Starting phenix.real_space_refine on Sun Aug 24 12:56:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8byp_16330/08_2025/8byp_16330_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8byp_16330/08_2025/8byp_16330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8byp_16330/08_2025/8byp_16330_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8byp_16330/08_2025/8byp_16330_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8byp_16330/08_2025/8byp_16330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8byp_16330/08_2025/8byp_16330.map" } resolution = 3.12 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= 0.002 sd= 0.154 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 12730 2.51 5 N 3214 2.21 5 O 3857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19836 Number of models: 1 Model: "" Number of chains: 2 Chain: "N" Number of atoms: 9554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1156, 9554 Classifications: {'peptide': 1156} Link IDs: {'PTRANS': 37, 'TRANS': 1118} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "X" Number of atoms: 10282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1265, 10282 Classifications: {'peptide': 1265} Link IDs: {'PTRANS': 46, 'TRANS': 1218} Chain breaks: 1 Time building chain proxies: 4.73, per 1000 atoms: 0.24 Number of scatterers: 19836 At special positions: 0 Unit cell: (108.15, 118.65, 168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 3857 8.00 N 3214 7.00 C 12730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS X 423 " - pdb=" SG CYS X 467 " distance=2.03 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: 1.76 Conformation dependent library (CDL) restraints added in 948.9 milliseconds Enol-peptide restraints added in 2.1 microseconds 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4654 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 33 sheets defined 32.6% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'N' and resid 59 through 63 Processing helix chain 'N' and resid 76 through 97 removed outlier: 4.090A pdb=" N VAL N 97 " --> pdb=" O ARG N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 109 Processing helix chain 'N' and resid 193 through 211 removed outlier: 3.831A pdb=" N GLY N 197 " --> pdb=" O ASP N 193 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS N 201 " --> pdb=" O GLY N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 244 Processing helix chain 'N' and resid 261 through 281 removed outlier: 3.614A pdb=" N LEU N 265 " --> pdb=" O ASN N 261 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU N 268 " --> pdb=" O PHE N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 302 Processing helix chain 'N' and resid 303 through 308 Processing helix chain 'N' and resid 311 through 319 removed outlier: 3.630A pdb=" N PHE N 315 " --> pdb=" O ASN N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 330 through 334 removed outlier: 3.717A pdb=" N TRP N 334 " --> pdb=" O ILE N 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 347 Processing helix chain 'N' and resid 406 through 411 Processing helix chain 'N' and resid 435 through 442 removed outlier: 3.735A pdb=" N ILE N 439 " --> pdb=" O ASP N 435 " (cutoff:3.500A) Processing helix chain 'N' and resid 475 through 484 removed outlier: 3.871A pdb=" N THR N 484 " --> pdb=" O LEU N 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 499 through 504 removed outlier: 3.765A pdb=" N SER N 504 " --> pdb=" O TYR N 500 " (cutoff:3.500A) Processing helix chain 'N' and resid 515 through 524 removed outlier: 3.957A pdb=" N ASN N 524 " --> pdb=" O GLU N 520 " (cutoff:3.500A) Processing helix chain 'N' and resid 533 through 554 Processing helix chain 'N' and resid 570 through 575 Processing helix chain 'N' and resid 582 through 591 removed outlier: 3.523A pdb=" N LEU N 589 " --> pdb=" O GLU N 585 " (cutoff:3.500A) Processing helix chain 'N' and resid 592 through 596 Processing helix chain 'N' and resid 623 through 654 Processing helix chain 'N' and resid 655 through 666 removed outlier: 3.798A pdb=" N LEU N 661 " --> pdb=" O GLN N 657 " (cutoff:3.500A) Processing helix chain 'N' and resid 667 through 689 removed outlier: 4.015A pdb=" N GLN N 674 " --> pdb=" O ASN N 670 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL N 679 " --> pdb=" O LEU N 675 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS N 682 " --> pdb=" O THR N 678 " (cutoff:3.500A) Processing helix chain 'N' and resid 694 through 739 removed outlier: 3.522A pdb=" N ARG N 700 " --> pdb=" O ASP N 696 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP N 710 " --> pdb=" O ASN N 706 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE N 711 " --> pdb=" O ARG N 707 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG N 714 " --> pdb=" O ASP N 710 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE N 715 " --> pdb=" O ILE N 711 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL N 739 " --> pdb=" O PHE N 735 " (cutoff:3.500A) Processing helix chain 'N' and resid 739 through 763 removed outlier: 3.634A pdb=" N ASN N 746 " --> pdb=" O LEU N 742 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS N 753 " --> pdb=" O ASN N 749 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU N 759 " --> pdb=" O ASN N 755 " (cutoff:3.500A) Processing helix chain 'N' and resid 768 through 775 removed outlier: 3.533A pdb=" N GLN N 772 " --> pdb=" O LEU N 768 " (cutoff:3.500A) Processing helix chain 'N' and resid 775 through 780 removed outlier: 3.521A pdb=" N TYR N 780 " --> pdb=" O LEU N 776 " (cutoff:3.500A) Processing helix chain 'N' and resid 784 through 788 Processing helix chain 'N' and resid 792 through 801 removed outlier: 3.814A pdb=" N PHE N 796 " --> pdb=" O ASN N 792 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS N 798 " --> pdb=" O SER N 794 " (cutoff:3.500A) Processing helix chain 'N' and resid 1003 through 1014 removed outlier: 3.583A pdb=" N ALA N1014 " --> pdb=" O ARG N1010 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 33 Processing helix chain 'X' and resid 84 through 105 removed outlier: 4.181A pdb=" N LYS X 105 " --> pdb=" O ARG X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 118 Processing helix chain 'X' and resid 171 through 177 removed outlier: 3.771A pdb=" N ILE X 175 " --> pdb=" O TYR X 171 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER X 176 " --> pdb=" O SER X 172 " (cutoff:3.500A) Processing helix chain 'X' and resid 220 through 237 removed outlier: 3.904A pdb=" N GLU X 228 " --> pdb=" O THR X 224 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL X 230 " --> pdb=" O MET X 226 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS X 231 " --> pdb=" O HIS X 227 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 271 Processing helix chain 'X' and resid 272 through 301 removed outlier: 