04415 / 2.77 ( 436) hydrogen bonds : angle 3.83539 / 2.46 ( 1242) *********************** 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 205 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.370 Fit side-chains REVERT: A 26 GLU cc_start: 0.7942 (pp20) cc_final: 0.7258 (pp20) REVERT: A 154 ASN cc_start: 0.8265 (t0) cc_final: 0.8058 (t0) REVERT: A 178 TYR cc_start: 0.9093 (t80) cc_final: 0.8824 (t80) REVERT: A 208 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8620 (tp) REVERT: A 254 MET cc_start: 0.8722 (tpt) cc_final: 0.7720 (tpt) REVERT: A 286 LYS cc_start: 0.8777 (mppt) cc_final: 0.8511 (mmtt) REVERT: A 378 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8323 (t0) REVERT: A 387 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8354 (t80) REVERT: A 439 GLU cc_start: 0.8169 (tp30) cc_final: 0.7827 (tp30) REVERT: A 542 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7425 (ttt90) REVERT: A 625 LEU cc_start: 0.8641 (mt) cc_final: 0.8343 (mp) REVERT: A 726 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8092 (ttpp) REVERT: A 773 GLU cc_start: 0.7636 (tp30) cc_final: 0.7185 (tp30) REVERT: A 827 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.5443 (m-80) REVERT: A 846 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7638 (pp) REVERT: A 885 GLU cc_start: 0.8214 (pp20) cc_final: 0.7549 (pm20) REVERT: A 952 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A 1008 ILE cc_start: 0.8830 (mt) cc_final: 0.8475 (mp) REVERT: A 1017 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8174 (mtmt) REVERT: A 1094 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8427 (ttmm) REVERT: A 1142 LYS cc_start: 0.8668 (mttt) cc_final: 0.8395 (mttp) outliers start: 36 outliers final: 21 residues processed: 195 average time/residue: 0.1190 time to fit residues: 31.2627 Evaluate side-chains 185 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 350 LYS Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 TYR 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 578 LYS 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 704 ILE 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 827 PHE 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 Chi-restraints excluded: chain A residue 1152 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3822 r_free = 0.3822 target = 0.170570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.136876 restraints weight = 11396.528| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.57 r_work: 0.3061 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10777 Z= 0.142 Angle : 0.754 12.598 14670 Z= 0.368 Chirality : 0.056 0.491 1615 Planarity : 0.003 0.023 1682 Dihedral : 15.059 172.612 1837 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.09 % Allowed : 15.62 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.25), residues: 1109 helix: 0.50 (0.20), residues: 721 sheet: -0.79 (0.98), residues: 30 loop : -2.38 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 978 TYR 0.016 0.001 TYR A 245 PHE 0.015 0.002 PHE A 556 TRP 0.010 0.002 TRP A 971 HIS 0.004 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (10777) covalent geometry : angle 0.75446 / 0.37 (14670) hydrogen bonds : bond 0.03848 / 2.43 ( 436) hydrogen bonds : angle 3.61798 / 2.32 ( 1242) *********************** 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 198 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 0.378 Fit side-chains REVERT: A 44 MET cc_start: 0.6583 (mmp) cc_final: 0.6095 (tpp) REVERT: A 154 ASN cc_start: 0.8011 (t0) cc_final: 0.7761 (t0) REVERT: A 208 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8592 (tp) REVERT: A 254 MET cc_start: 0.8679 (tpt) cc_final: 0.7536 (tpt) REVERT: A 286 LYS cc_start: 0.8765 (mppt) cc_final: 0.8492 (mmtt) REVERT: A 334 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: A 378 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.7750 (m110) REVERT: A 387 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8334 (t80) REVERT: A 393 ILE cc_start: 0.8928 (tt) cc_final: 0.8724 (tt) REVERT: A 406 MET cc_start: 0.7972 (mtp) cc_final: 0.7457 (ptp) REVERT: A 439 GLU cc_start: 0.8155 (tp30) cc_final: 0.7769 (tp30) REVERT: A 542 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7359 (ttt90) REVERT: A 631 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.6958 (pmt100) REVERT: A 714 LEU cc_start: 0.8213 (mt) cc_final: 0.7985 (mp) REVERT: A 726 