Starting phenix.real_space_refine on Wed Jun 18 01:39:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fn4_29305/06_2025/8fn4_29305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fn4_29305/06_2025/8fn4_29305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fn4_29305/06_2025/8fn4_29305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fn4_29305/06_2025/8fn4_29305.map" model { file = "/net/cci-nas-00/data/ceres_data/8fn4_29305/06_2025/8fn4_29305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fn4_29305/06_2025/8fn4_29305.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 118 5.16 5 C 13071 2.51 5 N 3630 2.21 5 O 3819 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20638 Number of models: 1 Model: "" Number of chains: 6 Chain: "1" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2525 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 17, 'TRANS': 301} Chain breaks: 1 Chain: "2" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2876 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 18, 'TRANS': 338} Chain breaks: 6 Chain: "3" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3705 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 20, 'TRANS': 459} Chain: "4" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5790 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 20, 'TRANS': 720} Chain breaks: 1 Chain: "5" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2163 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 15, 'TRANS': 260} Chain: "6" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3579 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 440} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 12.30, per 1000 atoms: 0.60 Number of scatterers: 20638 At special positions: 0 Unit cell: (114.696, 139.122, 190.098, 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 118 16.00 O 3819 8.00 N 3630 7.00 C 13071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.75 Conformation dependent library (CDL) restraints added in 3.4 seconds 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5010 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 11 sheets defined 61.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain '1' and resid 201 through 217 removed outlier: 3.743A pdb=" N LEU 1 207 " --> pdb=" O TYR 1 203 " (cutoff:3.500A) Processing helix chain '1' and resid 234 through 237 removed outlier: 3.939A pdb=" N MET 1 237 " --> pdb=" O PRO 1 234 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 234 through 237' Processing helix chain '1' and resid 245 through 253 removed outlier: 3.548A pdb=" N GLN 1 250 " --> pdb=" O SER 1 246 " (cutoff:3.500A) Processing helix chain '1' and resid 277 through 283 Processing helix chain '1' and resid 349 through 359 Processing helix chain '1' and resid 442 through 459 Processing helix chain '1' and resid 459 through 464 removed outlier: 3.882A pdb=" N VAL 1 464 " --> pdb=" O ALA 1 460 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 59 removed outlier: 3.692A pdb=" N TRP 2 58 " --> pdb=" O VAL 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 60 through 61 No H-bonds generated for 'chain '2' and resid 60 through 61' Processing helix chain '2' and resid 62 through 66 removed outlier: 3.801A pdb=" N LEU 2 66 " --> pdb=" O LEU 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 67 through 78 Processing helix chain '2' and resid 89 through 106 removed outlier: 4.461A pdb=" N GLN 2 106 " --> pdb=" O SER 2 102 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 234 removed outlier: 3.596A pdb=" N ILE 2 232 " --> pdb=" O CYS 2 228 " (cutoff:3.500A) Processing helix chain '2' and resid 264 through 274 Processing helix chain '2' and resid 284 through 286 No H-bonds generated for 'chain '2' and resid 284 through 286' Processing helix chain '2' and resid 287 through 298 removed outlier: 3.582A pdb=" N SER 2 293 " --> pdb=" O ALA 2 289 " (cutoff:3.500A) Processing helix chain '2' and resid 365 through 373 removed outlier: 4.443A pdb=" N ALA 2 371 " --> pdb=" O ARG 2 367 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR 2 372 " --> pdb=" O ILE 2 368 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 2 373 " --> pdb=" O ALA 2 369 " (cutoff:3.500A) Processing helix chain '2' and resid 456 through 473 Processing helix chain '3' and resid 4 through 19 Processing helix chain '3' and resid 24 through 34 Processing helix chain '3' and resid 38 through 62 removed outlier: 3.612A pdb=" N ALA 3 53 " --> pdb=" O THR 3 49 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU 3 54 " --> pdb=" O GLU 3 50 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN 3 59 " --> pdb=" O GLN 3 55 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N CYS 3 60 " --> pdb=" O GLN 3 56 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR 3 61 " --> pdb=" O ARG 3 57 " (cutoff:3.500A) Processing helix chain '3' and resid 65 through 76 removed outlier: 4.076A pdb=" N THR 3 76 " --> pdb=" O GLN 3 72 " (cutoff:3.500A) Processing helix chain '3' and resid 91 through 101 removed outlier: 3.545A pdb=" N PHE 3 101 " --> pdb=" O LEU 3 97 " (cutoff:3.500A) Processing helix chain '3' and resid 106 through 119 removed outlier: 3.850A pdb=" N TYR 3 110 " --> pdb=" O LEU 3 106 " (cutoff:3.500A) Processing helix chain '3' and resid 124 through 134 Processing helix chain '3' and resid 142 through 158 removed outlier: 3.660A pdb=" N ILE 3 146 " --> pdb=" O GLN 3 142 " (cutoff:3.500A) Proline residue: 3 152 - end of helix removed outlier: 3.864A pdb=" N GLU 3 156 " --> pdb=" O PRO 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 159 through 161 No H-bonds generated for 'chain '3' and resid 159 through 161' Processing helix chain '3' and resid 162 through 176 removed outlier: 3.910A pdb=" N HIS 3 168 " --> pdb=" O ARG 3 164 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE 3 176 " --> pdb=" O LEU 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 182 through 194 removed outlier: 3.640A pdb=" N VAL 3 186 " --> pdb=" O GLN 3 182 " (cutoff:3.500A) Processing helix chain '3' and resid 199 through 212 removed outlier: 4.172A pdb=" N GLU 3 212 " --> pdb=" O PHE 3 208 " (cutoff:3.500A) Processing helix chain '3' and resid 214 through 225 Processing helix chain '3' and resid 225 through 236 Processing helix chain '3' and resid 238 through 257 Processing helix chain '3' and resid 260 through 274 removed outlier: 3.677A pdb=" N SER 3 266 " --> pdb=" O ARG 3 262 " (cutoff:3.500A) Processing helix chain '3' and resid 279 through 291 Processing helix chain '3' and resid 297 through 308 Processing helix chain '3' and resid 319 through 335 removed outlier: 4.067A pdb=" N LEU 3 323 " --> pdb=" O LYS 3 319 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER 3 326 " --> pdb=" O GLY 3 322 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE 3 327 " --> pdb=" O LEU 3 323 " (cutoff:3.500A) Processing helix chain '3' and resid 340 through 352 removed outlier: 3.633A pdb=" N ALA 3 350 " --> pdb=" O THR 3 346 " (cutoff:3.500A) Processing helix chain '3' and resid 357 through 371 removed outlier: 3.873A pdb=" N ALA 3 361 " --> pdb=" O GLY 3 357 " (cutoff:3.500A) Processing helix chain '3' and resid 372 through 373 No H-bonds generated for 'chain '3' and resid 372 through 373' Processing helix chain '3' and resid 374 through 376 No H-bonds generated for 'chain '3' and resid 374 through 376' Processing helix chain '3' and resid 377 through 385 Processing helix chain '3' and resid 387 through 396 Processing helix chain '3' and resid 399 through 414 removed outlier: 3.775A pdb=" N HIS 3 412 " --> pdb=" O TYR 3 408 " (cutoff:3.500A) Processing helix chain '3' and resid 418 through 435 Proline residue: 3 427 - end of helix removed outlier: 3.573A pdb=" N VAL 3 433 " --> pdb=" O LEU 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 440 through 457 Processing helix chain '3' and resid 462 through 480 Processing helix chain '4' and resid 337 through 347 Processing helix chain '4' and resid 351 through 360 removed outlier: 3.623A pdb=" N PHE 4 356 " --> pdb=" O GLU 4 352 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN 4 360 " --> pdb=" O PHE 4 356 " (cutoff:3.500A) Processing helix chain '4' and resid 367 through 381 removed outlier: 3.907A pdb=" N GLU 4 380 " --> pdb=" O CYS 4 376 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS 4 381 " --> pdb=" O LEU 4 377 " (cutoff:3.500A) Processing helix chain '4' and resid 385 through 395 Processing helix chain '4' and resid 400 through 414 Processing helix chain '4' and resid 419 through 426 removed outlier: 3.530A pdb=" N ALA 4 425 " --> pdb=" O PRO 4 421 " (cutoff:3.500A) Processing helix chain '4' and resid 439 through 450 removed outlier: 3.619A pdb=" N LEU 4 443 " --> pdb=" O PRO 4 439 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE 4 450 " --> pdb=" O MET 4 446 " (cutoff:3.500A) Processing helix chain '4' and resid 468 through 487 removed outlier: 3.747A pdb=" N LYS 4 472 " --> pdb=" O GLU 4 468 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY 4 487 " --> pdb=" O SER 4 483 " (cutoff:3.500A) Processing helix chain '4' and resid 490 through 501 Processing helix chain '4' and resid 509 through 522 removed outlier: 3.716A pdb=" N GLN 4 521 " --> pdb=" O SER 4 517 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY 4 522 " --> pdb=" O ILE 4 518 " (cutoff:3.500A) Processing helix chain '4' and