Starting phenix.real_space_refine on Sat Sep 28 18:05:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/09_2024/8byp_16330_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/09_2024/8byp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/09_2024/8byp_16330.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/09_2024/8byp_16330.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/09_2024/8byp_16330_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byp_16330/09_2024/8byp_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 11.96, per 1000 atoms: 0.60 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: 5.13 Conformation dependent library (CDL) restraints added in 2.4 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: 3.02 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: 8.44 Time building geometry restraints manager: 5.98 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: 4.120 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: 0.000 Extract box with map and model: 0.920 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 48.000 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.470 ------------------------------------------------------------------------------- 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 20260 Z= 0.237 Angle : 0.636 12.132 27471 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 278 time to evaluate : 2.267 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: 0.2947 time to fit residues: 132.0185 Evaluate side-chains 227 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 223 time to evaluate : 2.305 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20260 Z= 0.156 Angle : 0.542 8.522 27471 Z= 0.293 Chirality : 0.045 0.165 3049 Planarity : 0.004 0.056 3547 Dihedral : 5.112 52.907 2618 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.47 % Allowed : 7.57 % Favored : 90.97 % 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: 1.05 (0.20), residues: 698 sheet: -1.12 (0.28), residues: 350 loop : -1.14 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 48 HIS 0.003 0.001 HIS X 562 PHE 0.027 0.001 PHE N 115 TYR 0.014 0.001 TYR X1267 ARG 0.004 0.000 ARG X 755 *********************** 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 fitting. rotamer outliers: 33 poor density : 276 time to evaluate : 2.204 Fit side-chains REVERT: N 335 ASP cc_start: 0.7253 (p0) cc_final: 0.7042 (p0) REVERT: N 439 ILE cc_start: 0.6696 (mt) cc_final: 0.6385 (mt) REVERT: N 530 THR cc_start: 0.8258 (m) cc_final: 0.7922 (m) REVERT: N 999 ASN cc_start: 0.8285 (t0) cc_final: 0.7942 (t0) REVERT: N 1157 LEU cc_start: 0.8910 (tt) cc_final: 0.8708 (tp) REVERT: N 1164 GLU cc_start: 0.7519 (pt0) cc_final: 0.7317 (pt0) REVERT: X 30 LYS cc_start: 0.8297 (mtmt) cc_final: 0.8086 (pttm) REVERT: X 240 SER cc_start: 0.8566 (t) cc_final: 0.8333 (t) REVERT: X 675 LEU cc_start: 0.8132 (tp) cc_final: 0.7890 (tt) REVERT: X 924 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6832 (mm-30) REVERT: X 1287 ARG cc_start: 0.7395 (mpt180) cc_final: 0.6898 (tmt170) outliers start: 33 outliers final: 21 residues processed: 292 average time/residue: 0.3025 time to fit residues: 138.1834 Evaluate side-chains 260 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 239 time to evaluate : 2.273 ------------------------------------------------------------------------------- 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 492 GLU 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 121 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 219 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 195 optimal weight: 0.1980 chunk 217 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 X1207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20260 Z= 0.321 Angle : 0.581 8.062 27471 Z= 0.313 Chirality : 0.047 0.176 3049 Planarity : 0.004 0.057 3547 Dihedral : 5.270 55.373 2616 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.09 % Allowed : 10.64 % Favored : 87.27 % 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: 1.08 (0.19), residues: 715 sheet: -1.04 (0.28), residues: 342 loop : -1.22 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X1056 HIS 0.004 0.001 HIS N 942 PHE 0.028 0.002 PHE N 115 TYR 0.016 0.001 TYR N 249 ARG 0.005 0.000 ARG N 336 *********************** 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 301 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 254 time to evaluate : 2.207 Fit side-chains REVERT: N 439 ILE cc_start: 0.6751 (mt) cc_final: 0.6431 (mt) REVERT: N 736 ASN cc_start: 0.7599 (t0) cc_final: 0.7345 (t0) REVERT: N 999 ASN cc_start: 0.8378 (t0) cc_final: 0.8035 (t0) REVERT: X 30 LYS cc_start: 