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8033 (ttpp) REVERT: A 773 GLU cc_start: 0.7596 (tp30) cc_final: 0.7215 (tp30) REVERT: A 827 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5469 (m-80) REVERT: A 885 GLU cc_start: 0.8161 (pp20) cc_final: 0.7496 (pm20) REVERT: A 952 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8357 (tt) REVERT: A 1008 ILE cc_start: 0.8815 (mt) cc_final: 0.8436 (mp) REVERT: A 1094 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8368 (ttmm) REVERT: A 1142 LYS cc_start: 0.8619 (mttt) cc_final: 0.8378 (mttp) outliers start: 32 outliers final: 19 residues processed: 189 average time/residue: 0.1158 time to fit residues: 29.5476 Evaluate side-chains 188 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 334 GLU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 403 THR 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 704 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 9 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN A 432 ASN A 830 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 = 0.3813 r_free = 0.3813 target = 0.169483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135111 restraints weight = 11367.319| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.59 r_work: 0.3083 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.4983 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= 0.152 Angle : 0.764 12.461 14670 Z= 0.373 Chirality : 0.057 0.502 1615 Planarity : 0.003 0.024 1682 Dihedral : 14.991 171.879 1837 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.99 % Allowed : 15.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.26), residues: 1109 helix: 0.58 (0.20), residues: 723 sheet: -0.69 (1.00), residues: 30 loop : -2.35 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 978 TYR 0.020 0.001 TYR A 245 PHE 0.016 0.002 PHE A 478 TRP 0.009 0.001 TRP A 971 HIS 0.004 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10777) covalent geometry : angle 0.76440 / 0.37 (14670) hydrogen bonds : bond 0.03813 / 2.43 ( 436) hydrogen bonds : angle 3.61439 / 2.32 ( 1242) *********************** 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 195 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.6657 (mmp) cc_final: 0.6202 (tpp) REVERT: A 154 ASN cc_start: 0.8019 (t0) cc_final: 0.7748 (t0) REVERT: A 208 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8586 (tp) REVERT: A 254 MET cc_start: 0.8703 (tpt) cc_final: 0.7627 (tpt) REVERT: A 286 LYS cc_start: 0.8750 (mppt) cc_final: 0.8486 (mmtt) REVERT: A 334 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: A 378 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.7722 (m110) REVERT: A 387 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8289 (t80) REVERT: A 393 ILE cc_start: 0.8977 (tt) cc_final: 0.8754 (tt) REVERT: A 406 MET cc_start: 0.7954 (mtp) cc_final: 0.7406 (ptp) REVERT: A 439 GLU cc_start: 0.8132 (tp30) cc_final: 0.7772 (tp30) REVERT: A 485 LYS cc_start: 0.8242 (ptmm) cc_final: 0.7907 (pttm) REVERT: A 542 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7373 (ttt90) REVERT: A 631 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.6963 (pmt100) REVERT: A 714 LEU cc_start: 0.8174 (mt) cc_final: 0.7933 (mp) REVERT: A 726 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8013 (ttpp) REVERT: A 773 GLU cc_start: 0.7590 (tp30) cc_final: 0.7163 (tp30) REVERT: A 805 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 827 PHE cc_start: 0.5901 (OUTLIER) cc_final: 0.5475 (m-80) REVERT: A 885 GLU cc_start: 0.8160 (pp20) cc_final: 0.7497 (pm20) REVERT: A 952 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8348 (tt) REVERT: A 1008 ILE cc_start: 0.8815 (mt) cc_final: 0.8428 (mp) REVERT: A 1017 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8192 (mtmt) REVERT: A 1094 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8335 (ttmm) REVERT: A 1142 LYS cc_start: 0.8616 (mttt) cc_final: 0.8372 (mttp) outliers start: 31 outliers final: 20 residues processed: 188 average time/residue: 0.1251 time to fit residues: 31.4623 Evaluate side-chains 191 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 387 TYR 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 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 704 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 PHE 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 Chi-restraints excluded: chain A residue 1152 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 6 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3744 r_free = 0.3744 target = 0.163151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.127234 restraints weight = 11442.122| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.67 r_work: 0.2957 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10777 Z= 0.254 Angle : 0.880 12.769 14670 Z= 0.421 Chirality : 0.068 0.742 1615 Planarity : 0.003 0.044 1682 Dihedral : 15.092 168.921 1837 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.18 % Allowed : 15.