resid 525 through 539 Processing helix chain '4' and resid 543 through 564 Proline residue: 4 552 - end of helix Processing helix chain '4' and resid 572 through 590 Processing helix chain '4' and resid 594 through 608 removed outlier: 3.880A pdb=" N ALA 4 598 " --> pdb=" O PHE 4 594 " (cutoff:3.500A) Processing helix chain '4' and resid 613 through 615 No H-bonds generated for 'chain '4' and resid 613 through 615' Processing helix chain '4' and resid 616 through 626 Processing helix chain '4' and resid 629 through 633 removed outlier: 4.124A pdb=" N ALA 4 632 " --> pdb=" O ARG 4 629 " (cutoff:3.500A) Processing helix chain '4' and resid 643 through 647 removed outlier: 3.990A pdb=" N GLN 4 646 " --> pdb=" O ASN 4 643 " (cutoff:3.500A) Processing helix chain '4' and resid 648 through 661 removed outlier: 4.137A pdb=" N GLY 4 653 " --> pdb=" O ASP 4 649 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU 4 654 " --> pdb=" O ASP 4 650 " (cutoff:3.500A) Processing helix chain '4' and resid 662 through 666 Processing helix chain '4' and resid 667 through 684 removed outlier: 3.828A pdb=" N LEU 4 683 " --> pdb=" O VAL 4 679 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG 4 684 " --> pdb=" O SER 4 680 " (cutoff:3.500A) Processing helix chain '4' and resid 689 through 704 removed outlier: 3.779A pdb=" N VAL 4 693 " --> pdb=" O PRO 4 689 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN 4 703 " --> pdb=" O VAL 4 699 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY 4 704 " --> pdb=" O TRP 4 700 " (cutoff:3.500A) Processing helix chain '4' and resid 711 through 720 removed outlier: 3.561A pdb=" N LYS 4 720 " --> pdb=" O ASP 4 716 " (cutoff:3.500A) Processing helix chain '4' and resid 721 through 725 Processing helix chain '4' and resid 726 through 737 Processing helix chain '4' and resid 738 through 740 No H-bonds generated for 'chain '4' and resid 738 through 740' Processing helix chain '4' and resid 744 through 751 Processing helix chain '4' and resid 762 through 781 removed outlier: 4.311A pdb=" N GLU 4 775 " --> pdb=" O PHE 4 771 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL 4 776 " --> pdb=" O GLY 4 772 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP 4 778 " --> pdb=" O GLY 4 774 " (cutoff:3.500A) Processing helix chain '4' and resid 783 through 799 removed outlier: 4.335A pdb=" N LEU 4 787 " --> pdb=" O LEU 4 783 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL 4 788 " --> pdb=" O SER 4 784 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA 4 789 " --> pdb=" O HIS 4 785 " (cutoff:3.500A) Processing helix chain '4' and resid 805 through 818 Processing helix chain '4' and resid 824 through 833 removed outlier: 3.829A pdb=" N PHE 4 830 " --> pdb=" O LEU 4 826 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR 4 832 " --> pdb=" O ASN 4 828 " (cutoff:3.500A) Processing helix chain '4' and resid 848 through 856 Processing helix chain '4' and resid 862 through 876 Processing helix chain '4' and resid 877 through 880 removed outlier: 4.161A pdb=" N LEU 4 880 " --> pdb=" O SER 4 877 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 877 through 880' Processing helix chain '4' and resid 884 through 893 removed outlier: 3.851A pdb=" N GLY 4 891 " --> pdb=" O LEU 4 887 " (cutoff:3.500A) Processing helix chain '4' and resid 899 through 913 removed outlier: 3.748A pdb=" N SER 4 908 " --> pdb=" O ASP 4 904 " (cutoff:3.500A) Processing helix chain '4' and resid 918 through 933 removed outlier: 4.221A pdb=" N LEU 4 932 " --> pdb=" O SER 4 928 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY 4 933 " --> pdb=" O PHE 4 929 " (cutoff:3.500A) Processing helix chain '4' and resid 936 through 950 removed outlier: 4.157A pdb=" N SER 4 945 " --> pdb=" O SER 4 941 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER 4 946 " --> pdb=" O ARG 4 942 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE 4 947 " --> pdb=" O MET 4 943 " (cutoff:3.500A) Processing helix chain '4' and resid 951 through 954 Processing helix chain '4' and resid 957 through 969 removed outlier: 3.527A pdb=" N VAL 4 961 " --> pdb=" O ALA 4 957 " (cutoff:3.500A) Processing helix chain '4' and resid 978 through 990 removed outlier: 3.650A pdb=" N LEU 4 983 " --> pdb=" O HIS 4 979 " (cutoff:3.500A) Processing helix chain '4' and resid 995 through 1009 removed outlier: 3.628A pdb=" N LEU 41004 " --> pdb=" O GLY 41000 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL 41005 " --> pdb=" O LYS 41001 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR 41009 " --> pdb=" O VAL 41005 " (cutoff:3.500A) Processing helix chain '4' and resid 1013 through 1030 removed outlier: 3.609A pdb=" N VAL 41017 " --> pdb=" O HIS 41013 " (cutoff:3.500A) Processing helix chain '4' and resid 1034 through 1048 Processing helix chain '4' and resid 1052 through 1064 removed outlier: 3.643A pdb=" N ARG 41056 " --> pdb=" O HIS 41052 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU 41057 " --> pdb=" O GLN 41053 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN 41058 " --> pdb=" O GLY 41054 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA 41061 " --> pdb=" O GLU 41057 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU 41062 " --> pdb=" O ASN 41058 " (cutoff:3.500A) Processing helix chain '4' and resid 1074 through 1085 Processing helix chain '5' and resid 34 through 51 removed outlier: 3.869A pdb=" N VAL 5 39 " --> pdb=" O ARG 5 35 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N HIS 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG 5 43 " --> pdb=" O VAL 5 39 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP 5 44 " --> pdb=" O HIS 5 40 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS 5 47 " --> pdb=" O ARG 5 43 " (cutoff:3.500A) Processing helix chain '5' and resid 67 through 71 Processing helix chain '5' and resid 91 through 93 No H-bonds generated for 'chain '5' and resid 91 through 93' Processing helix chain '5' and resid 94 through 107 removed outlier: 3.609A pdb=" N SER 5 101 " --> pdb=" O GLU 5 97 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N MET 5 102 " --> pdb=" O PHE 5 98 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG 5 103 " --> pdb=" O MET 5 99 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) Processing helix chain '5' and resid 115 through 120 Processing helix chain '5' and resid 147 through 159 removed outlier: 3.578A pdb=" N HIS 5 151 " --> pdb=" O ASN 5 147 " (cutoff:3.500A) Processing helix chain '5' and resid 180 through 185 removed outlier: 3.959A pdb=" N TYR 5 184 " --> pdb=" O PRO 5 180 " (cutoff:3.500A) Processing helix chain '5' and resid 198 through 210 Processing helix chain '5' and resid 212 through 216 removed outlier: 3.863A pdb=" N THR 5 215 " --> pdb=" O GLN 5 212 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU 5 216 " --> pdb=" O PRO 5 213 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 212 through 216' Processing helix chain '5' and resid 246 through 255 Processing helix chain '5' and resid 265 through 272 removed outlier: 3.512A pdb=" N LYS 5 270 " --> pdb=" O SER 5 266 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU 5 271 " --> pdb=" O GLU 5 267 " (cutoff:3.500A) Processing helix chain '5' and resid 274 through 278 Processing helix chain '6' and resid 62 through 81 removed outlier: 3.712A pdb=" N GLN 6 72 " --> pdb=" O THR 6 68 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY 6 81 " --> pdb=" O HIS 6 77 " (cutoff:3.500A) Processing helix chain '6' and resid 83 through 97 removed outlier: 3.656A pdb=" N ALA 6 87 " --> pdb=" O ASN 6 83 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA 6 96 " --> pdb=" O ARG 6 92 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 108 Processing helix chain '6' and resid 109 through 119 removed outlier: 3.635A pdb=" N ALA 6 116 " --> pdb=" O LEU 6 112 " (cutoff:3.500A) Processing helix chain '6' and resid 125 through 133 removed outlier: 3.692A pdb=" N ARG 6 129 " --> pdb=" O ALA 6 125 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP 6 133 " --> pdb=" O ARG 6 129 " (cutoff:3.500A) Processing helix chain '6' and resid 146 through 154 Processing helix chain '6' and resid 163 through 174 removed outlier: 3.534A pdb=" N GLU 6 167 " --> pdb=" O ARG 6 163 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS 6 172 " --> pdb=" O MET 6 168 " (cutoff:3.500A) Processing helix chain '6' and resid 181 through 196 removed outlier: 3.908A pdb=" N LYS 6 194 " --> pdb=" O SER 6 190 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR 6 195 " --> pdb=" O ALA 6 191 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY 6 196 " --> pdb=" O PHE 6 192 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 216 removed outlier: 4.511A pdb=" N VAL 6 216 " --> pdb=" O THR 6 212 " (cutoff:3.500A) Processing helix chain '6' and resid 222 through 235 removed outlier: 3.550A pdb=" N ILE 6 226 " --> pdb=" O ALA 6 222 " (cutoff:3.500A) Processing helix chain '6' and resid 238 through 252 removed outlier: 3.650A pdb=" N PHE 6 242 " --> pdb=" O ASP 6 238 " (cutoff:3.500A) Processing helix chain '6' and resid 257 through 270 Proline residue: 6 263 - end of helix Processing helix chain '6' and resid 276 through 290 removed outlier: 3.979A pdb=" N ALA 6 283 " --> pdb=" O SER 6 279 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR 6 284 " --> pdb=" O LYS 6 280 