Starting phenix.real_space_refine on Tue Jun 17 13:50:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8byp_16330/06_2025/8byp_16330_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8byp_16330/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8byp_16330/06_2025/8byp_16330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8byp_16330/06_2025/8byp_16330.map" model { file = "/net/cci-nas-00/data/ceres_data/8byp_16330/06_2025/8byp_16330_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8byp_16330/06_2025/8byp_16330_neut.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.70, per 1000 atoms: 0.74 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: 5.75 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.76 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: 12.12 Time building geometry restraints manager: 6.19 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: 153.540 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: 0.050 Extract box with map and model: 0.960 Check model and map are aligned: 0.230 Set scattering table: 0.230 Process input model: 56.660 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 215.570 ------------------------------------------------------------------------------- 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 : 9.76 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (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 TRP 0.018 0.001 TRP X1056 HIS 0.003 0.001 HIS X 227 PHE 0.019 0.001 PHE X 806 TYR 0.017 0.001 TYR X 139 ARG 0.009 0.000 ARG N 336 Details of bonding type rmsd hydrogen bonds : bond 0.20416 ( 747) hydrogen bonds : angle 7.75322 ( 2118) SS BOND : bond 0.00355 ( 1) SS BOND : angle 1.96788 ( 2) covalent geometry : bond 0.00365 (20260) covalent geometry : angle 0.63599 (27471) *********************** 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 : 3.521 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: 0.4283 time to fit residues: 192.8001 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 : 2.568 ------------------------------------------------------------------------------- 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 203 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 123 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 114 optimal weight: 0.0270 chunk 140 optimal weight: 0.2980 chunk 218 optimal weight: 6.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 43 HIS N 70 ASN N 343 ASN N 346 ASN N1017 ASN X 309 ASN X1207 ASN X1233 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.144713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125138 restraints weight = 25203.855| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.06 r_work: 0.3370 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20261 Z= 0.116 Angle : 0.543 8.570 27473 Z= 0.293 Chirality : 0.045 0.165 3049 Planarity : 0.004 0.056 3547 Dihedral : 5.116 52.848 2618 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.47 % Allowed : 7.61 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2413 helix: 1.06 (0.20), residues: 697 sheet: -1.12 (0.28), residues: 350 loop : -1.14 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 48 HIS 0.004 0.001 HIS X 562 PHE 0.028 0.001 PHE N 115 TYR 0.014 0.001 TYR X1267 ARG 0.004 0.000 ARG X 755 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 747) hydrogen bonds : angle 5.39265 ( 2118) SS BOND : bond 0.00590 ( 1) SS BOND : angle 0.88801 ( 2) covalent geometry : bond 0.00245 (20260) covalent geometry : angle 0.54293 (27471) *********************** 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 309 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 276 time to evaluate : 2.360 Fit side-chains REVERT: N 335 ASP cc_start: 0.7929 (p0) cc_final: 0.7694 (p0) REVERT: N 439 ILE cc_start: 0.6782 (mt) cc_final: 0.6444 (mt) REVERT: N 530 THR cc_start: 0.8426 (m) cc_final: 0.8107 (m) REVERT: N 600 GLU cc_start: 0.7332 (mp0) cc_final: 0.7001 (mm-30) REVERT: N 999 ASN cc_start: 0.8572 (t0) cc_final: 0.8314 (t0) REVERT: X 30 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8112 (pttm) REVERT: X 675 LEU cc_start: 0.8382 (tp) cc_final: 0.8177 (tt) REVERT: X 924 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7378 (mm-30) REVERT: X 1287 ARG cc_start: 0.7708 (mpt180) cc_final: 0.7022 (tmt170) outliers start: 33 outliers final: 20 residues processed: 292 average time/residue: 0.3199 time to fit residues: 147.7402 Evaluate