3.600A pdb=" N LYS X 276 " --> pdb=" O GLY X 272 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA X 277 " --> pdb=" O ILE X 273 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE X 278 " --> pdb=" O ASP X 274 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER X 280 " --> pdb=" O LYS X 276 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEU X 281 " --> pdb=" O ALA X 277 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN X 292 " --> pdb=" O GLU X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 302 through 305 removed outlier: 3.670A pdb=" N VAL X 305 " --> pdb=" O LEU X 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 302 through 305' Processing helix chain 'X' and resid 309 through 319 Processing helix chain 'X' and resid 331 through 344 Processing helix chain 'X' and resid 347 through 355 Processing helix chain 'X' and resid 473 through 475 No H-bonds generated for 'chain 'X' and resid 473 through 475' Processing helix chain 'X' and resid 559 through 567 removed outlier: 3.559A pdb=" N GLN X 567 " --> pdb=" O PHE X 563 " (cutoff:3.500A) Processing helix chain 'X' and resid 585 through 592 Processing helix chain 'X' and resid 602 through 608 removed outlier: 3.596A pdb=" N THR X 606 " --> pdb=" O ASN X 602 " (cutoff:3.500A) Processing helix chain 'X' and resid 618 through 635 removed outlier: 3.916A pdb=" N LEU X 624 " --> pdb=" O PHE X 620 " (cutoff:3.500A) Processing helix chain 'X' and resid 653 through 658 Processing helix chain 'X' and resid 669 through 676 removed outlier: 3.514A pdb=" N GLU X 674 " --> pdb=" O VAL X 670 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 738 removed outlier: 3.868A pdb=" N ALA X 710 " --> pdb=" O GLU X 706 " (cutoff:3.500A) Processing helix chain 'X' and resid 738 through 770 Processing helix chain 'X' and resid 777 through 819 removed outlier: 4.142A pdb=" N ILE X 781 " --> pdb=" O ASP X 777 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS X 809 " --> pdb=" O LYS X 805 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU X 810 " --> pdb=" O PHE X 806 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET X 819 " --> pdb=" O LEU X 815 " (cutoff:3.500A) Processing helix chain 'X' and resid 819 through 844 removed outlier: 3.619A pdb=" N VAL X 823 " --> pdb=" O MET X 819 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP X 825 " --> pdb=" O PRO X 821 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN X 826 " --> pdb=" O LYS X 822 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU X 844 " --> pdb=" O LYS X 840 " (cutoff:3.500A) Processing helix chain 'X' and resid 845 through 850 Processing helix chain 'X' and resid 850 through 865 Processing helix chain 'X' and resid 879 through 886 removed outlier: 4.374A pdb=" N ASN X 886 " --> pdb=" O ASP X 882 " (cutoff:3.500A) Processing helix chain 'X' and resid 886 through 892 Processing helix chain 'X' and resid 1091 through 1102 removed outlier: 3.631A pdb=" N TYR X1102 " --> pdb=" O LEU X1098 " (cutoff:3.500A) Processing helix chain 'X' and resid 1274 through 1280 removed outlier: 3.745A pdb=" N PHE X1278 " --> pdb=" O SER X1274 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN X1279 " --> pdb=" O ALA X1275 " (cutoff:3.500A) Processing helix chain 'X' and resid 1281 through 1284 Processing helix chain 'X' and resid 1287 through 1292 Processing sheet with id=AA1, first strand: chain 'N' and resid 18 through 22 removed outlier: 6.973A pdb=" N ILE N 44 " --> pdb=" O ILE N 40 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP N 45 " --> pdb=" O LEU N 147 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN N 158 " --> pdb=" O CYS N 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 125 through 126 removed outlier: 4.604A pdb=" N LYS N 125 " --> pdb=" O PHE N 141 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE N 141 " --> pdb=" O LYS N 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'N' and resid 183 through 184 removed outlier: 3.985A pdb=" N LYS N 363 " --> pdb=" O LYS N 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 219 through 224 removed outlier: 6.704A pdb=" N SER N 234 " --> pdb=" O TYR N 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 348 through 349 Processing sheet with id=AA6, first strand: chain 'N' and resid 390 through 394 removed outlier: 4.596A pdb=" N LEU N 390 " --> pdb=" O ASN N 385 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE N 469 " --> pdb=" O ILE N 380 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR N 382 " --> pdb=" O ILE N 469 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 494 through 496 removed outlier: 6.338A pdb=" N LYS N 494 " --> pdb=" O VAL N 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'N' and resid 555 through 556 Processing sheet with id=AA9, first strand: chain 'N' and resid 815 through 817 removed outlier: 5.386A pdb=" N LEU N 992 " --> pdb=" O LYS N 888 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS N 888 " --> pdb=" O LEU N 992 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA N 994 " --> pdb=" O TRP N 886 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP N 886 " --> pdb=" O ALA N 994 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 847 through 850 removed outlier: 3.990A pdb=" N ARG N 847 " --> pdb=" O LYS N 858 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N VAL N 855 " --> pdb=" O ALA N 994 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA N 994 " --> pdb=" O VAL N 855 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU N 992 " --> pdb=" O LYS N 888 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LYS N 888 " --> pdb=" O LEU N 992 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA N 994 " --> pdb=" O TRP N 886 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP N 886 " --> pdb=" O ALA N 994 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 820 through 824 removed outlier: 3.593A pdb=" N PHE N 831 " --> pdb=" O SER N 820 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 841 through 842 removed outlier: 6.500A pdb=" N LEU N 910 " --> pdb=" O LEU N 898 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN N 900 " --> pdb=" O TRP N 908 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TRP N 908 " --> pdb=" O ASN N 900 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 1036 through 1037 Processing sheet with id=AB5, first strand: chain 'N' and resid 1047 through 1049 removed outlier: 6.321A pdb=" N ILE N1057 " --> pdb=" O ILE N1153 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE N1134 " --> pdb=" O LEU N1141 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N LEU N1143 " --> pdb=" O LEU N1132 " (cutoff:3.500A) removed outlier: 15.086A pdb=" N LEU N1132 " --> pdb=" O LEU N1143 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER N1131 " --> pdb=" O ASN N1125 