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS 6 285 " --> pdb=" O ARG 6 281 " (cutoff:3.500A) Processing helix chain '6' and resid 291 through 293 No H-bonds generated for 'chain '6' and resid 291 through 293' Processing helix chain '6' and resid 294 through 309 removed outlier: 3.545A pdb=" N GLY 6 309 " --> pdb=" O PHE 6 305 " (cutoff:3.500A) Processing helix chain '6' and resid 312 through 326 removed outlier: 3.776A pdb=" N GLU 6 325 " --> pdb=" O ASN 6 321 " (cutoff:3.500A) Processing helix chain '6' and resid 334 through 346 removed outlier: 4.148A pdb=" N PHE 6 342 " --> pdb=" O THR 6 338 " (cutoff:3.500A) Processing helix chain '6' and resid 350 through 363 removed outlier: 3.727A pdb=" N ASP 6 354 " --> pdb=" O PRO 6 350 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN 6 355 " --> pdb=" O GLU 6 351 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU 6 361 " --> pdb=" O ALA 6 357 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA 6 362 " --> pdb=" O GLU 6 358 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL 6 363 " --> pdb=" O ARG 6 359 " (cutoff:3.500A) Processing helix chain '6' and resid 368 through 379 removed outlier: 3.610A pdb=" N SER 6 373 " --> pdb=" O ALA 6 369 " (cutoff:3.500A) Processing helix chain '6' and resid 386 through 400 removed outlier: 4.111A pdb=" N ARG 6 392 " --> pdb=" O GLU 6 388 " (cutoff:3.500A) Processing helix chain '6' and resid 405 through 419 Processing helix chain '6' and resid 423 through 434 removed outlier: 3.820A pdb=" N ALA 6 427 " --> pdb=" O GLN 6 423 " (cutoff:3.500A) Processing helix chain '6' and resid 435 through 441 removed outlier: 3.583A pdb=" N CYS 6 438 " --> pdb=" O VAL 6 435 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG 6 439 " --> pdb=" O TYR 6 436 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU 6 441 " --> pdb=" O CYS 6 438 " (cutoff:3.500A) Processing helix chain '6' and resid 442 through 456 Processing helix chain '6' and resid 460 through 474 Proline residue: 6 466 - end of helix Processing helix chain '6' and resid 474 through 480 Processing helix chain '6' and resid 481 through 483 No H-bonds generated for 'chain '6' and resid 481 through 483' Processing helix chain '6' and resid 484 through 496 removed outlier: 3.954A pdb=" N ASP 6 493 " --> pdb=" O GLU 6 489 " (cutoff:3.500A) Processing helix chain '6' and resid 500 through 509 removed outlier: 3.649A pdb=" N SER 6 509 " --> pdb=" O GLN 6 505 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 156 through 158 removed outlier: 6.542A pdb=" N LEU 1 342 " --> pdb=" O LEU 1 325 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR 1 327 " --> pdb=" O LEU 1 340 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU 1 340 " --> pdb=" O THR 1 327 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP 1 329 " --> pdb=" O VAL 1 338 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL 1 338 " --> pdb=" O TRP 1 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 156 through 158 removed outlier: 6.542A pdb=" N LEU 1 342 " --> pdb=" O LEU 1 325 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR 1 327 " --> pdb=" O LEU 1 340 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU 1 340 " --> pdb=" O THR 1 327 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP 1 329 " --> pdb=" O VAL 1 338 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL 1 338 " --> pdb=" O TRP 1 329 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE 1 227 " --> pdb=" O TYR 1 425 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TYR 1 425 " --> pdb=" O PHE 1 227 " (cutoff:3.500A) removed outlier: 9.294A pdb=" N LYS 1 229 " --> pdb=" O VAL 1 423 " (cutoff:3.500A) removed outlier: 12.515A pdb=" N VAL 1 423 " --> pdb=" O LYS 1 229 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU 1 383 " --> pdb=" O LEU 1 411 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU 1 380 " --> pdb=" O LYS 1 299 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LYS 1 299 " --> pdb=" O LEU 1 380 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR 1 382 " --> pdb=" O THR 1 297 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP 1 310 " --> pdb=" O VAL 1 315 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL 1 315 " --> pdb=" O ASP 1 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 362 through 363 Processing sheet with id=AA4, first strand: chain '2' and resid 178 through 179 removed outlier: 7.187A pdb=" N LEU 2 178 " --> pdb=" O ILE 2 347 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP 2 339 " --> pdb=" O ALA 2 360 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA 2 360 " --> pdb=" O ASP 2 339 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL 2 358 " --> pdb=" O PHE 2 341 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL 2 343 " --> pdb=" O TYR 2 356 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR 2 356 " --> pdb=" O VAL 2 343 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N HIS 2 345 " --> pdb=" O LEU 2 354 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU 2 354 " --> pdb=" O HIS 2 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 178 through 179 removed outlier: 7.187A pdb=" N LEU 2 178 " --> pdb=" O ILE 2 347 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP 2 339 " --> pdb=" O ALA 2 360 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA 2 360 " --> pdb=" O ASP 2 339 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL 2 358 " --> pdb=" O PHE 2 341 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL 2 343 " --> pdb=" O TYR 2 356 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR 2 356 " --> pdb=" O VAL 2 343 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N HIS 2 345 " --> pdb=" O LEU 2 354 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU 2 354 " --> pdb=" O HIS 2 345 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TYR 2 441 " --> pdb=" O ALA 2 245 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N LYS 2 247 " --> pdb=" O LEU 2 439 " (cutoff:3.500A) removed outlier: 12.841A pdb=" N LEU 2 439 " --> pdb=" O LYS 2 247 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR 2 416 " --> pdb=" O PRO 2 446 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N CYS 2 399 " --> pdb=" O LEU 2 427 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS 2 406 " --> pdb=" O GLU 2 305 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU 2 305 " --> pdb=" O LYS 2 406 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ALA 2 408 " --> pdb=" O GLN 2 303 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLN 2 303 " --> pdb=" O ALA 2 408 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N LYS 2 410 " --> pdb=" O SER 2 301 " (cutoff:3.500A) removed outlier: 9.546A pdb=" N SER 2 301 " --> pdb=" O LYS 2 410 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET 2 333 " --> pdb=" O GLU 2 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 190 through 191 Processing sheet with id=AA7, first strand: chain '5' and resid 57 through 61 removed outlier: 6.600A pdb=" N ALA 5 13 " --> pdb=" O HIS 5 59 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N MET 5 61 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL 5 15 " --> pdb=" O MET 5 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain '5' and resid 131 through 134 removed outlier: 6.185A pdb=" N ILE 5 138 " --> pdb=" O PHE 5 170 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU 5 172 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL 5 140 " --> pdb=" O LEU 5 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 192 through 196 removed outlier: 6.010A pdb=" N LEU 5 193 " --> pdb=" O VAL 5 220 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU 5 222 " --> pdb=" O LEU 5 193 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N THR 5 195 " --> pdb=" O LEU 5 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain '5' and resid 228 through 229 removed outlier: 6.007A pdb=" N VAL 5 240 " --> pdb=" O ILE 5 261 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL 5 263 " --> pdb=" O VAL 5 240 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL 5 242 " --> pdb=" O VAL 5 263 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3186 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: 7.47 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6779 1.34 - 1.45: 2447 1.45 - 1.57: 11615 1.57 - 1.69: 0 1.69 - 1.81: 180 Bond restraints: 21021 Sorted by residual: bond pdb=" CA ARG 4 502 " pdb=" C ARG 4 502 " ideal model delta sigma weight residual 1.522 1.477 0.045 1.41e-02 5.03e+03 1.03e+01 bond pdb=" C ARG 4 502 " pdb=" N ALA 4 503 " ideal model delta sigma weight residual 1.331 1.309 0.022 1.29e-02 6.01e+03 2.86e+00 bond pdb=" C ARG 4 502 " pdb=" O ARG 4 502 " ideal model delta sigma weight residual 1.236 1.218 0.018 1.28e-02 6.10e+03 2.01e+00 bond pdb=" CA PRO 1 285 " pdb=" C PRO 1 285 " ideal model delta sigma weight residual 1.526 1.515 0.011 8.50e-03 1.38e+04 1.66e+00 bond pdb=" C GLN 1 279 " pdb=" O GLN 1 279 " ideal model delta sigma weight residual 1.244 1.231 0.012 1.00e-02 1.00e+04 1.52e+00 ... (remaining 21016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 27938 1.64 - 3.27: 468 3.27 - 4.91: 59 4.91 - 6.55: 10 6.55 - 8.18: 3 Bond angle restraints: 28478 Sorted by residual: angle pdb=" N GLY 1 282 " pdb=" CA GLY 1 282 " pdb=" C GLY 1 282 " ideal model delta sigma weight residual 113.24 108.46 4.78 1.31e+00 5.83e-01 1.33e+01 angle pdb=" CA GLN 1 