side-chains 259 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 2.199 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain N residue 431 LEU Chi-restraints excluded: chain N residue 454 LEU Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 986 ASP Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 324 ARG Chi-restraints excluded: chain X residue 385 LEU 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 904 ASP 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 1259 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 164 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 208 ASN X 353 GLN X 396 ASN X1008 HIS X1207 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.137841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118186 restraints weight = 25240.931| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.03 r_work: 0.3277 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 20261 Z= 0.234 Angle : 0.603 8.615 27473 Z= 0.325 Chirality : 0.048 0.178 3049 Planarity : 0.004 0.057 3547 Dihedral : 5.365 55.036 2616 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.18 % Allowed : 10.86 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.17), residues: 2413 helix: 1.02 (0.19), residues: 716 sheet: -0.98 (0.28), residues: 348 loop : -1.25 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X1056 HIS 0.004 0.001 HIS N 942 PHE 0.028 0.002 PHE N 115 TYR 0.017 0.002 TYR N 249 ARG 0.006 0.001 ARG N 336 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 747) hydrogen bonds : angle 5.24231 ( 2118) SS BOND : bond 0.00854 ( 1) SS BOND : angle 0.44708 ( 2) covalent geometry : bond 0.00561 (20260) covalent geometry : angle 0.60333 (27471) *********************** 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 302 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 253 time to evaluate : 2.248 Fit side-chains REVERT: N 439 ILE cc_start: 0.6824 (mt) cc_final: 0.6477 (mt) REVERT: N 530 THR cc_start: 0.8543 (m) cc_final: 0.8265 (m) REVERT: N 600 GLU cc_start: 0.7124 (mp0) cc_final: 0.6856 (mm-30) REVERT: N 689 ASN cc_start: 0.6686 (m-40) cc_final: 0.6474 (m110) REVERT: N 736 ASN cc_start: 0.8000 (t0) cc_final: 0.7784 (t0) REVERT: N 999 ASN cc_start: 0.8712 (t0) cc_final: 0.8455 (t0) REVERT: X 30 LYS cc_start: 0.8374 (mtmt) cc_final: 0.8065 (pttm) REVERT: X 52 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8387 (mm-30) REVERT: X 399 GLN cc_start: 0.8172 (tt0) cc_final: 0.7899 (tt0) REVERT: X 675 LEU cc_start: 0.8421 (tp) cc_final: 0.8208 (tt) REVERT: X 1036 LYS cc_start: 0.8279 (mttt) cc_final: 0.7916 (mttt) outliers start: 49 outliers final: 35 residues processed: 282 average time/residue: 0.3131 time to fit residues: 140.7129 Evaluate side-chains 269 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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 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 747 VAL Chi-restraints excluded: chain N residue 986 ASP Chi-restraints excluded: chain N residue 1062 ASN 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 324 ARG Chi-restraints excluded: chain X residue 332 THR 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 645 SER 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 844 GLU 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 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1259 THR Chi-restraints excluded: chain X residue 1305 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 91 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 721 GLN X1207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.139357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119965 restraints weight = 25254.246| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.07 r_work: 0.3316 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1433 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= 0.131 Angle : 0.533 9.713 27473 Z= 0.287 Chirality : 0.045 0.171 3049 Planarity : 0.004 0.067 3547 Dihedral : 5.182 57.511 2616 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.00 % Allowed : 12.68 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2413 helix: 1.28 (0.19), residues: 715 sheet: -1.09 (0.28), residues: 342 loop : -1.21 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 992 HIS 0.003 0.001 HIS X 739 PHE 0.032 0.001 PHE N 115 TYR 0.013 0.001 TYR N 249 ARG 0.004 0.000 ARG N 336 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 747) hydrogen