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASN N1125 " --> pdb=" O SER N1131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 1100 through 1101 Processing sheet with id=AB7, first strand: chain 'N' and resid 1160 through 1161 Processing sheet with id=AB8, first strand: chain 'X' and resid 144 through 150 removed outlier: 4.913A pdb=" N ILE X 145 " --> pdb=" O GLU X 141 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU X 141 " --> pdb=" O ILE X 145 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA X 138 " --> pdb=" O ARG X 23 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N THR X 21 " --> pdb=" O GLN X 140 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLN X 42 " --> pdb=" O ILE X 49 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE X 49 " --> pdb=" O GLN X 42 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP X 48 " --> pdb=" O ILE X 155 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 123 through 125 Processing sheet with id=AC1, first strand: chain 'X' and resid 191 through 192 Processing sheet with id=AC2, first strand: chain 'X' and resid 195 through 196 Processing sheet with id=AC3, first strand: chain 'X' and resid 245 through 246 Processing sheet with id=AC4, first strand: chain 'X' and resid 321 through 324 Processing sheet with id=AC5, first strand: chain 'X' and resid 468 through 471 removed outlier: 8.911A pdb=" N ILE X 553 " --> pdb=" O PHE X 419 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS X 421 " --> pdb=" O ILE X 553 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 582 through 583 Processing sheet with id=AC7, first strand: chain 'X' and resid 906 through 909 removed outlier: 8.177A pdb=" N ALA X 902 " --> pdb=" O ASP X1081 " (cutoff:3.500A) removed outlier: 9.728A pdb=" N ASP X1081 " --> pdb=" O ALA X 902 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 906 through 909 removed outlier: 8.177A pdb=" N ALA X 902 " --> pdb=" O ASP X1081 " (cutoff:3.500A) removed outlier: 9.728A pdb=" N ASP X1081 " --> pdb=" O ALA X 902 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU X1080 " --> pdb=" O LYS X 967 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS X 967 " --> pdb=" O LEU X1080 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLN X1082 " --> pdb=" O TRP X 965 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TRP X 965 " --> pdb=" O GLN X1082 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N SER X1038 " --> pdb=" O GLU X1049 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU X1049 " --> pdb=" O SER X1038 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL X1040 " --> pdb=" O ILE X1047 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 917 through 919 removed outlier: 6.878A pdb=" N ILE X 994 " --> pdb=" O LEU X 983 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU X 985 " --> pdb=" O TRP X 992 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TRP X 992 " --> pdb=" O GLU X 985 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 1121 through 1123 Processing sheet with id=AD2, first strand: chain 'X' and resid 1121 through 1123 removed outlier: 3.625A pdb=" N ILE X1201 " --> pdb=" O THR X1224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 1134 through 1139 Processing sheet with id=AD4, first strand: chain 'X' and resid 1154 through 1156 Processing sheet with id=AD5, first strand: chain 'X' and resid 1228 through 1230 Processing sheet with id=AD6, first strand: chain 'X' and resid 1256 through 1260 779 hydrogen bonds defined for protein. 2118 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.08 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3439 1.32 - 1.45: 5408 1.45 - 1.57: 11354 1.57 - 1.70: 0 1.70 - 1.83: 59 Bond restraints: 20260 Sorted by residual: bond pdb=" N CYS N 88 " pdb=" CA CYS N 88 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.20e-02 6.94e+03 1.26e+01 bond pdb=" C LEU X 624 " pdb=" O LEU X 624 " ideal model delta sigma weight residual 1.237 1.198 0.038 1.17e-02 7.31e+03 1.07e+01 bond pdb=" C PHE X 806 " pdb=" O PHE X 806 " ideal model delta sigma weight residual 1.236 1.194 0.043 1.32e-02 5.74e+03 1.05e+01 bond pdb=" N ILE N 87 " pdb=" CA ILE N 87 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.20e-02 6.94e+03 9.55e+00 bond pdb=" C PRO X 599 " pdb=" O PRO X 599 " ideal model delta sigma weight residual 1.239 1.201 0.038 1.27e-02 6.20e+03 8.86e+00 ... (remaining 20255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 27104 2.43 - 4.85: 322 4.85 - 7.28: 40 7.28 - 9.71: 4 9.71 - 12.13: 1 Bond angle restraints: 27471 Sorted by residual: angle pdb=" N PRO X 424 " pdb=" CA PRO X 424 " pdb=" C PRO X 424 " ideal model delta sigma weight residual 111.38 123.51 -12.13 1.59e+00 3.96e-01 5.82e+01 angle pdb=" N ILE X 869 " pdb=" CA ILE X 869 " pdb=" CB ILE X 869 " ideal model delta sigma weight residual 110.72 118.28 -7.56 1.09e+00 8.42e-01 4.81e+01 angle pdb=" N ASN X 602 " pdb=" CA ASN X 602 " pdb=" C ASN X 602 " ideal model delta sigma weight residual 114.62 108.39 6.23 1.14e+00 7.69e-01 2.99e+01 angle pdb=" CA PHE X 600 " pdb=" CB PHE X 600 " pdb=" CG PHE X 600 " ideal model delta sigma weight residual 113.80 108.43 5.37 1.00e+00 1.00e+00 2.89e+01 angle pdb=" C CYS X 423 " pdb=" N PRO X 424 " pdb=" CA PRO X 424 " ideal model delta sigma weight residual 119.85 125.11 -5.26 1.01e+00 9.80e-01 2.71e+01 ... (remaining 27466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10950 17.97 - 35.93: 1042 35.93 - 53.90: 148 53.90 - 71.86: 41 71.86 - 89.83: 18 Dihedral angle restraints: 12199 sinusoidal: 4997 harmonic: 7202 Sorted by residual: dihedral pdb=" CA LYS N 223 " pdb=" C LYS N 223 " pdb=" N LEU N 224 " pdb=" CA LEU N 224 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA TYR X 139 " pdb=" C TYR X 139 " pdb=" N GLN X 140 " pdb=" CA GLN X 140 " ideal model delta harmonic sigma weight residual -180.00 -158.13 -21.87 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA MET X 22 " pdb=" C MET X 22 " pdb=" N ARG X 23 " pdb=" CA ARG X 23 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 12196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2666 0.071 - 0.143: 361 0.143 - 0.214: 15 0.214 - 0.286: 4 0.286 - 0.357: 3 Chirality restraints: 3049 Sorted by residual: chirality pdb=" CA PRO X 424 " pdb=" N PRO X 424 " pdb=" C PRO X 424 " pdb=" CB PRO X 424 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA ASP X1306 " pdb=" N ASP X1306 " pdb=" C ASP X1306 " pdb=" CB ASP X1306 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASP X1304 " pdb=" N ASP X1304 " pdb=" C ASP X1304 " pdb=" CB ASP X1304 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 3046 not shown) Planarity restraints: 3547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP X1304 " 0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C ASP X1304 " -0.074 