279 " pdb=" C GLN 1 279 " pdb=" N PRO 1 280 " ideal model delta sigma weight residual 120.77 117.32 3.45 9.70e-01 1.06e+00 1.27e+01 angle pdb=" N VAL 4 501 " pdb=" CA VAL 4 501 " pdb=" C VAL 4 501 " ideal model delta sigma weight residual 111.77 108.48 3.29 1.04e+00 9.25e-01 1.00e+01 angle pdb=" N ALA 1 284 " pdb=" CA ALA 1 284 " pdb=" C ALA 1 284 " ideal model delta sigma weight residual 109.48 113.91 -4.43 1.44e+00 4.82e-01 9.47e+00 angle pdb=" N ASN 3 3 " pdb=" CA ASN 3 3 " pdb=" C ASN 3 3 " ideal model delta sigma weight residual 111.00 119.18 -8.18 2.80e+00 1.28e-01 8.54e+00 ... (remaining 28473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 11758 17.96 - 35.93: 811 35.93 - 53.89: 187 53.89 - 71.86: 25 71.86 - 89.82: 11 Dihedral angle restraints: 12792 sinusoidal: 5104 harmonic: 7688 Sorted by residual: dihedral pdb=" CA ILE 4 751 " pdb=" C ILE 4 751 " pdb=" N ASP 4 752 " pdb=" CA ASP 4 752 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ALA 5 73 " pdb=" C ALA 5 73 " pdb=" N ASP 5 74 " pdb=" CA ASP 5 74 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA TYR 6 334 " pdb=" C TYR 6 334 " pdb=" N ILE 6 335 " pdb=" CA ILE 6 335 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 12789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2020 0.031 - 0.062: 896 0.062 - 0.092: 245 0.092 - 0.123: 106 0.123 - 0.154: 10 Chirality restraints: 3277 Sorted by residual: chirality pdb=" CB ILE 4 751 " pdb=" CA ILE 4 751 " pdb=" CG1 ILE 4 751 " pdb=" CG2 ILE 4 751 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN 3 3 " pdb=" N ASN 3 3 " pdb=" C ASN 3 3 " pdb=" CB ASN 3 3 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CB VAL 4 426 " pdb=" CA VAL 4 426 " pdb=" CG1 VAL 4 426 " pdb=" CG2 VAL 4 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 3274 not shown) Planarity restraints: 3678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU 3 362 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C LEU 3 362 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU 3 362 " 0.011 2.00e-02 2.50e+03 pdb=" N THR 3 363 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL 4 501 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.73e+00 pdb=" C VAL 4 501 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL 4 501 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG 4 502 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE 4 366 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO 4 367 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO 4 367 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO 4 367 " 0.022 5.00e-02 4.00e+02 ... (remaining 3675 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2489 2.75 - 3.28: 21433 3.28 - 3.82: 33333 3.82 - 4.36: 38156 4.36 - 4.90: 65200 Nonbonded interactions: 160611 Sorted by model distance: nonbonded pdb=" OD1 ASP 6 105 " pdb=" OG SER 6 108 " model vdw 2.208 3.040 nonbonded pdb=" ND2 ASN 4 899 " pdb=" O VAL 6 58 " model vdw 2.214 3.120 nonbonded pdb=" OE1 GLN 5 174 " pdb=" OH TYR 5 184 " model vdw 2.225 3.040 nonbonded pdb=" NZ LYS 4 863 " pdb=" O SER 6 59 " model vdw 2.226 3.120 nonbonded pdb=" O ILE 2 456 " pdb=" OG1 THR 2 460 " model vdw 2.230 3.040 ... (remaining 160606 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 48.880 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.003 0.045 21021 Z= 0.150 Angle : 0.545 8.185 28478 Z= 0.299 Chirality : 0.039 0.154 3277 Planarity : 0.004 0.040 3678 Dihedral : 13.163 89.819 7782 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.80 % Allowed : 8.40 % Favored : 90.80 % 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: -0.53 (0.17), residues: 2597 helix: 0.44 (0.14), residues: 1466 sheet: -0.52 (0.35), residues: 219 loop : -1.53 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 4 700 HIS 0.002 0.001 HIS 2 48 PHE 0.021 0.001 PHE 5 165 TYR 0.012 0.001 TYR 1 247 ARG 0.003 0.000 ARG 6 233 Details of bonding type rmsd hydrogen bonds : bond 0.14566 ( 1071) hydrogen bonds : angle 6.05520 ( 3186) covalent geometry : bond 0.00319 (21021) covalent geometry : angle 0.54523 (28478) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 230 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 309 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8327 (mt) REVERT: 1 311 ASN cc_start: 0.7497 (p0) cc_final: 0.7217 (p0) REVERT: 2 235 MET cc_start: -0.0313 (tpp) cc_final: -0.1328 (tpt) REVERT: 2 455 ASP cc_start: 0.5367 (t70) cc_final: 0.5033 (m-30) REVERT: 3 122 MET cc_start: 0.7760 (mtt) cc_final: 0.7453 (mtp) REVERT: 4 355 MET cc_start: 0.8373 (mpp) cc_final: 0.7683 (mpp) REVERT: 4 603 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6996 (t-170) REVERT: 4 709 THR cc_start: 0.8798 (t) cc_final: 0.8407 (m) REVERT: 6 307 TYR cc_start: 0.8282 (m-80) cc_final: 0.7198 (m-80) outliers start: 18 outliers final: 4 residues processed: 242 average time/residue: 0.3312 time to fit residues: 129.2366 Evaluate side-chains 171 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 165 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 309 LEU Chi-restraints excluded: chain 4 residue 430 PHE Chi-restraints excluded: chain 4 residue 603 HIS Chi-restraints excluded: chain 5 residue 159 GLU Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 367 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 106 GLN ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.130594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105294 restraints weight = 42817.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.103482 restraints weight = 34241.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.104928 restraints weight = 34674.546| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21021 Z= 0.219 Angle : 0.642 13.483 28478 Z= 0.333 Chirality : 0.043 0.163 3277 Planarity : 0.005 0.047 3678 Dihedral : 5.300 51.582 2870 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.55 % Allowed : 12.06 % Favored : 85.40 % 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: -0.51 (0.17), residues: 2597 helix: 0.50 (0.14), residues: 1482 sheet: -0.73 (0.33), residues: 253 loop : -1.59 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 2 443 HIS 0.005 0.001 HIS 5 236 PHE 0.028 0.002 PHE 5 165 TYR 0.017 0.002 TYR 6 495 ARG 0.005 0.000 ARG 5 94 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 1071) hydrogen bonds : angle 4.91194 ( 3186) covalent geometry : bond 0.00514 (21021) covalent geometry : angle 0.64188 (28478) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 138 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7681 (tp) REVERT: 1 309 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8428 (mt) REVERT: 1 376 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: 2 219 MET cc_start: 0.7382 (mmp) cc_final: 0.6931 (mtt) REVERT: 2 235 MET cc_start: -0.2299 (tpp) cc_final: -0.2793 (tpt) REVERT: 2 419 LEU cc_start: 0.5197 (tp) cc_final: 0.4685 (mt) REVERT: 2 455 ASP cc_start: 0.5829 (t70) cc_final: 0.5532 (m-30) REVERT: 3 122 MET cc_start: 0.7945 (mtt) cc_final: 0.7611 (mtp) REVERT: 3 330 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7175 (mt0) REVERT: 3 447 LEU cc_start: 0.7680 (mt) cc_final: 0.7143 (tp) REVERT: 4 355 MET cc_start: 0.8287 (mpp) cc_final: 0.7571 (mpp) REVERT: 4 603 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6736 (t-170) REVERT: 5 70 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8503 (tt) REVERT: 5 86 MET cc_start: 0.7600 (mmt) cc_final: 0.6954 (mmt) REVERT: 6 307 TYR cc_start: 0.8166 (m-80) cc_final: 0.7357 (m-80) outliers start: 57 outliers final: 27 residues processed: 223 average time/residue: 0.3692 time to fit residues: 133.2346 Evaluate side-chains 199 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 138 LEU Chi-restraints excluded: chain 1 residue 309 LEU Chi-restraints excluded: chain 1 residue 376 GLU Chi-restraints excluded: chain 1 residue 426 SER Chi-restraints excluded: chain 2 residue 120 ILE Chi-restraints excluded: chain 2 residue 293 SER Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 79 LEU Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 330 GLN Chi-restraints excluded: chain 4 residue 405 THR Chi-restraints excluded: chain 4 residue 430 PHE Chi-restraints excluded: chain 4 residue 603 HIS Chi-restraints excluded: chain 4 residue 693 VAL Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 988 VAL Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 159 GLU Chi-restraints excluded: chain 5 residue 240 VAL Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 284 THR Chi-restraints excluded: chain 6 residue 291 ASP Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 352 LEU Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain 6 residue 367 HIS Chi-restraints excluded: chain 6 residue 410 VAL Chi-restraints excluded: chain 6 residue 477 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 103 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 198 optimal weight: 0.4980 chunk 223 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 403 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.131537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104676 restraints weight = 42501.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.105294 restraints weight = 35997.