bonds : angle 4.96136 ( 2118) SS BOND : bond 0.00627 ( 1) SS BOND : angle 0.36964 ( 2) covalent geometry : bond 0.00300 (20260) covalent geometry : angle 0.53321 (27471) *********************** 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 303 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 2.406 Fit side-chains REVERT: N 280 LYS cc_start: 0.6803 (pttp) cc_final: 0.5387 (tmtt) REVERT: N 530 THR cc_start: 0.8459 (m) cc_final: 0.8132 (m) REVERT: N 600 GLU cc_start: 0.7200 (mp0) cc_final: 0.6837 (mm-30) REVERT: N 617 MET cc_start: 0.1749 (mmt) cc_final: 0.0580 (ptt) REVERT: N 689 ASN cc_start: 0.6396 (m-40) cc_final: 0.6192 (m110) REVERT: N 999 ASN cc_start: 0.8491 (t0) cc_final: 0.8230 (t0) REVERT: N 1043 ASP cc_start: 0.7516 (p0) cc_final: 0.7316 (p0) REVERT: X 30 LYS cc_start: 0.8305 (mtmt) cc_final: 0.7973 (pttm) REVERT: X 211 LYS cc_start: 0.6097 (ttmm) cc_final: 0.5784 (mtpp) REVERT: X 239 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8371 (mm) REVERT: X 399 GLN cc_start: 0.8122 (tt0) cc_final: 0.7777 (tt0) REVERT: X 675 LEU cc_start: 0.8290 (tp) cc_final: 0.8080 (tt) REVERT: X 948 MET cc_start: 0.8512 (mtp) cc_final: 0.8147 (ttm) outliers start: 45 outliers final: 31 residues processed: 287 average time/residue: 0.3222 time to fit residues: 147.1300 Evaluate side-chains 268 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 3.118 ------------------------------------------------------------------------------- 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 162 LEU 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 473 LEU Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 747 VAL Chi-restraints excluded: chain N residue 822 SER Chi-restraints excluded: chain N residue 867 ASN Chi-restraints excluded: chain N residue 986 ASP 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 239 ILE 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 922 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 75 optimal weight: 0.4980 chunk 221 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 547 ASN N1017 ASN X 322 GLN X1207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120882 restraints weight = 25186.232| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.06 r_work: 0.3320 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20261 Z= 0.132 Angle : 0.526 8.089 27473 Z= 0.285 Chirality : 0.045 0.184 3049 Planarity : 0.004 0.067 3547 Dihedral : 5.118 59.980 2616 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.36 % Allowed : 13.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 2413 helix: 1.36 (0.19), residues: 718 sheet: -1.11 (0.28), residues: 360 loop : -1.18 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 992 HIS 0.002 0.001 HIS X 562 PHE 0.016 0.001 PHE N 733 TYR 0.017 0.001 TYR X 139 ARG 0.006 0.000 ARG N 336 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 747) hydrogen bonds : angle 4.82947 ( 2118) SS BOND : bond 0.00602 ( 1) SS BOND : angle 0.54800 ( 2) covalent geometry : bond 0.00304 (20260) covalent geometry : angle 0.52590 (27471) *********************** 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 301 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 248 time to evaluate : 2.620 Fit side-chains REVERT: N 99 GLU cc_start: 0.7938 (mp0) cc_final: 0.7710 (mp0) REVERT: N 280 LYS cc_start: 0.6866 (pttp) cc_final: 0.5413 (tmtt) REVERT: N 530 THR cc_start: 0.8466 (m) cc_final: 0.8178 (m) REVERT: N 600 GLU cc_start: 0.7113 (mp0) cc_final: 0.6785 (mm-30) REVERT: N 617 MET cc_start: 0.1761 (mmt) cc_final: 0.0712 (ppp) REVERT: N 689 ASN cc_start: 0.6539 (m-40) cc_final: 0.6329 (m110) REVERT: N 999 ASN cc_start: 0.8500 (t0) cc_final: 0.8065 (t0) REVERT: X 30 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7972 (pttm) REVERT: X 211 LYS cc_start: 0.5657 (ttmm) cc_final: 0.5295 (mtpp) REVERT: X 216 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7640 (pt0) REVERT: X 239 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8312 (mm) REVERT: X 399 GLN cc_start: 0.8027 (tt0) cc_final: 0.7694 (tt0) REVERT: X 603 MET cc_start: 0.7888 (mmm) cc_final: 0.7428 (tpp) REVERT: X 675 LEU cc_start: 0.8287 (tp) cc_final: 0.8063 (tt) outliers start: 53 outliers final: 38 residues processed: 277 average time/residue: 0.3505 time to fit residues: 158.2672 Evaluate side-chains 279 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 2.874 ------------------------------------------------------------------------------- 