2.00e-02 2.50e+03 pdb=" O ASP X1304 " 0.029 2.00e-02 2.50e+03 pdb=" N GLU X1305 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR X 771 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C TYR X 771 " -0.063 2.00e-02 2.50e+03 pdb=" O TYR X 771 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS X 772 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 429 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ALA N 429 " 0.055 2.00e-02 2.50e+03 pdb=" O ALA N 429 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU N 430 " -0.018 2.00e-02 2.50e+03 ... (remaining 3544 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1498 2.74 - 3.28: 20486 3.28 - 3.82: 32288 3.82 - 4.36: 41007 4.36 - 4.90: 70400 Nonbonded interactions: 165679 Sorted by model distance: nonbonded pdb=" OD1 ASP X1007 " pdb=" N HIS X1008 " model vdw 2.198 3.120 nonbonded pdb=" O ASP N 606 " pdb=" ND2 ASN N 750 " model vdw 2.210 3.120 nonbonded pdb=" OH TYR X 246 " pdb=" O ALA X 732 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR N 51 " pdb=" OE1 GLU N 176 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR N 512 " pdb=" O LYS N 572 " model vdw 2.230 3.040 ... (remaining 165674 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: 1.830 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.340 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 : 0.004 0.057 20261 Z= 0.187 Angle : 0.636 12.132 27473 Z= 0.381 Chirality : 0.048 0.357 3049 Planarity : 0.004 0.063 3547 Dihedral : 14.534 89.826 7542 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.40 % Allowed : 0.80 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.17), residues: 2413 helix: 0.46 (0.20), residues: 699 sheet: -1.19 (0.27), residues: 359 loop : -1.22 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 336 TYR 0.017 0.001 TYR X 139 PHE 0.019 0.001 PHE X 806 TRP 0.018 0.001 TRP X1056 HIS 0.003 0.001 HIS X 227 Details of bonding type rmsd covalent geometry : bond 0.00365 (20260) covalent geometry : angle 0.63599 (27471) SS BOND : bond 0.00355 ( 1) SS BOND : angle 1.96788 ( 2) hydrogen bonds : bond 0.20416 ( 747) hydrogen bonds : angle 7.75322 ( 2118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 278 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: N 335 ASP cc_start: 0.7332 (p0) cc_final: 0.7063 (p0) REVERT: N 530 THR cc_start: 0.8096 (m) cc_final: 0.7832 (m) REVERT: N 999 ASN cc_start: 0.8410 (t0) cc_final: 0.8049 (t0) REVERT: X 240 SER cc_start: 0.8311 (t) cc_final: 0.8095 (t) REVERT: X 265 GLU cc_start: 0.7913 (tt0) cc_final: 0.7675 (tt0) REVERT: X 829 ASN cc_start: 0.7397 (t0) cc_final: 0.7194 (t0) REVERT: X 1163 TYR cc_start: 0.6889 (m-80) cc_final: 0.6665 (m-80) outliers start: 9 outliers final: 4 residues processed: 285 average time/residue: 0.1487 time to fit residues: 67.0809 Evaluate side-chains 227 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 223 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 624 LEU Chi-restraints excluded: chain X residue 806 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 ASN N 225 GLN N 343 ASN N 346 ASN N1017 ASN X 309 ASN X1092 GLN X1207 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.134199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114600 restraints weight = 25648.636| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.03 r_work: 0.3228 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 20261 Z= 0.349 Angle : 0.720 11.874 27473 Z= 0.385 Chirality : 0.053 0.201 3049 Planarity : 0.005 0.066 3547 Dihedral : 5.905 54.680 2618 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.09 % Allowed : 9.57 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.16), residues: 2413 helix: 0.39 (0.19), residues: 718 sheet: -1.32 (0.27), residues: 345 loop : -1.42 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 324 TYR 0.023 0.002 TYR N 190 PHE 0.024 0.002 PHE X 187 TRP 0.014 0.002 TRP X 992 HIS 0.007 0.001 HIS N 942 Details of bonding type rmsd covalent geometry : bond 0.00839 (20260) covalent geometry : angle 0.72002 (27471) SS BOND : bond 0.00910 ( 1) SS BOND : angle 0.90157 ( 2) hydrogen bonds : bond 0.05953 ( 747) hydrogen bonds : angle 5.71006 ( 2118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 254 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: N 439 ILE cc_start: 0.7168 (mt) cc_final: 0.6812 (mt) REVERT: N 530 THR cc_start: 0.8578 (m) cc_final: 0.8317 (m) REVERT: N 689 ASN cc_start: 0.6921 (m-40) cc_final: 0.6702 (m110) REVERT: N 895 SER cc_start: 0.8345 (t) cc_final: 0.8104 (m) REVERT: N 949 ASP cc_start: 0.8914 (t70) cc_final: 0.8685 (t0) REVERT: N 999 ASN cc_start: 0.8776 (t0) cc_final: 0.8556 (t0) REVERT: X 239 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8410 (mm) REVERT: X 240 SER cc_start: 0.8816 (t) cc_final: 0.8611 (t) REVERT: X 675 LEU cc_start: 0.8469 (tp) cc_final: 0.8256 (tt) outliers start: 47 outliers final: 32 residues processed: 280 average time/residue: 0.1512 time to fit residues: 66.8518 Evaluate side-chains 251 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 218 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 454 LEU Chi-restraints excluded: chain N residue 464 THR Chi-restraints excluded: chain N residue 469 ILE Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 625 ASP Chi-restraints excluded: chain N residue 665 CYS Chi-restraints excluded: chain N residue 822 SER Chi-restraints excluded: chain N residue 986 ASP Chi-restraints excluded: chain N residue 1062 ASN Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 324 ARG Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 470 VAL Chi-restraints excluded: chain X residue 571 GLU Chi-restraints excluded: chain X residue 679 THR Chi-restraints excluded: chain X residue 806 PHE Chi-restraints excluded: chain X residue 825 ASP Chi-restraints excluded: chain X residue 904 ASP Chi-restraints excluded: chain X residue 922 ASP Chi-restraints excluded: chain X residue 943 THR Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 999 SER Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1305 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 196 optimal weight: 1.9990 chunk 108 optimal weight: 0.0030 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 GLN N 290 ASN N 750 ASN N 942 HIS X 396 ASN X1207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122000 restraints weight = 25257.431| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.04 r_work: 0.3312 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20261 Z= 0.116 Angle : 0.530 8.714 27473 Z= 0.287 Chirality : 0.045 0.173 3049 Planarity : 0.004 0.065 3547 Dihedral : 5.278 59.754 2616 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.91 % Allowed : 11.88 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.17), residues: 2413 helix: 1.05 (0.19), residues: 718 sheet: -1.27 (0.28), residues: 348 loop : -1.28 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 336 TYR 0.016 0.001 TYR N 38 PHE 0.033 0.001 PHE N 252 TRP 0.009 0.001 TRP X 48 HIS 0.004 0.001 HIS X1008 Details of bonding type rmsd covalent geometry : bond 0.00252 (20260) covalent geometry : angle 0.52969 (27471) SS BOND : bond 0.00494 ( 1) SS BOND : angle 0.20835 ( 2) hydrogen bonds : bond 0.04328 ( 747) hydrogen bonds : angle 5.10829 ( 2118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 0.838 Fit side-chains REVERT: N 439 ILE cc_start: 0.6821 (mt) cc_final: 0.6476 (mt) REVERT: N 530 THR cc_start: 0.8476 (m) cc_final: 0.8135 (m) REVERT: X 30 LYS cc_start: 0.8324 (mtmt) cc_final: 0.8051 (pttm) REVERT: X 211 LYS cc_start: 0.5808 (ttmm) cc_final: 0.5461 (mtpp) REVERT: X 675 LEU cc_start: 0.8372 (tp) cc_final: 0.8159 (tt) outliers start: 43 outliers final: 25 residues processed: 291 average time/residue: 0.1432 time to fit residues: 66.7453 Evaluate side-chains 246 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 751 ILE Chi-restraints excluded: chain N residue 884 ASP Chi-restraints excluded: chain N residue 986 ASP Chi-restraints excluded: chain N residue 1115 ASN Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 309 ASN Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 470 VAL Chi-restraints excluded: chain X residue 569 ILE Chi-restraints excluded: chain X residue 571 GLU Chi-restraints excluded: chain X residue 806 PHE Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 999 SER Chi-restraints excluded: chain X residue 1207 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 236 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 chunk 214 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 689 ASN X1207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121548 restraints weight = 25116.309| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.04 r_work: 0.3315 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20261 Z= 0.129 Angle : 0.526 8.212 27473 Z= 0.285 Chirality : 0.045 0.173 3049 Planarity : 0.004 0.068 3547 Dihedral : 5.185 58.374 2616 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.45 % Allowed : 13.08 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.17), residues: 2413 helix: 1.25 (0.20), residues: 712 sheet: -1.19 (0.27), residues: 359 loop : -1.24 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 336 TYR 0.015 0.001 TYR N 416 PHE 0.024 0.001 PHE N 252 TRP 0.009 0.001 TRP X 992 HIS 0.003 0.001 HIS X 562 Details of bonding type rmsd covalent geometry : bond 0.00294 (20260) covalent geometry : angle 0.52559 (27471) SS BOND : bond 0.00643 ( 1) SS BOND : angle 0.48764 ( 2) hydrogen bonds : bond 0.04120 ( 747) hydrogen bonds : angle 4.93009 ( 2118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 242 time to evaluate : 0.825 Fit side-chains REVERT: X 30 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8035 (pttm) REVERT: X 211 LYS cc_start: 0.6171 (ttmm) cc_final: 0.5878 (mtpp) REVERT: X 239 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8311 (mm) REVERT: X 399 GLN cc_start: 0.8077 (tt0) cc_final: 0.7773 (tt0) REVERT: X 675 LEU cc_start: 0.8377 (tp) cc_final: 0.8162 (tt) outliers start: 55 outliers final: 38 residues processed: 274 average time/residue: 0.1515 time to fit residues: 66.2325 Evaluate side-chains 266 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 464 THR Chi-restraints excluded: chain N residue 469 ILE Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 751 ILE Chi-restraints excluded: chain N residue 807 ILE Chi-restraints excluded: chain N residue 867 ASN Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 986 ASP Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 309 ASN Chi-restraints excluded: chain X residue 324 ARG Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 470 VAL Chi-restraints excluded: chain X residue 569 ILE Chi-restraints excluded: chain X residue 571 GLU Chi-restraints excluded: chain X residue 679 THR Chi-restraints excluded: chain X residue 806 PHE Chi-restraints excluded: chain X residue 825 ASP Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1259 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 218 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 164 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 GLN X 322 GLN X 721 GLN X 890 ASN X1119 ASN X1207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114072 restraints weight = 25624.601| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.03 r_work: 0.3217 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 20261 Z= 0.330 Angle : 0.675 11.625 27473 Z= 0.362 Chirality : 0.051 0.203 3049 Planarity : 0.005 0.076 3547 Dihedral : 5.678 56.059 2616 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.03 % Allowed : 13.75 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.17), residues: 2413 helix: 0.71 (0.19), residues: 739 sheet: -1.13 (0.28), residues: 364 loop : -1.43 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 367 TYR 0.021 0.002 TYR X1239 PHE 0.025 0.002 PHE X 187 TRP 0.017 0.002 TRP X1056 HIS 0.004 0.001 HIS X 739 Details of bonding type rmsd covalent geometry : bond 0.00800 (20260) covalent geometry : angle 0.67522 (27471) SS BOND : bond 0.00879 ( 1) SS BOND : angle 1.15709 ( 2) hydrogen bonds : bond 0.05075 ( 747) hydrogen bonds : angle 5.21525 ( 2118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 0.938 Fit side-chains REVERT: N 118 ASP cc_start: 0.6222 (OUTLIER) cc_final: 0.4251 (m-30) REVERT: N 895 SER cc_start: 0.8415 (t) cc_final: 0.8131 (m) REVERT: N 1043 ASP cc_start: 0.7577 (p0) cc_final: 0.7372 (p0) REVERT: X 30 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8077 (pttm) REVERT: X 239 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8417 (mt) REVERT: X 399 GLN cc_start: 0.8228 (tt0) cc_final: 0.7886 (tt0) REVERT: X 603 MET cc_start: 0.7937 (mmm) cc_final: 0.7518 (tpp) REVERT: X 1265 HIS cc_start: 0.4076 (OUTLIER) cc_final: 0.3800 (m170) outliers start: 68 outliers final: 44 residues processed: 268 average time/residue: 0.1493 time to fit residues: 64.1504 Evaluate side-chains 266 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 219 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 454 LEU Chi-restraints excluded: chain N residue 464 THR Chi-restraints excluded: chain N residue 469 ILE Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain N residue 510 LEU Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 625 ASP Chi-restraints excluded: chain N residue 665 CYS Chi-restraints excluded: chain N residue 807 ILE Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 946 LEU Chi-restraints excluded: chain N residue 986 ASP Chi-restraints excluded: chain N residue 1055 ASP Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 309 