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.105884 restraints weight = 31151.199| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21021 Z= 0.132 Angle : 0.569 11.599 28478 Z= 0.291 Chirality : 0.041 0.181 3277 Planarity : 0.004 0.047 3678 Dihedral : 5.114 55.263 2870 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.97 % Allowed : 13.93 % Favored : 84.10 % 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: -0.24 (0.17), residues: 2597 helix: 0.69 (0.14), residues: 1489 sheet: -0.44 (0.34), residues: 228 loop : -1.49 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 4 700 HIS 0.005 0.001 HIS 5 12 PHE 0.020 0.001 PHE 5 165 TYR 0.017 0.001 TYR 6 307 ARG 0.003 0.000 ARG 2 87 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 1071) hydrogen bonds : angle 4.54386 ( 3186) covalent geometry : bond 0.00296 (21021) covalent geometry : angle 0.56908 (28478) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 309 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8373 (mt) REVERT: 1 376 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: 2 235 MET cc_start: -0.2188 (tpp) cc_final: -0.2823 (tpt) REVERT: 2 237 MET cc_start: -0.0461 (ttm) cc_final: -0.0784 (ttm) REVERT: 2 455 ASP cc_start: 0.6031 (t70) cc_final: 0.5727 (m-30) REVERT: 3 122 MET cc_start: 0.8072 (mtt) cc_final: 0.7724 (mtp) REVERT: 3 330 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7192 (mt0) REVERT: 3 447 LEU cc_start: 0.7613 (mt) cc_final: 0.7092 (tp) REVERT: 4 355 MET cc_start: 0.8397 (mpp) cc_final: 0.7592 (mpp) REVERT: 4 550 MET cc_start: 0.7714 (mpp) cc_final: 0.7256 (mpp) REVERT: 4 603 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6658 (t70) REVERT: 5 86 MET cc_start: 0.7599 (mmt) cc_final: 0.6826 (mmt) REVERT: 5 159 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: 6 307 TYR cc_start: 0.8146 (m-80) cc_final: 0.7723 (m-80) outliers start: 44 outliers final: 15 residues processed: 220 average time/residue: 0.4114 time to fit residues: 151.8389 Evaluate side-chains 183 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 309 LEU Chi-restraints excluded: chain 1 residue 376 GLU Chi-restraints excluded: chain 2 residue 120 ILE Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 293 SER Chi-restraints excluded: chain 3 residue 330 GLN Chi-restraints excluded: chain 4 residue 405 THR Chi-restraints excluded: chain 4 residue 430 PHE Chi-restraints excluded: chain 4 residue 603 HIS Chi-restraints excluded: chain 4 residue 796 VAL Chi-restraints excluded: chain 4 residue 825 SER Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 1084 LEU Chi-restraints excluded: chain 5 residue 38 LEU Chi-restraints excluded: chain 5 residue 83 PHE Chi-restraints excluded: chain 5 residue 159 GLU Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 367 HIS Chi-restraints excluded: chain 6 residue 477 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 50 optimal weight: 30.0000 chunk 224 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 242 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.130405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.103636 restraints weight = 43048.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102956 restraints weight = 35334.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.103695 restraints weight = 34195.586| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21021 Z= 0.164 Angle : 0.570 9.607 28478 Z= 0.295 Chirality : 0.041 0.174 3277 Planarity : 0.004 0.045 3678 Dihedral : 5.131 56.441 2870 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.90 % Allowed : 14.52 % Favored : 82.58 % 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: -0.20 (0.17), residues: 2597 helix: 0.73 (0.14), residues: 1491 sheet: -0.52 (0.34), residues: 240 loop : -1.45 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 2 443 HIS 0.004 0.001 HIS 4 738 PHE 0.021 0.001 PHE 5 165 TYR 0.025 0.002 TYR 4 860 ARG 0.006 0.000 ARG 1 339 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 1071) hydrogen bonds : angle 4.44394 ( 3186) covalent geometry : bond 0.00381 (21021) covalent geometry : angle 0.57048 (28478) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 138 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7626 (tp) REVERT: 1 309 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8379 (mt) REVERT: 1 376 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8225 (pt0) REVERT: 2 219 MET cc_start: 0.7376 (mmp) cc_final: 0.7001 (mtt) REVERT: 2 235 MET cc_start: -0.2176 (tpp) cc_final: -0.2721 (tpt) REVERT: 2 455 ASP cc_start: 0.6083 (t70) cc_final: 0.5789 (m-30) REVERT: 3 45 MET cc_start: 0.8345 (mmm) cc_final: 0.8087 (mmm) REVERT: 3 122 MET cc_start: 0.8091 (mtt) cc_final: 0.7746 (mtp) REVERT: 3 330 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: 3 447 LEU cc_start: 0.7705 (mt) cc_final: 0.7193 (tp) REVERT: 4 355 MET cc_start: 0.8438 (mpp) cc_final: 0.7627 (mpp) REVERT: 4 419 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8161 (mm) REVERT: 4 550 MET cc_start: 0.7745 (mpp) cc_final: 0.7400 (mpp) REVERT: 4 603 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6635 (t-170) REVERT: 5 70 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8534 (tt) outliers start: 65 outliers final: 32 residues processed: 228 average time/residue: 0.4907 time to fit residues: 185.1835 Evaluate side-chains 199 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 138 LEU Chi-restraints excluded: chain 1 residue 309 LEU Chi-restraints excluded: chain 1 residue 311 ASN Chi-restraints excluded: chain 1 residue 376 GLU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 426 SER Chi-restraints excluded: chain 1 residue 439 THR Chi-restraints excluded: chain 2 residue 120 ILE Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 292 LEU Chi-restraints excluded: chain 3 residue 330 GLN Chi-restraints excluded: chain 4 residue 405 THR Chi-restraints excluded: chain 4 residue 419 LEU Chi-restraints excluded: chain 4 residue 430 PHE Chi-restraints excluded: chain 4 residue 576 VAL Chi-restraints excluded: chain 4 residue 603 HIS Chi-restraints excluded: chain 4 residue 693 VAL Chi-restraints excluded: chain 4 residue 796 VAL Chi-restraints excluded: chain 4 residue 825 SER Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 934 VAL Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1083 LEU Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 83 PHE Chi-restraints excluded: chain 5 residue 159 GLU Chi-restraints excluded: chain 6 residue 165 VAL Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 293 MET Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain 6 residue 367 HIS Chi-restraints excluded: chain 6 residue 404 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 248 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 395 HIS 5 151 HIS ** 6 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.130653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.103911 restraints weight = 43164.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.104381 restraints weight = 35704.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.104988 restraints weight = 31493.725| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21021 Z= 0.152 Angle : 0.574 12.797 28478 Z= 0.292 Chirality : 0.041 0.189 3277 Planarity : 0.004 0.046 3678 Dihedral : 5.114 59.314 2870 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.99 % Allowed : 15.19 % Favored : 81.82 % 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: -0.13 (0.17), residues: 2597 helix: 0.79 (0.14), residues: 1496 sheet: -0.47 (0.34), residues: 240 loop : -1.45 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 2 443 HIS 0.003 0.001 HIS 3 321 PHE 0.019 0.001 PHE 5 165 TYR 0.025 0.001 TYR 4 860 ARG 0.005 0.000 ARG 1 339 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 1071) hydrogen bonds : angle 4.38337 ( 3186) covalent geometry : bond 0.00351 (21021) covalent geometry : angle 0.57442 (28478) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 138 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7415 (tp) REVERT: 1 309 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8369 (mt) REVERT: 1 441 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8097 (t) REVERT: 1 473 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5939 (pp) REVERT: 2 219 MET cc_start: 0.7358 (mmp) cc_final: 0.6974 (mtt) REVERT: 2 235 MET cc_start: -0.2186 (tpp) cc_final: -0.2721 (tpt) REVERT: 2 237 MET cc_start: -0.0593 (ttm) cc_final: -0.0976 (ttm) REVERT: 2 455 ASP cc_start: 0.6117 (t70) cc_final: 0.5854 (m-30) REVERT: 3 45 MET cc_start: 0.8303 (mmm) cc_final: 0.8038 (mmm) REVERT: 3 122 MET cc_start: 0.7993 (mtt) cc_final: 0.7647 (mtp) REVERT: 3 330 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: 3 447 LEU cc_start: 0.7731 (mt) cc_final: 0.7238 (tp) REVERT: 4 355 MET cc_start: 0.8390 (mpp) cc_final: 0.7629 (mpp) REVERT: 4 419 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8103 (mm) REVERT: 4 550 MET cc_start: 0.7698 (mpp) cc_final: 0.7489 (mpp) REVERT: 4 603 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6594 (t-170) REVERT: 4 654 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7956 (mt-10) REVERT: 4 1023 GLN cc_start: 0.8701 (tp40) cc_final: 0.7789 (tp40) REVERT: 5 70 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8507 (tt) REVERT: 5 151 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7532 (t-170) REVERT: 6 328 ASP cc_start: 0.8326 (m-30) cc_final: 0.8074 (m-30) outliers start: 67 outliers final: 35 residues processed: 231 average time/residue: 0.3973 time to fit residues: 156.2499 Evaluate side-chains 205 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 7.