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 159 VAL 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 464 THR Chi-restraints excluded: chain N residue 469 ILE Chi-restraints excluded: chain N residue 473 LEU 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 747 VAL 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 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 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 1259 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 161 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 0.0370 chunk 180 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 290 ASN N 942 HIS X 918 ASN X1207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123049 restraints weight = 25097.621| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.05 r_work: 0.3327 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1665 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= 0.112 Angle : 0.509 8.574 27473 Z= 0.274 Chirality : 0.044 0.171 3049 Planarity : 0.004 0.064 3547 Dihedral : 5.009 59.685 2616 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.49 % Allowed : 14.33 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2413 helix: 1.51 (0.19), residues: 718 sheet: -1.11 (0.28), residues: 360 loop : -1.17 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 992 HIS 0.002 0.001 HIS X 562 PHE 0.014 0.001 PHE N 733 TYR 0.014 0.001 TYR X 139 ARG 0.006 0.000 ARG N 336 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 747) hydrogen bonds : angle 4.71821 ( 2118) SS BOND : bond 0.00527 ( 1) SS BOND : angle 0.48140 ( 2) covalent geometry : bond 0.00250 (20260) covalent geometry : angle 0.50874 (27471) *********************** 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 312 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 256 time to evaluate : 2.293 Fit side-chains REVERT: N 530 THR cc_start: 0.8444 (m) cc_final: 0.8155 (m) REVERT: N 617 MET cc_start: 0.1934 (mmt) cc_final: 0.0787 (ppp) REVERT: N 630 GLU cc_start: 0.7904 (pp20) cc_final: 0.7637 (pp20) REVERT: N 999 ASN cc_start: 0.8428 (t0) cc_final: 0.8125 (t0) REVERT: X 30 LYS cc_start: 0.8274 (mtmt) cc_final: 0.8006 (pttm) REVERT: X 211 LYS cc_start: 0.5690 (ttmm) cc_final: 0.5341 (mtpp) REVERT: X 216 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7605 (pt0) REVERT: X 239 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8298 (mm) REVERT: X 399 GLN cc_start: 0.7998 (tt0) cc_final: 0.7665 (tt0) REVERT: X 675 LEU cc_start: 0.8341 (tp) cc_final: 0.8116 (tt) REVERT: X 762 MET cc_start: 0.7496 (mmm) cc_final: 0.7254 (mmm) REVERT: X 918 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7725 (p0) REVERT: X 1208 GLU cc_start: 0.6857 (tp30) cc_final: 0.6097 (tt0) REVERT: X 1239 TYR cc_start: 0.8965 (p90) cc_final: 0.8584 (p90) REVERT: X 1265 HIS cc_start: 0.4110 (OUTLIER) cc_final: 0.3814 (m170) outliers start: 56 outliers final: 39 residues processed: 289 average time/residue: 0.2940 time to fit residues: 137.2029 Evaluate side-chains 281 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 2.195 ------------------------------------------------------------------------------- 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 159 VAL Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 307 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 747 VAL Chi-restraints excluded: chain N residue 822 SER Chi-restraints excluded: chain N residue 867 ASN 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 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 569 ILE Chi-restraints excluded: chain X residue 571 GLU Chi-restraints excluded: chain X residue 645 SER 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 948 MET 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 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 60 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 174 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 887 GLN ** X 918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120400 restraints weight = 25196.922| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.04 r_work: 0.3307 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20261 Z= 0.163 Angle : 0.537 9.071 27473 Z= 0.289 Chirality : 0.046 0.170 3049 Planarity : 0.004 0.066 3547 Dihedral : 5.104 59.855 2616 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.63 % Allowed : 14.73 