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.25), residues: 1109 helix: 0.30 (0.19), residues: 727 sheet: -0.78 (0.98), residues: 30 loop : -2.47 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 377 TYR 0.018 0.002 TYR A 677 PHE 0.020 0.002 PHE A 556 TRP 0.007 0.002 TRP A 971 HIS 0.006 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 (10777) covalent geometry : angle 0.88004 / 0.42 (14670) hydrogen bonds : bond 0.04427 / 2.80 ( 436) hydrogen bonds : angle 3.89773 / 2.52 ( 1242) ********************** 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 197 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.348 Fit side-chains REVERT: A 44 MET cc_start: 0.6821 (mmp) cc_final: 0.6345 (tpp) REVERT: A 154 ASN cc_start: 0.8248 (t0) cc_final: 0.8025 (t0) REVERT: A 208 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8623 (tp) REVERT: A 234 LYS cc_start: 0.8108 (mppt) cc_final: 0.7535 (mppt) REVERT: A 254 MET cc_start: 0.8820 (tpt) cc_final: 0.7857 (tpt) REVERT: A 286 LYS cc_start: 0.8737 (mppt) cc_final: 0.8477 (mmtt) REVERT: A 334 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: A 378 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8338 (t0) REVERT: A 393 ILE cc_start: 0.9138 (tt) cc_final: 0.8831 (tt) REVERT: A 439 GLU cc_start: 0.8152 (tp30) cc_final: 0.7759 (tp30) REVERT: A 459 ASP cc_start: 0.8025 (t0) cc_final: 0.7438 (m-30) REVERT: A 625 LEU cc_start: 0.8679 (mt) cc_final: 0.8400 (mp) REVERT: A 726 LYS cc_start: 0.8378 (mtpp) cc_final: 0.8103 (ttpp) REVERT: A 736 ILE cc_start: 0.8599 (mp) cc_final: 0.8384 (mp) REVERT: A 773 GLU cc_start: 0.7608 (tp30) cc_final: 0.7181 (tp30) REVERT: A 827 PHE cc_start: 0.6024 (OUTLIER) cc_final: 0.5452 (m-80) REVERT: A 885 GLU cc_start: 0.8232 (pp20) cc_final: 0.7567 (pm20) REVERT: A 1008 ILE cc_start: 0.8855 (mt) cc_final: 0.8485 (mp) REVERT: A 1094 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8423 (ttmm) REVERT: A 1142 LYS cc_start: 0.8694 (mttt) cc_final: 0.8423 (mttp) outliers start: 33 outliers final: 23 residues processed: 186 average time/residue: 0.1208 time to fit residues: 30.1569 Evaluate side-chains 192 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 231 ILE 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 535 LEU 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 631 ARG Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 702 ILE Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 795 ASP Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 827 PHE 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 Chi-restraints excluded: chain A residue 1152 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 55 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 41 optimal weight: 0.0050 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 378 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.174340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.140704 restraints weight = 11459.988| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.54 r_work: 0.3174 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10777 Z= 0.127 Angle : 0.740 12.761 14670 Z= 0.362 Chirality : 0.053 0.372 1615 Planarity : 0.003 0.027 1682 Dihedral : 15.060 173.659 1837 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.80 % Allowed : 16.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.26), residues: 1109 helix: 0.75 (0.20), residues: 725 sheet: -0.72 (1.13), residues: 24 loop : -2.34 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 322 TYR 0.019 0.001 TYR A 245 PHE 0.014 0.001 PHE A 478 TRP 0.010 0.002 TRP A 971 HIS 0.005 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (10777) covalent geometry : angle 0.73974 / 0.36 (14670) hydrogen bonds : bond 0.03577 / 2.28 ( 436) hydrogen bonds : angle 3.55332 / 2.29 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2319.28 seconds wall clock time: 40 minutes 38.66 seconds (2438.66 seconds total)