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 138 LEU Chi-restraints excluded: chain 1 residue 309 LEU Chi-restraints excluded: chain 1 residue 311 ASN Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 426 SER Chi-restraints excluded: chain 1 residue 439 THR Chi-restraints excluded: chain 1 residue 441 VAL Chi-restraints excluded: chain 1 residue 473 LEU Chi-restraints excluded: chain 2 residue 120 ILE Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 282 ILE Chi-restraints excluded: chain 2 residue 293 SER Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 292 LEU Chi-restraints excluded: chain 3 residue 330 GLN Chi-restraints excluded: chain 4 residue 405 THR Chi-restraints excluded: chain 4 residue 419 LEU Chi-restraints excluded: chain 4 residue 430 PHE Chi-restraints excluded: chain 4 residue 576 VAL Chi-restraints excluded: chain 4 residue 603 HIS Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 693 VAL Chi-restraints excluded: chain 4 residue 753 ASP Chi-restraints excluded: chain 4 residue 796 VAL Chi-restraints excluded: chain 4 residue 825 SER Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 934 VAL Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1083 LEU Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 83 PHE Chi-restraints excluded: chain 5 residue 151 HIS Chi-restraints excluded: chain 5 residue 159 GLU Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 165 VAL Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 293 MET Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 327 ILE Chi-restraints excluded: chain 6 residue 367 HIS Chi-restraints excluded: chain 6 residue 404 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 178 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 128 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 29 ASN 5 151 HIS ** 6 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.132474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105635 restraints weight = 42798.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.105486 restraints weight = 36753.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.105994 restraints weight = 35764.018| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21021 Z= 0.108 Angle : 0.550 11.466 28478 Z= 0.277 Chirality : 0.040 0.178 3277 Planarity : 0.004 0.048 3678 Dihedral : 4.940 59.612 2870 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.81 % Allowed : 15.94 % Favored : 81.24 % 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: 0.07 (0.17), residues: 2597 helix: 0.94 (0.14), residues: 1499 sheet: -0.31 (0.35), residues: 228 loop : -1.36 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 986 HIS 0.004 0.001 HIS 5 151 PHE 0.013 0.001 PHE 5 165 TYR 0.022 0.001 TYR 4 860 ARG 0.007 0.000 ARG 1 339 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 1071) hydrogen bonds : angle 4.19394 ( 3186) covalent geometry : bond 0.00235 (21021) covalent geometry : angle 0.54955 (28478) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 183 time to evaluate : 3.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 138 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7497 (tp) REVERT: 1 309 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8298 (mt) REVERT: 1 441 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8110 (t) REVERT: 1 473 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5939 (pp) REVERT: 2 235 MET cc_start: -0.2002 (tpp) cc_final: -0.2590 (tpt) REVERT: 3 45 MET cc_start: 0.8300 (mmm) cc_final: 0.8044 (mmm) REVERT: 3 122 MET cc_start: 0.8019 (mtt) cc_final: 0.7671 (mtp) REVERT: 3 330 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7798 (mt0) REVERT: 3 447 LEU cc_start: 0.7758 (mt) cc_final: 0.7268 (tp) REVERT: 4 355 MET cc_start: 0.8331 (mpp) cc_final: 0.7547 (mpp) REVERT: 4 419 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8148 (mm) REVERT: 4 550 MET cc_start: 0.7639 (mpp) cc_final: 0.7424 (mpp) REVERT: 4 603 HIS cc_start: 0.6834 (OUTLIER) cc_final: 0.6530 (t-170) REVERT: 4 654 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: 4 1023 GLN cc_start: 0.8658 (tp40) cc_final: 0.7747 (tp40) REVERT: 5 70 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8502 (tp) REVERT: 5 159 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: 5 239 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7643 (t0) REVERT: 6 302 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7888 (t80) REVERT: 6 328 ASP cc_start: 0.8290 (m-30) cc_final: 0.8063 (m-30) REVERT: 6 390 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7401 (m-80) outliers start: 63 outliers final: 29 residues processed: 236 average time/residue: 0.4564 time to fit residues: 183.0536 Evaluate side-chains 209 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 138 LEU Chi-restraints excluded: chain 1 residue 309 LEU Chi-restraints excluded: chain 1 residue 311 ASN Chi-restraints excluded: chain 1 residue 441 VAL Chi-restraints excluded: chain 1 residue 455 LEU Chi-restraints excluded: chain 1 residue 473 LEU Chi-restraints excluded: chain 2 residue 120 ILE Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 282 ILE Chi-restraints excluded: chain 2 residue 293 SER Chi-restraints excluded: chain 2 residue 422 THR Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 330 GLN Chi-restraints excluded: chain 4 residue 405 THR Chi-restraints excluded: chain 4 residue 419 LEU Chi-restraints excluded: chain 4 residue 430 PHE Chi-restraints excluded: chain 4 residue 497 VAL Chi-restraints excluded: chain 4 residue 603 HIS Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 693 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 796 VAL Chi-restraints excluded: chain 4 residue 825 SER Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 929 PHE Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 1083 LEU Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 83 PHE Chi-restraints excluded: chain 5 residue 159 GLU Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 5 residue 239 ASP Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 293 MET Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain 6 residue 367 HIS Chi-restraints excluded: chain 6 residue 390 PHE Chi-restraints excluded: chain 6 residue 404 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 104 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 180 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 335 ASN ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 362 GLN 5 151 HIS ** 6 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.130082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.103102 restraints weight = 43257.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.103277 restraints weight = 35265.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.103934 restraints weight = 33411.454| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21021 Z= 0.171 Angle : 0.597 14.850 28478 Z= 0.302 Chirality : 0.041 0.185 3277 Planarity : 0.004 0.049 3678 Dihedral : 5.065 59.282 2870 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.95 % Allowed : 16.57 % Favored : 80.48 % 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: -0.03 (0.17), residues: 2597 helix: 0.89 (0.14), residues: 1496 sheet: -0.53 (0.33), residues: 241 loop : -1.40 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 443 HIS 0.004 0.001 HIS 3 321 PHE 0.016 0.001 PHE 5 165 TYR 0.025 0.002 TYR 4 860 ARG 0.006 0.000 ARG 6 344 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 1071) hydrogen bonds : angle 4.32899 ( 3186) covalent geometry : bond 0.00400 (21021) covalent geometry : angle 0.59732 (28478) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 170 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 309 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8338 (mt) REVERT: 1 441 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.8036 (t) REVERT: 1 473 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5947 (pp) REVERT: 2 219 MET cc_start: 0.7374 (mmp) cc_final: 0.7024 (mtt) REVERT: 2 235 MET cc_start: -0.2136 (tpp) cc_final: -0.2871 (tpt) REVERT: 2 237 MET cc_start: -0.0659 (ttm) cc_final: -0.0986 (ttm) REVERT: 3 45 MET cc_start: 0.8314 (mmm) cc_final: 0.8063 (mmm) REVERT: 3 122 MET cc_start: 0.8070 (mtt) cc_final: 0.7707 (mtp) REVERT: 3 330 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7830 (mt0) REVERT: 3 447 LEU cc_start: 0.7754 (mt) cc_final: 0.7254 (tp) REVERT: 4 355 MET cc_start: 0.8370 (mpp) cc_final: 0.7570 (mpp) REVERT: 4 419 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8059 (mm) REVERT: 4 603 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6614 (t-170) REVERT: 4 654 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: 4 943 MET cc_start: 0.8575 (tpp) cc_final: 0.8228 (tpt) REVERT: 4 1023 GLN cc_start: 0.8679 (tp40) cc_final: 0.7776 (tp40) REVERT: 5 70 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8516 (tt) REVERT: 5 239 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7848 (t0) REVERT: 6 88 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8332 (mt0) REVERT: 6 307 TYR cc_start: 0.8307 (m-80) cc_final: 0.8050 (m-80) REVERT: 6 321 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8168 (t0) REVERT: 6 328 ASP cc_start: 0.8338 (m-30) cc_final: 0.8110 (m-30) outliers start: 66 outliers