0.8236 (mtmt) cc_final: 0.8025 (pttm) REVERT: X 52 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7843 (mm-30) REVERT: X 240 SER cc_start: 0.8595 (t) cc_final: 0.8371 (t) REVERT: X 399 GLN cc_start: 0.7807 (tt0) cc_final: 0.7518 (tt0) REVERT: X 675 LEU cc_start: 0.8179 (tp) cc_final: 0.7939 (tt) REVERT: X 874 ASN cc_start: 0.8154 (p0) cc_final: 0.7895 (p0) REVERT: X 948 MET cc_start: 0.8390 (mtp) cc_final: 0.8188 (ttm) REVERT: X 1036 LYS cc_start: 0.8024 (mttt) cc_final: 0.7654 (mttt) outliers start: 47 outliers final: 33 residues processed: 281 average time/residue: 0.3126 time to fit residues: 138.7790 Evaluate side-chains 272 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 239 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 232 optimal weight: 0.0470 chunk 114 optimal weight: 0.8980 chunk 208 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 689 ASN X 353 GLN X 721 GLN X1207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20260 Z= 0.179 Angle : 0.526 9.123 27471 Z= 0.284 Chirality : 0.045 0.174 3049 Planarity : 0.004 0.068 3547 Dihedral : 5.114 57.305 2616 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.96 % Allowed : 12.19 % Favored : 85.85 % 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: 1.32 (0.19), residues: 715 sheet: -1.06 (0.28), residues: 346 loop : -1.18 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 992 HIS 0.003 0.001 HIS X1008 PHE 0.031 0.001 PHE N 115 TYR 0.013 0.001 TYR N 249 ARG 0.004 0.000 ARG N 336 *********************** 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 fitting. rotamer outliers: 44 poor density : 259 time to evaluate : 2.360 Fit side-chains REVERT: N 280 LYS cc_start: 0.6953 (pttp) cc_final: 0.5576 (tmtt) REVERT: N 617 MET cc_start: 0.2292 (mmt) cc_final: 0.1032 (ptt) REVERT: N 736 ASN cc_start: 0.7594 (t0) cc_final: 0.7366 (t0) REVERT: N 999 ASN cc_start: 0.8159 (t0) cc_final: 0.7723 (t0) REVERT: N 1043 ASP cc_start: 0.7205 (p0) cc_final: 0.6998 (p0) REVERT: N 1157 LEU cc_start: 0.8934 (tt) cc_final: 0.8705 (tp) REVERT: X 211 LYS cc_start: 0.6109 (ttmm) cc_final: 0.5786 (mtpp) REVERT: X 239 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8003 (mm) REVERT: X 399 GLN cc_start: 0.7782 (tt0) cc_final: 0.7472 (tt0) REVERT: X 590 LEU cc_start: 0.8078 (mt) cc_final: 0.7865 (mt) REVERT: X 675 LEU cc_start: 0.8118 (tp) cc_final: 0.7886 (tt) REVERT: X 948 MET cc_start: 0.8347 (mtp) cc_final: 0.8033 (ttm) outliers start: 44 outliers final: 29 residues processed: 287 average time/residue: 0.2992 time to fit residues: 135.5050 Evaluate side-chains 268 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 238 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 625 ASP Chi-restraints excluded: chain N residue 747 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 58 optimal weight: 0.0050 overall best weight: 1.7398 ------------------------------------------------------------------------------- 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 509 GLN X1207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20260 Z= 0.231 Angle : 0.543 8.085 27471 Z= 0.292 Chirality : 0.046 0.181 3049 Planarity : 0.004 0.068 3547 Dihedral : 5.158 59.193 2616 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.36 % Allowed : 13.00 % Favored : 84.65 % 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: -0.62 (0.17), residues: 2413 helix: 1.34 (0.19), residues: 715 sheet: -1.12 (0.28), residues: 360 loop : -1.19 (0.16), residues: 1338 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 0.016 0.001 PHE X 187 TYR 0.020 0.001 TYR X 139 ARG 0.007 0.000 ARG N 336 *********************** 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 297 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 244 time to evaluate : 2.280 Fit side-chains REVERT: N 96 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8113 (m-40) REVERT: N 280 LYS cc_start: 0.6978 (pttp) cc_final: 0.5571 (tmtt) REVERT: N 439 ILE cc_start: 0.6530 (mt) cc_final: 0.6313 (mt) REVERT: N 736 ASN cc_start: 0.7616 (t0) cc_final: 0.7385 (t0) REVERT: N 999 ASN cc_start: 0.8218 (t0) cc_final: 0.7918 (t0) REVERT: N 1043 ASP cc_start: 0.7199 (p0) cc_final: 0.6998 (p0) REVERT: X 30 LYS cc_start: 0.8280 (pttm) cc_final: 0.8025 (mtmt) REVERT: X 211 LYS cc_start: 0.5737 (ttmm) cc_final: 0.5398 (mtpp) REVERT: X 239 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8080 (mm) REVERT: X 399 GLN cc_start: 0.7726 (tt0) cc_final: 0.7426 (tt0) REVERT: X 675 LEU cc_start: 0.8136 (tp) cc_final: 0.7903 (tt) REVERT: X 948 MET cc_start: 0.8282 (mtp) cc_final: 0.8030 (ttm) outliers start: 53 outliers final: 41 residues processed: 274 average time/residue: 