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2413 helix: 1.38 (0.19), residues: 724 sheet: -1.10 (0.28), residues: 359 loop : -1.20 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 45 HIS 0.003 0.001 HIS X 739 PHE 0.025 0.001 PHE N 685 TYR 0.017 0.001 TYR X 139 ARG 0.008 0.000 ARG N 336 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 747) hydrogen bonds : angle 4.75538 ( 2118) SS BOND : bond 0.00596 ( 1) SS BOND : angle 0.71931 ( 2) covalent geometry : bond 0.00387 (20260) covalent geometry : angle 0.53701 (27471) *********************** 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: 59 poor density : 246 time to evaluate : 2.424 Fit side-chains REVERT: N 96 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8219 (m-40) REVERT: N 118 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.4173 (m-30) REVERT: N 530 THR cc_start: 0.8483 (m) cc_final: 0.8193 (m) REVERT: N 600 GLU cc_start: 0.7259 (mp0) cc_final: 0.7009 (mm-30) REVERT: N 617 MET cc_start: 0.1818 (mmt) cc_final: 0.1193 (tmm) REVERT: N 999 ASN cc_start: 0.8529 (t0) cc_final: 0.8313 (t0) REVERT: X 30 LYS cc_start: 0.8301 (mtmt) cc_final: 0.8008 (pttm) REVERT: X 239 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8345 (mm) REVERT: X 399 GLN cc_start: 0.8063 (tt0) cc_final: 0.7728 (tt0) REVERT: X 603 MET cc_start: 0.7859 (mmm) cc_final: 0.7427 (tpp) REVERT: X 1208 GLU cc_start: 0.7027 (tp30) cc_final: 0.6188 (tt0) REVERT: X 1265 HIS cc_start: 0.4223 (OUTLIER) cc_final: 0.3879 (m170) outliers start: 59 outliers final: 46 residues processed: 277 average time/residue: 0.3182 time to fit residues: 141.0095 Evaluate side-chains 291 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 241 time to evaluate : 2.417 ------------------------------------------------------------------------------- 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 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 160 LEU Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 307 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 473 LEU 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 747 VAL 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 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 569 ILE Chi-restraints excluded: chain X residue 571 GLU Chi-restraints excluded: chain X residue 645 SER 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 948 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 154 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 225 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 224 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 689 ASN N 737 ASN X 721 GLN X 918 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.142513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123011 restraints weight = 25235.706| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.05 r_work: 0.3340 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20261 Z= 0.112 Angle : 0.509 9.357 27473 Z= 0.275 Chirality : 0.044 0.173 3049 Planarity : 0.004 0.065 3547 Dihedral : 4.962 58.330 2616 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.36 % Allowed : 15.31 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2413 helix: 1.60 (0.19), residues: 717 sheet: -1.08 (0.28), residues: 360 loop : -1.17 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 45 HIS 0.002 0.001 HIS X 562 PHE 0.021 0.001 PHE N 685 TYR 0.013 0.001 TYR X 139 ARG 0.008 0.000 ARG N 336 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 747) hydrogen bonds : angle 4.64252 ( 2118) SS BOND : bond 0.00523 ( 1) SS BOND : angle 0.54029 ( 2) covalent geometry : bond 0.00249 (20260) covalent geometry : angle 0.50946 (27471) *********************** 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 296 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 2.494 Fit side-chains REVERT: N 96 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8206 (m-40) REVERT: N 118 ASP cc_start: 0.5444 (OUTLIER) cc_final: 0.3747 (m-30) REVERT: N 530 THR cc_start: 0.8445 (m) cc_final: 0.8156 (m) REVERT: N 600 GLU cc_start: 0.7119 (mp0) cc_final: 0.6828 (mm-30) REVERT: N 617 MET cc_start: 0.1833 (mmt) cc_final: 0.1264 (tmm) REVERT: N 999 ASN cc_start: 0.8453 (t0) cc_final: 0.8177 (t0) REVERT: X 30 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8000 (pttm) REVERT: X 239 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8297 (mm) REVERT: X 399 GLN cc_start: 0.7991 (tt0) cc_final: 0.7690 (tt0) REVERT: X 603 