ASN Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 470 VAL Chi-restraints excluded: chain X residue 569 ILE Chi-restraints excluded: chain X residue 571 GLU Chi-restraints excluded: chain X residue 679 THR Chi-restraints excluded: chain X residue 685 VAL Chi-restraints excluded: chain X residue 806 PHE Chi-restraints excluded: chain X residue 825 ASP Chi-restraints excluded: chain X residue 904 ASP Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1265 HIS Chi-restraints excluded: chain X residue 1305 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 23 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 140 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 227 optimal weight: 0.7980 chunk 239 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 GLN N 689 ASN X 353 GLN X 887 GLN X1207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119610 restraints weight = 25124.361| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.03 r_work: 0.3294 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20261 Z= 0.129 Angle : 0.537 8.550 27473 Z= 0.290 Chirality : 0.045 0.180 3049 Planarity : 0.004 0.071 3547 Dihedral : 5.301 58.723 2616 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.67 % Allowed : 15.53 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.17), residues: 2413 helix: 1.16 (0.19), residues: 728 sheet: -1.26 (0.28), residues: 356 loop : -1.33 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 367 TYR 0.015 0.001 TYR N 249 PHE 0.036 0.001 PHE N 252 TRP 0.010 0.001 TRP X 992 HIS 0.004 0.001 HIS X1008 Details of bonding type rmsd covalent geometry : bond 0.00294 (20260) covalent geometry : angle 0.53664 (27471) SS BOND : bond 0.00627 ( 1) SS BOND : angle 0.74218 ( 2) hydrogen bonds : bond 0.04076 ( 747) hydrogen bonds : angle 4.89450 ( 2118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 234 time to evaluate : 0.807 Fit side-chains REVERT: N 200 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: N 249 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8616 (t80) REVERT: N 680 LEU cc_start: 0.8308 (tp) cc_final: 0.8100 (tp) REVERT: X 30 LYS cc_start: 0.8355 (mtmt) cc_final: 0.8045 (pttm) REVERT: X 141 GLU cc_start: 0.6585 (mp0) cc_final: 0.6324 (mt-10) REVERT: X 399 GLN cc_start: 0.8136 (tt0) cc_final: 0.7799 (tt0) REVERT: X 603 MET cc_start: 0.7874 (mmm) cc_final: 0.7539 (tpp) REVERT: X 675 LEU cc_start: 0.8371 (tp) cc_final: 0.8160 (tt) REVERT: X 1137 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: X 1208 GLU cc_start: 0.7007 (tp30) cc_final: 0.6287 (tt0) REVERT: X 1265 HIS cc_start: 0.4197 (OUTLIER) cc_final: 0.3809 (m170) outliers start: 60 outliers final: 40 residues processed: 272 average time/residue: 0.1437 time to fit residues: 63.0113 Evaluate side-chains 265 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 249 TYR Chi-restraints excluded: chain N residue 273 GLU Chi-restraints excluded: chain N residue 307 ILE Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 469 ILE Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 751 ILE Chi-restraints excluded: chain N residue 807 ILE Chi-restraints excluded: chain N residue 822 SER Chi-restraints excluded: chain N residue 867 ASN Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 986 ASP Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 309 ASN Chi-restraints excluded: chain X residue 324 ARG Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 470 VAL Chi-restraints excluded: chain X residue 569 ILE Chi-restraints excluded: chain X residue 571 GLU Chi-restraints excluded: chain X residue 679 THR Chi-restraints excluded: chain X residue 685 VAL Chi-restraints excluded: chain X residue 806 PHE Chi-restraints excluded: chain X residue 825 ASP Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1137 GLU Chi-restraints excluded: chain X residue 1265 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 39 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 143 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 GLN N 689 ASN X1119 ASN X1207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117572 restraints weight = 25398.966| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.03 r_work: 0.3264 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20261 Z= 0.189 Angle : 0.576 9.415 27473 Z= 0.308 Chirality : 0.047 0.178 3049 Planarity : 0.004 0.073 3547 Dihedral : 5.374 59.276 2616 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.12 % Allowed : 15.40 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.17), residues: 2413 helix: 1.10 (0.19), residues: 728 sheet: -1.17 (0.28), residues: 358 loop : -1.34 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 336 TYR 0.015 0.001 TYR N 249 PHE 0.038 0.002 PHE N 252 TRP 0.012 0.001 TRP N 45 HIS 0.003 0.001 HIS X 739 Details of bonding type rmsd covalent geometry : bond 0.00453 (20260) covalent geometry : angle 0.57563 (27471) SS BOND : bond 0.00708 ( 1) SS BOND : angle 0.94752 ( 2) hydrogen bonds : bond 0.04320 ( 747) hydrogen bonds : angle 4.91171 ( 2118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 235 time to evaluate : 0.808 Fit side-chains REVERT: N 118 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.4216 (m-30) REVERT: N 200 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: N 249 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8647 (t80) REVERT: N 390 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7467 (tt) REVERT: N 608 ILE cc_start: 0.8096 (pt) cc_final: 0.7865 (pt) REVERT: N 680 LEU cc_start: 0.8282 (tp) cc_final: 0.8062 (tp) REVERT: N 920 GLU cc_start: 0.8383 (pt0) cc_final: 0.8080 (pt0) REVERT: N 1006 GLU cc_start: 0.8549 (tt0) cc_final: 0.8322 (tt0) REVERT: X 30 LYS cc_start: 0.8361 (mtmt) cc_final: 0.8060 (pttm) REVERT: X 141 GLU cc_start: 0.6680 (mp0) cc_final: 0.6437 (mt-10) REVERT: X 144 ASN cc_start: 0.6913 (t0) cc_final: 0.6700 (t0) REVERT: X 239 ILE cc_start: 0.8740 (mm) cc_final: 0.8349 (mt) REVERT: X 399 GLN cc_start: 0.8132 (tt0) cc_final: 0.7792 (tt0) REVERT: X 603 MET cc_start: 0.7831 (mmm) cc_final: 0.7576 (tpp) REVERT: X 658 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7278 (mt) REVERT: X 1137 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7764 (pt0) REVERT: X 1208 GLU cc_start: 0.7160 (tp30) cc_final: 0.6417 (tt0) REVERT: X 1265 HIS cc_start: 0.4308 (OUTLIER) cc_final: 0.3844 (m170) outliers start: 70 outliers final: 46 residues processed: 281 average time/residue: 0.1453 time to fit residues: 65.4486 Evaluate side-chains 276 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 249 TYR Chi-restraints excluded: chain N residue 273 GLU Chi-restraints excluded: chain N residue 307 ILE Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 454 LEU Chi-restraints excluded: chain N residue 464 THR Chi-restraints excluded: chain N residue 469 ILE Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 