0.2996 time to fit residues: 131.3052 Evaluate side-chains 279 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 236 time to evaluate : 2.421 ------------------------------------------------------------------------------- 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 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 497 THR Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 625 ASP Chi-restraints excluded: chain N residue 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 1062 ASN 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 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 Chi-restraints excluded: chain X residue 1305 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 233 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 942 HIS X1207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20260 Z= 0.355 Angle : 0.600 10.206 27471 Z= 0.322 Chirality : 0.048 0.186 3049 Planarity : 0.004 0.069 3547 Dihedral : 5.454 57.344 2616 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.94 % Allowed : 13.93 % Favored : 83.13 % 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: -0.80 (0.17), residues: 2413 helix: 1.06 (0.19), residues: 726 sheet: -1.04 (0.28), residues: 346 loop : -1.31 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X1056 HIS 0.003 0.001 HIS N 43 PHE 0.022 0.002 PHE X 187 TYR 0.021 0.002 TYR X 139 ARG 0.005 0.000 ARG N 336 *********************** 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 306 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 240 time to evaluate : 2.236 Fit side-chains REVERT: N 118 ASP cc_start: 0.5882 (OUTLIER) cc_final: 0.3973 (m-30) REVERT: N 999 ASN cc_start: 0.8378 (t0) cc_final: 0.8084 (t0) REVERT: N 1006 GLU cc_start: 0.8250 (tt0) cc_final: 0.8040 (tt0) REVERT: X 211 LYS cc_start: 0.5689 (ttmm) cc_final: 0.5451 (mtpp) REVERT: X 239 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8076 (mt) REVERT: X 399 GLN cc_start: 0.7756 (tt0) cc_final: 0.7448 (tt0) REVERT: X 603 MET cc_start: 0.7795 (mmm) cc_final: 0.7354 (tpp) REVERT: X 1208 GLU cc_start: 0.6746 (tp30) cc_final: 0.6121 (tt0) REVERT: X 1265 HIS cc_start: 0.3823 (OUTLIER) cc_final: 0.3602 (m170) outliers start: 66 outliers final: 47 residues processed: 279 average time/residue: 0.2951 time to fit residues: 131.4759 Evaluate side-chains 275 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 225 time to evaluate : 2.332 ------------------------------------------------------------------------------- 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 118 ASP Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 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 497 THR Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 625 ASP Chi-restraints excluded: chain N residue 665 CYS Chi-restraints excluded: chain N residue 747 VAL Chi-restraints excluded: chain N residue 807 ILE Chi-restraints excluded: chain N residue 822 SER Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 946 LEU Chi-restraints excluded: chain N residue 986 ASP Chi-restraints excluded: chain N residue 1050 PHE Chi-restraints excluded: chain N residue 1062 ASN Chi-restraints excluded: chain N residue 1098 LEU 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 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 904 ASP Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1265 HIS Chi-restraints excluded: chain X residue 1305 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 232 optimal weight: 0.0170 chunk 145 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 290 ASN N 737 ASN X 887 GLN X1207 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20260 Z= 0.238 Angle : 0.551 9.396 27471 Z= 0.296 Chirality : 0.046 0.178 3049 Planarity : 0.004 0.069 3547 Dihedral : 5.302 58.885 2616 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % 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: -0.72 (0.17), residues: 2413 helix: 1.21 (0.19), residues: 725 sheet: -1.06 (0.28), residues: 354 loop : -1.30 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 45 HIS 0.003 0.001 HIS X 739 PHE 0.016 0.001 PHE X 187 TYR 0.017 0.001 TYR X 139 ARG 0.008 0.000 ARG N 336 *********************** 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 281 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 228 time to evaluate : 2.363 Fit side-chains REVERT: N 680 LEU cc_start: 0.7943 (tp) cc_final: 0.7725 (tp) REVERT: N 999 ASN cc_start: 0.8189 (t0) cc_final: 0.7830 (t0) REVERT: X 211 LYS cc_start: 0.5607 (ttmm) cc_final: 0.5378 (mtpp) REVERT: X 239 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8049 (mt) REVERT: X 399 GLN cc_start: 0.7712 (tt0) cc_final: 