MET cc_start: 0.7852 (mmm) cc_final: 0.7420 (tpp) REVERT: X 1208 GLU cc_start: 0.7017 (tp30) cc_final: 0.6653 (pm20) REVERT: X 1239 TYR cc_start: 0.8975 (p90) cc_final: 0.8674 (p90) REVERT: X 1265 HIS cc_start: 0.4223 (OUTLIER) cc_final: 0.3882 (m170) outliers start: 53 outliers final: 42 residues processed: 274 average time/residue: 0.2962 time to fit residues: 131.6714 Evaluate side-chains 276 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 2.274 ------------------------------------------------------------------------------- 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 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 160 LEU Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 307 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 473 LEU Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 747 VAL 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 946 LEU 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 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 569 ILE Chi-restraints excluded: chain X residue 645 SER 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 948 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 30 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 890 ASN X1119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119496 restraints weight = 25287.406| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.04 r_work: 0.3296 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20261 Z= 0.182 Angle : 0.557 9.540 27473 Z= 0.299 Chirality : 0.046 0.181 3049 Planarity : 0.004 0.068 3547 Dihedral : 5.125 58.975 2616 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.45 % Allowed : 15.53 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2413 helix: 1.42 (0.19), residues: 724 sheet: -1.09 (0.28), residues: 359 loop : -1.22 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 45 HIS 0.004 0.001 HIS X 739 PHE 0.029 0.002 PHE N 685 TYR 0.016 0.001 TYR X 139 ARG 0.008 0.000 ARG N 336 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 747) hydrogen bonds : angle 4.73660 ( 2118) SS BOND : bond 0.00585 ( 1) SS BOND : angle 0.76331 ( 2) covalent geometry : bond 0.00435 (20260) covalent geometry : angle 0.55679 (27471) *********************** 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: 55 poor density : 236 time to evaluate : 2.232 Fit side-chains REVERT: N 96 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.8226 (m-40) REVERT: N 118 ASP cc_start: 0.5893 (OUTLIER) cc_final: 0.4008 (m-30) REVERT: N 530 THR cc_start: 0.8495 (m) cc_final: 0.8191 (m) REVERT: N 600 GLU cc_start: 0.7100 (mp0) cc_final: 0.6761 (mm-30) REVERT: N 617 MET cc_start: 0.1857 (mmt) cc_final: 0.1207 (tmm) REVERT: N 646 ILE cc_start: 0.8494 (tp) cc_final: 0.8125 (tp) REVERT: N 999 ASN cc_start: 0.8542 (t0) cc_final: 0.8162 (t0) REVERT: X 30 LYS cc_start: 0.8318 (mtmt) cc_final: 0.8019 (pttm) REVERT: X 239 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8258 (mt) REVERT: X 399 GLN cc_start: 0.8037 (tt0) cc_final: 0.7702 (tt0) REVERT: X 603 MET cc_start: 0.7867 (mmm) cc_final: 0.7466 (tpp) REVERT: X 1208 GLU cc_start: 0.7049 (tp30) cc_final: 0.6696 (pm20) REVERT: X 1265 HIS cc_start: 0.4325 (OUTLIER) cc_final: 0.3934 (m170) outliers start: 55 outliers final: 43 residues processed: 269 average time/residue: 0.2930 time to fit residues: 126.8659 Evaluate side-chains 283 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 2.223 ------------------------------------------------------------------------------- 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 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 160 LEU Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 307 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 473 LEU Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 747 VAL 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 946 LEU Chi-restraints excluded: chain N residue 975 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 187 PHE Chi-restraints excluded: chain X residue 239 ILE 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 645 SER 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 948 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 173 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 215 optimal weight: 0.0040 chunk 56 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 689 ASN X 918 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122868 restraints