final: 43 residues processed: 228 average time/residue: 0.5769 time to fit residues: 223.2009 Evaluate side-chains 216 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 162 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 309 LEU Chi-restraints excluded: chain 1 residue 311 ASN Chi-restraints excluded: chain 1 residue 383 LEU Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 426 SER Chi-restraints excluded: chain 1 residue 441 VAL Chi-restraints excluded: chain 1 residue 473 LEU Chi-restraints excluded: chain 2 residue 120 ILE Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 282 ILE Chi-restraints excluded: chain 2 residue 293 SER Chi-restraints excluded: chain 2 residue 455 ASP Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 16 MET Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 292 LEU Chi-restraints excluded: chain 3 residue 330 GLN Chi-restraints excluded: chain 4 residue 405 THR Chi-restraints excluded: chain 4 residue 419 LEU Chi-restraints excluded: chain 4 residue 430 PHE Chi-restraints excluded: chain 4 residue 497 VAL Chi-restraints excluded: chain 4 residue 576 VAL Chi-restraints excluded: chain 4 residue 603 HIS Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 693 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 731 THR Chi-restraints excluded: chain 4 residue 743 VAL Chi-restraints excluded: chain 4 residue 787 LEU Chi-restraints excluded: chain 4 residue 796 VAL Chi-restraints excluded: chain 4 residue 825 SER Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 1084 LEU Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 83 PHE Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 239 ASP Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 88 GLN Chi-restraints excluded: chain 6 residue 132 ILE Chi-restraints excluded: chain 6 residue 140 LYS Chi-restraints excluded: chain 6 residue 165 VAL Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 293 MET Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 321 ASN Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain 6 residue 367 HIS Chi-restraints excluded: chain 6 residue 404 PHE Chi-restraints excluded: chain 6 residue 407 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 81 optimal weight: 0.9980 chunk 216 optimal weight: 0.8980 chunk 195 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 29 ASN ** 6 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.132431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105622 restraints weight = 42872.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.106199 restraints weight = 35939.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.106783 restraints weight = 34128.100| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21021 Z= 0.110 Angle : 0.573 13.360 28478 Z= 0.285 Chirality : 0.040 0.200 3277 Planarity : 0.004 0.050 3678 Dihedral : 4.802 52.487 2867 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.37 % Allowed : 17.55 % Favored : 80.08 % 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: 0.21 (0.17), residues: 2597 helix: 1.05 (0.14), residues: 1501 sheet: -0.30 (0.35), residues: 229 loop : -1.30 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 4 986 HIS 0.007 0.001 HIS 3 321 PHE 0.012 0.001 PHE 5 165 TYR 0.023 0.001 TYR 4 860 ARG 0.002 0.000 ARG 2 87 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 1071) hydrogen bonds : angle 4.18043 ( 3186) covalent geometry : bond 0.00242 (21021) covalent geometry : angle 0.57334 (28478) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 138 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7417 (tp) REVERT: 1 309 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8334 (mt) REVERT: 1 441 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.8001 (t) REVERT: 1 473 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5954 (pp) REVERT: 2 219 MET cc_start: 0.7256 (mmp) cc_final: 0.6930 (mtt) REVERT: 2 235 MET cc_start: -0.1892 (tpp) cc_final: -0.2698 (tpt) REVERT: 2 237 MET cc_start: -0.0462 (ttm) cc_final: -0.0815 (ttm) REVERT: 3 45 MET cc_start: 0.8318 (mmm) cc_final: 0.8078 (mmm) REVERT: 3 122 MET cc_start: 0.7955 (mtt) cc_final: 0.7595 (mtp) REVERT: 3 330 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7789 (mt0) REVERT: 3 447 LEU cc_start: 0.7738 (mt) cc_final: 0.7246 (tp) REVERT: 4 419 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8035 (mm) REVERT: 4 550 MET cc_start: 0.7624 (mpp) cc_final: 0.7267 (mpp) REVERT: 4 603 HIS cc_start: 0.6751 (OUTLIER) cc_final: 0.6426 (t70) REVERT: 4 654 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: 4 943 MET cc_start: 0.8541 (tpp) cc_final: 0.8179 (tpt) REVERT: 4 1023 GLN cc_start: 0.8626 (tp40) cc_final: 0.7706 (tp40) REVERT: 5 70 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8484 (tp) REVERT: 5 239 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7610 (t0) REVERT: 6 302 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7884 (t80) REVERT: 6 307 TYR cc_start: 0.8198 (m-80) cc_final: 0.7904 (m-80) REVERT: 6 321 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8111 (t0) REVERT: 6 390 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7346 (m-80) outliers start: 53 outliers final: 35 residues processed: 227 average time/residue: 0.2844 time to fit residues: 106.3118 Evaluate side-chains 218 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 138 LEU Chi-restraints excluded: chain 1 residue 309 LEU Chi-restraints excluded: chain 1 residue 311 ASN Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 439 THR Chi-restraints excluded: chain 1 residue 441 VAL Chi-restraints excluded: chain 1 residue 473 LEU Chi-restraints excluded: chain 2 residue 120 ILE Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 282 ILE Chi-restraints excluded: chain 2 residue 293 SER Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 330 GLN Chi-restraints excluded: chain 3 residue 390 MET Chi-restraints excluded: chain 4 residue 405 THR Chi-restraints excluded: chain 4 residue 419 LEU Chi-restraints excluded: chain 4 residue 430 PHE Chi-restraints excluded: chain 4 residue 497 VAL Chi-restraints excluded: chain 4 residue 576 VAL Chi-restraints excluded: chain 4 residue 603 HIS Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 693 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 743 VAL Chi-restraints excluded: chain 4 residue 787 LEU Chi-restraints excluded: chain 4 residue 825 SER Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 880 LEU Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 929 PHE Chi-restraints excluded: chain 4 residue 934 VAL Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 1083 LEU Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 83 PHE Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 239 ASP Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 140 LYS Chi-restraints excluded: chain 6 residue 293 MET Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 321 ASN Chi-restraints excluded: chain 6 residue 367 HIS Chi-restraints excluded: chain 6 residue 390 PHE Chi-restraints excluded: chain 6 residue 404 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 38 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 445 GLN 5 214 HIS 5 264 GLN ** 6 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.127376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100509 restraints weight = 43640.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.100398 restraints weight = 36472.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.100742 restraints weight = 37585.681| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 21021 Z= 0.286 Angle : 0.707 13.432 28478 Z= 0.360 Chirality : 0.045 0.191 3277 Planarity : 0.005 0.049 3678 Dihedral : 5.259 55.662 2867 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.59 % Favored : 92.38 % Rotamer: Outliers : 2.95 % Allowed : 17.06 % Favored : 79.99 % 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: -0.36 (0.17), residues: 2597 helix: 0.62 (0.14), residues: 1489 sheet: -0.71 (0.34), residues: 240 loop : -1.52 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 2 443 HIS 0.008 0.001 HIS 5 236 PHE 0.033 0.002 PHE 6 479 TYR 0.017 0.002 TYR 1 247 ARG 0.005 0.001 ARG 6 344 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 1071) hydrogen bonds : angle 4.63883 ( 3186) covalent geometry : bond 0.00667 (21021) covalent geometry : angle 0.70701 (28478) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 162 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 138 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7933 (mm) REVERT: 1 309 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8459 (mt) REVERT: 1 441 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8082 (t) REVERT: 1 473 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5966 (pp) REVERT: 2 219 MET cc_start: 0.7429 (mmp) cc_final: 0.7010 (mtt) REVERT: 2 235 MET cc_start: -0.2226 (tpp) cc_final: -0.2845 (tpt) REVERT: 2 356 TYR cc_start: 0.7901 (m-10) cc_final: 0.7585 (m-10) REVERT: 3 45 MET cc_start: 0.8325 (mmm) cc_final: 0.8065 (mmm) REVERT: 3 122 MET cc_start: 0.8068 (mtt) cc_final: 0.7724 (mtp) REVERT: 3 330 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: 3 447 LEU cc_start: 0.7825 (mt) cc_final: 0.7365 (tp) REVERT: 4 355 MET cc_start: 0.8328 (mpp) cc_final: 0.7545 (mpp) REVERT: 4 419 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8065 (mm) REVERT: 4 654 