0.7417 (tt0) REVERT: X 603 MET cc_start: 0.7675 (mmm) cc_final: 0.7284 (tpp) REVERT: X 1208 GLU cc_start: 0.6857 (tp30) cc_final: 0.6243 (tt0) outliers start: 53 outliers final: 42 residues processed: 260 average time/residue: 0.3037 time to fit residues: 125.9302 Evaluate side-chains 269 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 2.476 ------------------------------------------------------------------------------- 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 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 454 LEU Chi-restraints excluded: chain N residue 464 THR Chi-restraints excluded: chain N residue 469 ILE Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain N residue 526 SER Chi-restraints excluded: chain N residue 624 ILE Chi-restraints excluded: chain N residue 625 ASP 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 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 571 GLU Chi-restraints excluded: chain X residue 679 THR Chi-restraints excluded: chain X residue 685 VAL Chi-restraints excluded: chain X residue 806 PHE Chi-restraints excluded: chain X residue 825 ASP Chi-restraints excluded: chain X residue 963 SER Chi-restraints excluded: chain X residue 984 VAL Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1305 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 0.2980 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.0670 chunk 147 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 816 ASN X1207 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20260 Z= 0.145 Angle : 0.514 9.314 27471 Z= 0.276 Chirality : 0.044 0.166 3049 Planarity : 0.004 0.067 3547 Dihedral : 5.001 57.789 2616 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.05 % Allowed : 15.75 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.17), residues: 2413 helix: 1.52 (0.20), residues: 717 sheet: -1.13 (0.28), residues: 360 loop : -1.16 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 45 HIS 0.003 0.001 HIS N 478 PHE 0.014 0.001 PHE N 695 TYR 0.016 0.001 TYR X1267 ARG 0.008 0.000 ARG N 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 252 time to evaluate : 2.517 Fit side-chains REVERT: N 999 ASN cc_start: 0.8047 (t0) cc_final: 0.7756 (t0) REVERT: N 1006 GLU cc_start: 0.8050 (tt0) cc_final: 0.7721 (tt0) REVERT: X 211 LYS cc_start: 0.5640 (ttmm) cc_final: 0.5417 (mtpp) REVERT: X 216 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7000 (pt0) REVERT: X 359 VAL cc_start: 0.7702 (OUTLIER) cc_final: 0.7466 (m) REVERT: X 399 GLN cc_start: 0.7618 (tt0) cc_final: 0.7363 (tt0) REVERT: X 603 MET cc_start: 0.7612 (mmm) cc_final: 0.7260 (tpp) REVERT: X 1239 TYR cc_start: 0.8647 (p90) cc_final: 0.8423 (p90) outliers start: 46 outliers final: 34 residues processed: 277 average time/residue: 0.2953 time to fit residues: 131.2508 Evaluate side-chains 262 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 162 LEU Chi-restraints excluded: chain N residue 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 747 VAL Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 1055 ASP Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 324 ARG Chi-restraints excluded: chain X residue 331 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 chunk 204 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20260 Z= 0.195 Angle : 0.535 10.837 27471 Z= 0.286 Chirality : 0.045 0.176 3049 Planarity : 0.004 0.067 3547 Dihedral : 5.018 56.850 2616 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.91 % Allowed : 16.47 % Favored : 81.62 % 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: -0.50 (0.17), residues: 2413 helix: 1.49 (0.19), residues: 719 sheet: -1.10 (0.28), residues: 355 loop : -1.16 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 45 HIS 0.003 0.001 HIS X 739 PHE 0.028 0.001 PHE N 705 TYR 0.015 0.001 TYR X 139 ARG 0.009 0.000 ARG N 336 *********************** 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 283 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 240 time to evaluate : 2.245 Fit side-chains REVERT: N 118 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.4130 (m-30) REVERT: N 617 MET cc_start: 0.2203 (mmt) cc_final: 0.1518 (tmm) REVERT: N 646 ILE cc_start: 0.8246 (tp) cc_final: 0.7978 (tp) REVERT: N 999 ASN cc_start: 0.8170 (t0) cc_final: 0.7867 (t0) REVERT: X 211 LYS cc_start: 0.5673 (ttmm) cc_final: 0.5471 (mtpp) REVERT: X 359 VAL cc_start: 0.7758 (OUTLIER) cc_final: 0.7540 (m) REVERT: X 367 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7943 (mtp85) REVERT: X 399 GLN cc_start: 0.7635 (tt0) cc_final: 0.7401 (tt0) REVERT: X 603 MET cc_start: 0.7617 (mmm) cc_final: 0.7313 (tpp) REVERT: X 1239 TYR cc_start: 0.8709 (p90) cc_final: 0.8463 (p90) outliers start: 43 outliers final: 36 residues processed: 266 average time/residue: 0.2956 time to fit residues: 125.7881 Evaluate side-chains 273 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 2.