weight = 24930.874| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.06 r_work: 0.3345 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20261 Z= 0.108 Angle : 0.510 9.547 27473 Z= 0.275 Chirality : 0.044 0.173 3049 Planarity : 0.004 0.067 3547 Dihedral : 4.925 56.620 2616 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.14 % Allowed : 16.11 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2413 helix: 1.65 (0.19), residues: 716 sheet: -1.08 (0.28), residues: 360 loop : -1.14 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 45 HIS 0.002 0.001 HIS X 739 PHE 0.016 0.001 PHE N 685 TYR 0.015 0.001 TYR N 249 ARG 0.009 0.000 ARG N 336 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 747) hydrogen bonds : angle 4.59872 ( 2118) SS BOND : bond 0.00470 ( 1) SS BOND : angle 0.51351 ( 2) covalent geometry : bond 0.00239 (20260) covalent geometry : angle 0.51038 (27471) ********************** 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 290 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 242 time to evaluate : 5.347 Fit side-chains REVERT: N 96 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8176 (m-40) REVERT: N 118 ASP cc_start: 0.5319 (OUTLIER) cc_final: 0.3814 (m-30) REVERT: N 530 THR cc_start: 0.8421 (m) cc_final: 0.8124 (m) REVERT: N 617 MET cc_start: 0.1798 (mmt) cc_final: 0.1184 (tmm) REVERT: N 646 ILE cc_start: 0.8408 (tp) cc_final: 0.8067 (tp) REVERT: N 999 ASN cc_start: 0.8438 (t0) cc_final: 0.8118 (t0) REVERT: X 30 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7965 (pttm) REVERT: X 239 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8300 (mm) REVERT: X 359 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7684 (m) REVERT: X 399 GLN cc_start: 0.7929 (tt0) cc_final: 0.7593 (tt0) REVERT: X 603 MET cc_start: 0.7802 (mmm) cc_final: 0.7392 (tpp) REVERT: X 918 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7404 (p0) REVERT: X 1208 GLU cc_start: 0.7180 (tp30) cc_final: 0.6626 (pm20) REVERT: X 1239 TYR cc_start: 0.8967 (p90) cc_final: 0.8599 (p90) REVERT: X 1265 HIS cc_start: 0.4111 (OUTLIER) cc_final: 0.3757 (m170) outliers start: 48 outliers final: 40 residues processed: 271 average time/residue: 0.3786 time to fit residues: 170.4827 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 : 2.689 ------------------------------------------------------------------------------- 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 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 160 LEU Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 307 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 473 LEU 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 747 VAL Chi-restraints excluded: chain N residue 867 ASN Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 946 LEU 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 187 PHE Chi-restraints excluded: chain X residue 239 ILE Chi-restraints excluded: chain X residue 359 VAL 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 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 948 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 69 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 233 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 200 optimal weight: 0.0570 chunk 133 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 918 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123336 restraints weight = 25109.779| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.04 r_work: 0.3340 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20261 Z= 0.115 Angle : 0.511 9.496 27473 Z= 0.276 Chirality : 0.044 0.186 3049 Planarity : 0.004 0.065 3547 Dihedral : 4.892 55.677 2616 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.36 % Allowed : 15.89 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.17), residues: 2413 helix: 1.67 (0.19), residues: 716 sheet: -1.05 (0.28), residues: 360 loop : -1.13 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 45 HIS 0.002 0.001 HIS X 739 PHE 0.019 0.001 PHE N 685 TYR 0.014 0.001 TYR X1267 ARG 0.009 0.000 ARG N 336 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 747) hydrogen bonds : angle 4.57530 ( 2118) SS BOND : bond 0.00486 ( 1) SS BOND : angle 0.52580 ( 2) covalent geometry : bond 0.00258 (20260) covalent geometry : angle 0.51142 (27471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11409.12 seconds wall clock time: 204 minutes 40.09 seconds (12280.09 seconds total)