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: 4 860 TYR cc_start: 0.8579 (t80) cc_final: 0.8366 (t80) REVERT: 4 943 MET cc_start: 0.8566 (tpp) cc_final: 0.8278 (tpt) REVERT: 5 70 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8541 (tt) REVERT: 5 239 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8027 (t70) REVERT: 6 307 TYR cc_start: 0.8325 (m-80) cc_final: 0.8098 (m-80) REVERT: 6 321 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8244 (t0) outliers start: 66 outliers final: 47 residues processed: 219 average time/residue: 0.3177 time to fit residues: 118.3952 Evaluate side-chains 214 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 157 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 138 LEU Chi-restraints excluded: chain 1 residue 269 CYS Chi-restraints excluded: chain 1 residue 309 LEU Chi-restraints excluded: chain 1 residue 311 ASN Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 426 SER Chi-restraints excluded: chain 1 residue 439 THR Chi-restraints excluded: chain 1 residue 441 VAL Chi-restraints excluded: chain 1 residue 473 LEU Chi-restraints excluded: chain 2 residue 120 ILE Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 282 ILE Chi-restraints excluded: chain 2 residue 293 SER Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 79 LEU Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 292 LEU Chi-restraints excluded: chain 3 residue 330 GLN Chi-restraints excluded: chain 4 residue 405 THR Chi-restraints excluded: chain 4 residue 419 LEU Chi-restraints excluded: chain 4 residue 430 PHE Chi-restraints excluded: chain 4 residue 497 VAL Chi-restraints excluded: chain 4 residue 576 VAL Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 693 VAL Chi-restraints excluded: chain 4 residue 718 ILE Chi-restraints excluded: chain 4 residue 731 THR Chi-restraints excluded: chain 4 residue 743 VAL Chi-restraints excluded: chain 4 residue 787 LEU Chi-restraints excluded: chain 4 residue 796 VAL Chi-restraints excluded: chain 4 residue 825 SER Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 880 LEU Chi-restraints excluded: chain 4 residue 892 VAL Chi-restraints excluded: chain 4 residue 934 VAL Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 4 residue 996 ASP Chi-restraints excluded: chain 4 residue 1006 LEU Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 83 PHE Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 239 ASP Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 71 LEU Chi-restraints excluded: chain 6 residue 140 LYS Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 293 MET Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 321 ASN Chi-restraints excluded: chain 6 residue 347 ILE Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain 6 residue 367 HIS Chi-restraints excluded: chain 6 residue 404 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 23 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 74 optimal weight: 0.0050 chunk 79 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 192 optimal weight: 0.2980 chunk 24 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 603 HIS ** 6 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.132145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.105318 restraints weight = 43431.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.104455 restraints weight = 34578.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.105070 restraints weight = 36437.566| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21021 Z= 0.114 Angle : 0.614 15.889 28478 Z= 0.303 Chirality : 0.040 0.207 3277 Planarity : 0.004 0.049 3678 Dihedral : 4.844 54.914 2865 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.01 % Allowed : 18.54 % Favored : 79.46 % 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: 0.09 (0.17), residues: 2597 helix: 0.95 (0.14), residues: 1503 sheet: -0.42 (0.34), residues: 235 loop : -1.33 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP 1 329 HIS 0.003 0.001 HIS 5 151 PHE 0.010 0.001 PHE 5 165 TYR 0.031 0.001 TYR 2 466 ARG 0.007 0.000 ARG 2 355 Details of bonding type rmsd hydrogen bonds : bond 0.03131 ( 1071) hydrogen bonds : angle 4.26209 ( 3186) covalent geometry : bond 0.00245 (21021) covalent geometry : angle 0.61395 (28478) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 138 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7601 (tp) REVERT: 1 309 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8367 (mt) REVERT: 1 441 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.7997 (t) REVERT: 1 473 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5854 (pp) REVERT: 2 219 MET cc_start: 0.7469 (mmp) cc_final: 0.7007 (mtt) REVERT: 2 235 MET cc_start: -0.1955 (tpp) cc_final: -0.2738 (tpt) REVERT: 2 237 MET cc_start: -0.0790 (ttm) cc_final: -0.1104 (ttm) REVERT: 2 351 MET cc_start: 0.7168 (tpt) cc_final: 0.5264 (ttt) REVERT: 2 356 TYR cc_start: 0.8031 (m-10) cc_final: 0.7698 (m-10) REVERT: 3 45 MET cc_start: 0.8227 (mmm) cc_final: 0.7989 (mmm) REVERT: 3 122 MET cc_start: 0.8000 (mtt) cc_final: 0.7645 (mtp) REVERT: 3 447 LEU cc_start: 0.7809 (mt) cc_final: 0.7363 (tp) REVERT: 4 355 MET cc_start: 0.8327 (mpp) cc_final: 0.7502 (mpp) REVERT: 4 419 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7985 (mm) REVERT: 4 550 MET cc_start: 0.7715 (mpp) cc_final: 0.7459 (mpp) REVERT: 4 654 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: 4 943 MET cc_start: 0.8521 (tpp) cc_final: 0.8170 (tpt) REVERT: 5 70 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8425 (tp) REVERT: 5 91 MET cc_start: 0.6896 (tpp) cc_final: 0.6678 (tpp) REVERT: 6 302 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7986 (t80) REVERT: 6 307 TYR cc_start: 0.8189 (m-80) cc_final: 0.7874 (m-80) REVERT: 6 321 ASN cc_start: 0.8373 (OUTLIER) cc_final: 0.8128 (t0) outliers start: 45 outliers final: 31 residues processed: 213 average time/residue: 0.3353 time to fit residues: 119.3636 Evaluate side-chains 209 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 138 LEU Chi-restraints excluded: chain 1 residue 309 LEU Chi-restraints excluded: chain 1 residue 311 ASN Chi-restraints excluded: chain 1 residue 423 VAL Chi-restraints excluded: chain 1 residue 426 SER Chi-restraints excluded: chain 1 residue 439 THR Chi-restraints excluded: chain 1 residue 441 VAL Chi-restraints excluded: chain 1 residue 473 LEU Chi-restraints excluded: chain 2 residue 120 ILE Chi-restraints excluded: chain 2 residue 209 ILE Chi-restraints excluded: chain 2 residue 282 ILE Chi-restraints excluded: chain 2 residue 293 SER Chi-restraints excluded: chain 2 residue 459 LEU Chi-restraints excluded: chain 3 residue 79 LEU Chi-restraints excluded: chain 3 residue 170 LEU Chi-restraints excluded: chain 4 residue 405 THR Chi-restraints excluded: chain 4 residue 419 LEU Chi-restraints excluded: chain 4 residue 430 PHE Chi-restraints excluded: chain 4 residue 497 VAL Chi-restraints excluded: chain 4 residue 654 GLU Chi-restraints excluded: chain 4 residue 743 VAL Chi-restraints excluded: chain 4 residue 787 LEU Chi-restraints excluded: chain 4 residue 825 SER Chi-restraints excluded: chain 4 residue 834 LEU Chi-restraints excluded: chain 4 residue 934 VAL Chi-restraints excluded: chain 4 residue 961 VAL Chi-restraints excluded: chain 5 residue 70 LEU Chi-restraints excluded: chain 5 residue 83 PHE Chi-restraints excluded: chain 5 residue 192 VAL Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 5 residue 271 LEU Chi-restraints excluded: chain 6 residue 140 LYS Chi-restraints excluded: chain 6 residue 195 THR Chi-restraints excluded: chain 6 residue 216 VAL Chi-restraints excluded: chain 6 residue 293 MET Chi-restraints excluded: chain 6 residue 302 PHE Chi-restraints excluded: chain 6 residue 321 ASN Chi-restraints excluded: chain 6 residue 364 VAL Chi-restraints excluded: chain 6 residue 367 HIS Chi-restraints excluded: chain 6 residue 404 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 21 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 150 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 114 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 29 ASN ** 6 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.132372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.105194 restraints weight = 43347.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104731 restraints weight = 34999.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.105672 restraints weight = 33804.951| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21021 Z= 0.113 Angle : 0.597 12.707 28478 Z= 0.295 Chirality : 0.040 0.196 3277 Planarity : 0.004 0.050 3678 Dihedral : 4.733 54.414 2865 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 1.97 % Allowed : 18.45 % Favored : 79.59 % 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: 0.24 (0.17), residues: 2597 helix: 1.07 (0.14), residues: 1499 sheet: -0.35 (0.34), residues: 240 loop : -1.26 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 1 329 HIS 0.006 0.001 HIS 3 321 PHE 0.016 0.001 PHE 6 382 TYR 0.016 0.001 TYR 4 860 ARG 0.002 0.000 ARG 2 87 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 1071) hydrogen bonds : angle 4.16896 ( 3186) covalent geometry : bond 0.00253 (21021) covalent geometry : angle 0.59684 (28478) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7838.66 seconds wall clock time: 146 minutes 53.72 seconds (8813.72 seconds total)