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 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 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 762 ILE Chi-restraints excluded: chain N residue 945 THR Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 1055 ASP Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 324 ARG 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 0.8980 chunk 139 optimal weight: 0.0570 chunk 108 optimal weight: 0.0370 chunk 159 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20260 Z= 0.152 Angle : 0.520 11.724 27471 Z= 0.278 Chirality : 0.044 0.171 3049 Planarity : 0.004 0.067 3547 Dihedral : 4.895 54.871 2616 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.87 % Allowed : 16.73 % Favored : 81.40 % 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: -0.43 (0.17), residues: 2413 helix: 1.59 (0.19), residues: 716 sheet: -1.07 (0.28), residues: 360 loop : -1.12 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 45 HIS 0.003 0.001 HIS X1008 PHE 0.014 0.001 PHE X 806 TYR 0.014 0.001 TYR X1267 ARG 0.010 0.000 ARG N 336 ********************** 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 279 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 237 time to evaluate : 2.458 Fit side-chains REVERT: N 96 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8125 (m-40) REVERT: N 118 ASP cc_start: 0.5473 (OUTLIER) cc_final: 0.3862 (m-30) REVERT: N 617 MET cc_start: 0.2146 (mmt) cc_final: 0.1464 (tmm) REVERT: N 646 ILE cc_start: 0.8149 (tp) cc_final: 0.7883 (tp) REVERT: N 999 ASN cc_start: 0.8098 (t0) cc_final: 0.7783 (t0) REVERT: X 52 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7710 (mm-30) REVERT: X 211 LYS cc_start: 0.5665 (ttmm) cc_final: 0.5462 (mtpp) REVERT: X 359 VAL cc_start: 0.7629 (OUTLIER) cc_final: 0.7403 (m) REVERT: X 399 GLN cc_start: 0.7613 (tt0) cc_final: 0.7382 (tt0) REVERT: X 603 MET cc_start: 0.7585 (mmm) cc_final: 0.7279 (tpp) REVERT: X 1137 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7245 (pt0) REVERT: X 1239 TYR cc_start: 0.8693 (p90) cc_final: 0.8427 (p90) outliers start: 42 outliers final: 36 residues processed: 264 average time/residue: 0.2964 time to fit residues: 124.2695 Evaluate side-chains 268 residues out of total 2247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 228 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 96 ASN Chi-restraints excluded: chain N residue 118 ASP Chi-restraints excluded: chain N residue 145 ILE Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 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 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 945 THR Chi-restraints excluded: chain N residue 975 LEU Chi-restraints excluded: chain N residue 1055 ASP Chi-restraints excluded: chain N residue 1168 ILE Chi-restraints excluded: chain X residue 22 MET Chi-restraints excluded: chain X residue 149 LEU Chi-restraints excluded: chain X residue 175 ILE Chi-restraints excluded: chain X residue 187 PHE Chi-restraints excluded: chain X residue 324 ARG 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 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 984 VAL Chi-restraints excluded: chain X residue 1029 THR Chi-restraints excluded: chain X residue 1084 SER Chi-restraints excluded: chain X residue 1137 GLU Chi-restraints excluded: chain X residue 1259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 5.9990 chunk 58 optimal weight: 0.0980 chunk 176 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.139323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.119772 restraints weight = 25311.444| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.04 r_work: 0.3280 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20260 Z= 0.278 Angle : 0.567 9.608 27471 Z= 0.304 Chirality : 0.047 0.175 3049 Planarity : 0.004 0.067 3547 Dihedral : 5.106 56.167 2616 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.05 % Allowed : 16.69 % Favored : 81.26 % 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: -0.56 (0.17), residues: 2413 helix: 1.40 (0.19), residues: 721 sheet: -1.07 (0.28), residues: 356 loop : -1.19 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 45 HIS 0.003 0.001 HIS X 739 PHE 0.019 0.002 PHE N 733 TYR 0.028 0.001 TYR N 416 ARG 0.010 0.000 ARG N 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4227.08 seconds wall clock time: 76 minutes 53.42 seconds (4613.42 seconds total)