751 ILE Chi-restraints excluded: chain N residue 762 ILE Chi-restraints excluded: chain N residue 781 THR Chi-restraints excluded: chain N residue 807 ILE Chi-restraints excluded: chain N residue 822 SER Chi-restraints excluded: chain N residue 867 ASN Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 986 ASP Chi-restraints excluded: chain N residue 1050 PHE Chi-restraints excluded: chain N residue 1055 ASP Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 309 ASN Chi-restraints excluded: chain X residue 324 ARG Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 470 VAL Chi-restraints excluded: chain X residue 569 ILE Chi-restraints excluded: chain X residue 571 GLU Chi-restraints excluded: chain X residue 658 LEU Chi-restraints excluded: chain X residue 679 THR Chi-restraints excluded: chain X residue 685 VAL Chi-restraints excluded: chain X residue 806 PHE Chi-restraints excluded: chain X residue 825 ASP Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1137 GLU Chi-restraints excluded: chain X residue 1265 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 171 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 233 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 160 optimal weight: 0.9990 chunk 121 optimal weight: 0.0060 chunk 1 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 GLN N 547 ASN N 737 ASN N1017 ASN X 918 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121699 restraints weight = 25233.935| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.05 r_work: 0.3327 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20261 Z= 0.107 Angle : 0.531 11.319 27473 Z= 0.283 Chirality : 0.044 0.156 3049 Planarity : 0.004 0.071 3547 Dihedral : 5.107 58.009 2616 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.36 % Allowed : 16.42 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.17), residues: 2413 helix: 1.41 (0.20), residues: 720 sheet: -1.22 (0.28), residues: 352 loop : -1.27 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 336 TYR 0.015 0.001 TYR X1267 PHE 0.035 0.001 PHE N 252 TRP 0.027 0.001 TRP N 45 HIS 0.003 0.001 HIS N 478 Details of bonding type rmsd covalent geometry : bond 0.00234 (20260) covalent geometry : angle 0.53107 (27471) SS BOND : bond 0.00536 ( 1) SS BOND : angle 0.62628 ( 2) hydrogen bonds : bond 0.03771 ( 747) hydrogen bonds : angle 4.73202 ( 2118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 0.805 Fit side-chains REVERT: N 118 ASP cc_start: 0.5577 (OUTLIER) cc_final: 0.4016 (m-30) REVERT: N 249 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8653 (t80) REVERT: N 390 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7471 (tt) REVERT: N 608 ILE cc_start: 0.8092 (pt) cc_final: 0.7879 (pt) REVERT: N 646 ILE cc_start: 0.8451 (tp) cc_final: 0.8067 (tp) REVERT: N 895 SER cc_start: 0.8318 (t) cc_final: 0.8075 (m) REVERT: N 1006 GLU cc_start: 0.8531 (tt0) cc_final: 0.8306 (tt0) REVERT: X 30 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8020 (pttm) REVERT: X 399 GLN cc_start: 0.7961 (tt0) cc_final: 0.7643 (tt0) REVERT: X 603 MET cc_start: 0.7748 (mmm) cc_final: 0.7521 (tpp) REVERT: X 658 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7174 (mt) REVERT: X 918 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7634 (p0) REVERT: X 1137 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7545 (pt0) REVERT: X 1208 GLU cc_start: 0.7212 (tp30) cc_final: 0.6838 (pm20) REVERT: X 1265 HIS cc_start: 0.4077 (OUTLIER) cc_final: 0.3809 (m170) outliers start: 53 outliers final: 39 residues processed: 281 average time/residue: 0.1426 time to fit residues: 64.3554 Evaluate side-chains 272 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 249 TYR Chi-restraints excluded: chain N residue 307 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 469 ILE Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 751 ILE Chi-restraints excluded: chain N residue 762 ILE Chi-restraints excluded: chain N residue 781 THR Chi-restraints excluded: chain N residue 867 ASN Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 1013 GLU Chi-restraints excluded: chain N residue 1055 ASP Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 309 ASN Chi-restraints excluded: chain X residue 324 ARG Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 423 CYS Chi-restraints excluded: chain X residue 470 VAL Chi-restraints excluded: chain X residue 569 ILE Chi-restraints excluded: chain X residue 658 LEU Chi-restraints excluded: chain X residue 679 THR Chi-restraints excluded: chain X residue 685 VAL Chi-restraints excluded: chain X residue 806 PHE Chi-restraints excluded: chain X residue 825 ASP Chi-restraints excluded: chain X residue 918 ASN Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1137 GLU Chi-restraints excluded: chain X residue 1265 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 183 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 192 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 GLN N 689 ASN N 750 ASN X 918 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115471 restraints weight = 25414.026| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.02 r_work: 0.3236 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 20261 Z= 0.277 Angle : 0.648 11.154 27473 Z= 0.344 Chirality : 0.050 0.183 3049 Planarity : 0.004 0.074 3547 Dihedral : 5.480 59.902 2616 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.76 % Allowed : 16.07 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.17), residues: 2413 helix: 0.91 (0.19), residues: 742 sheet: -0.95 (0.29), residues: 353 loop : -1.39 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 336 TYR 0.022 0.002 TYR X1239 PHE 0.040 0.002 PHE N 252 TRP 0.034 0.002 TRP N 45 HIS 0.003 0.001 HIS X 739 Details of bonding type rmsd covalent geometry : bond 0.00674 (20260) covalent geometry : angle 0.64790 (27471) SS BOND : bond 0.00754 ( 1) SS BOND : angle 1.10099 ( 2) hydrogen bonds : bond 0.04662 ( 747) hydrogen bonds : angle 5.01742 ( 2118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 0.975 Fit side-chains REVERT: N 118 ASP cc_start: 0.5979 (OUTLIER) cc_final: 0.4213 (m-30) REVERT: N 200 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: N 390 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7439 (tt) REVERT: N 630 GLU cc_start: 0.7916 (pp20) cc_final: 0.7677 (pp20) REVERT: N 895 SER cc_start: 0.8636 (t) cc_final: 0.8272 (m) REVERT: N 920 GLU cc_start: 0.8401 (pt0) cc_final: 0.8117 (pt0) REVERT: X 30 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8063 (pttm) REVERT: X 144 ASN cc_start: 0.7008 (t0) cc_final: 0.6712 (t0) REVERT: X 239 ILE cc_start: 0.8773 (mm) cc_final: 0.8455 (mt) REVERT: X 329 LYS cc_start: 0.7692 (ttpp) cc_final: 0.7104 (tttm) REVERT: X 399 GLN cc_start: 0.8186 (tt0) cc_final: 0.7826 (tt0) REVERT: X 658 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7295 (mt) REVERT: X 918 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7590 (p0) REVERT: X 1137 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7770 (pt0) REVERT: X 1208 GLU cc_start: 0.7110 (tp30) cc_final: 0.6438 (tt0) REVERT: X 1265 HIS cc_start: 0.4249 (OUTLIER) cc_final: 0.3774 (m170) outliers start: 62 outliers final: 45 residues processed: 270 average time/residue: 0.1330 time to fit residues: 57.9919 Evaluate side-chains 276 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 200 GLU Chi-restraints excluded: chain N residue 273 GLU Chi-restraints excluded: chain N residue 307 ILE Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 464 THR Chi-restraints excluded: chain N residue 469 ILE Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain N residue 510 LEU Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 590 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 751 ILE Chi-restraints excluded: chain N residue 762 ILE Chi-restraints excluded: chain N residue 781 THR Chi-restraints excluded: chain N residue 807 ILE Chi-restraints excluded: chain N residue 822 SER Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 946 LEU Chi-restraints excluded: chain N residue 1050 PHE Chi-restraints excluded: chain N residue 1055 ASP Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 309 ASN Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 423 CYS Chi-restraints excluded: chain X residue 470 VAL Chi-restraints excluded: chain X residue 569 ILE Chi-restraints excluded: chain X residue 658 LEU Chi-restraints excluded: chain X residue 679 THR Chi-restraints excluded: chain X residue 685 VAL Chi-restraints excluded: chain X residue 806 PHE Chi-restraints excluded: chain X residue 825 ASP Chi-restraints excluded: chain X residue 918 ASN Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1137 GLU Chi-restraints excluded: chain X residue 1265 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 177 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120873 restraints weight = 25070.365| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.03 r_work: 0.3316 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20261 Z= 0.118 Angle : 0.552 10.198 27473 Z= 0.295 Chirality : 0.045 0.184 3049 Planarity : 0.004 0.072 3547 Dihedral : 5.142 57.738 2614 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.05 % Allowed : 17.31 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.17), residues: 2413 helix: 1.35 (0.20), residues: 716 sheet: -1.21 (0.29), residues: 350 loop : -1.28 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 336 TYR 0.015 0.001 TYR X1267 PHE 0.039 0.001 PHE N 252 TRP 0.037 0.001 TRP N 45 HIS 0.003 0.001 HIS X1008 Details of bonding type rmsd covalent geometry : bond 0.00264 (20260) covalent geometry : angle 0.55188 (27471) SS BOND : bond 0.00557 ( 1) SS BOND : angle 0.62215 ( 2) hydrogen bonds : bond 0.03891 ( 747) hydrogen bonds : angle 4.80055 ( 2118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.723 Fit side-chains REVERT: N 118 ASP cc_start: 0.5637 (OUTLIER) cc_final: 0.4073 (m-30) REVERT: N 390 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7447 (tt) REVERT: N 606 ASP cc_start: 0.8057 (t0) cc_final: 0.7803 (t0) REVERT: N 617 MET cc_start: 0.1959 (mmt) cc_final: 0.1108 (tmm) REVERT: N 646 ILE cc_start: 0.8487 (tp) cc_final: 0.8072 (tp) REVERT: N 895 SER cc_start: 0.8575 (t) cc_final: 0.8232 (m) REVERT: X 30 LYS cc_start: 0.8351 (mtmt) cc_final: 0.8035 (pttm) REVERT: X 144 ASN cc_start: 0.6744 (t0) cc_final: 0.6469 (t0) REVERT: X 239 ILE cc_start: 0.8719 (mm) cc_final: 0.8336 (mt) REVERT: X 399 GLN cc_start: 0.8002 (tt0) cc_final: 0.7667 (tt0) REVERT: X 658 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7157 (mt) REVERT: X 1137 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: X 1163 TYR cc_start: 0.7420 (m-80) cc_final: 0.7032 (m-80) REVERT: X 1208 GLU cc_start: 0.7164 (tp30) cc_final: 0.6793 (pm20) REVERT: X 1265 HIS cc_start: 0.4203 (OUTLIER) cc_final: 0.3790 (m170) outliers start: 46 outliers final: 39 residues processed: 266 average time/residue: 0.1128 time to fit residues: 48.2651 Evaluate side-chains 272 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 123 LEU Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 307 ILE Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain N residue 390 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 469 ILE Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 751 ILE Chi-restraints excluded: chain N residue 762 ILE Chi-restraints excluded: chain N residue 781 THR Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 1055 ASP Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 309 ASN Chi-restraints excluded: chain X residue 324 ARG Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 423 CYS Chi-restraints excluded: chain X residue 470 VAL Chi-restraints excluded: chain X residue 569 ILE Chi-restraints excluded: chain X residue 658 LEU Chi-restraints excluded: chain X residue 679 THR Chi-restraints excluded: chain X residue 685 VAL Chi-restraints excluded: chain X residue 806 PHE Chi-restraints excluded: chain X residue 825 ASP Chi-restraints excluded: chain X residue 918 ASN Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1137 GLU Chi-restraints excluded: chain X residue 1265 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 219 optimal weight: 2.9990 chunk 215 optimal weight: 0.2980 chunk 240 optimal weight: 2.9990 chunk 164 optimal weight: 0.0000 chunk 57 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 184 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 150 GLN X 918 ASN X1057 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121260 restraints weight = 25389.395| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.06 r_work: 0.3304 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20261 Z= 0.123 Angle : 0.541 12.047 27473 Z= 0.289 Chirality : 0.045 0.172 3049 Planarity : 0.004 0.072 3547 Dihedral : 5.006 55.465 2614 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.14 % Allowed : 17.36 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.17), residues: 2413 helix: 1.47 (0.20), residues: 712 sheet: -1.18 (0.29), residues: 350 loop : -1.24 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 336 TYR 0.015 0.001 TYR X1267 PHE 0.038 0.001 PHE N 252 TRP 0.033 0.001 TRP N 45 HIS 0.003 0.001 HIS N 478 Details of bonding type rmsd covalent geometry : bond 0.00279 (20260) covalent geometry : angle 0.54148 (27471) SS BOND : bond 0.00529 ( 1) SS BOND : angle 0.55823 ( 2) hydrogen bonds : bond 0.03839 ( 747) hydrogen bonds : angle 4.73262 ( 2118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4706.69 seconds wall clock time: 82 minutes 6.25 seconds (4926.25 seconds total)