Starting phenix.real_space_refine on Wed Jun 25 15:41:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk4_32558/06_2025/7wk4_32558.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk4_32558/06_2025/7wk4_32558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wk4_32558/06_2025/7wk4_32558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk4_32558/06_2025/7wk4_32558.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk4_32558/06_2025/7wk4_32558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk4_32558/06_2025/7wk4_32558.cif" } resolution = 3.69 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= 0.006 sd= 0.102 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 143 5.16 5 C 18904 2.51 5 N 4917 2.21 5 O 5577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 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: 29541 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4736 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 27, 'TRANS': 553} Chain: "B" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 54, 'TRANS': 1002} Chain breaks: 7 Chain: "D" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'PTRANS': 54, 'TRANS': 1002} Chain breaks: 7 Time building chain proxies: 16.27, per 1000 atoms: 0.55 Number of scatterers: 29541 At special positions: 0 Unit cell: (151.927, 138.811, 233.902, 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 143 16.00 O 5577 8.00 N 4917 7.00 C 18904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.04 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.04 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.04 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: 6.15 Conformation dependent library (CDL) restraints added in 3.4 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 47 sheets defined 25.7% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.658A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 removed outlier: 3.835A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.525A pdb=" N GLN A 76 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.863A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.646A pdb=" N ASN A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 149 removed outlier: 4.069A pdb=" N ASN A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 3.519A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.596A pdb=" N LEU A 179 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.804A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 removed outlier: 4.077A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 204' Processing helix chain 'A' and resid 220 through 248 removed outlier: 4.246A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.658A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.977A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 removed outlier: 3.797A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.503A pdb=" N VAL A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 382 removed outlier: 3.822A pdb=" N PHE A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.524A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.545A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.000A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.572A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 removed outlier: 4.155A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.512A pdb=" N MET A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.968A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.805A pdb=" N ILE A 484 " --> pdb=" O MET A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.697A pdb=" N SER A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 503' Processing helix chain 'A' and resid 515 through 530 removed outlier: 4.134A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.948A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.645A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.719A pdb=" N LYS B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.804A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 386 through 390' Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.719A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.524A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.945A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.517A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.720A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.533A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.511A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.607A pdb=" N ALA B 924 " --> pdb=" O GLN B 920 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.667A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.762A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.843A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.556A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.510A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 removed outlier: 3.516A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.649A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.604A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 746 through 751' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.530A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.619A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.541A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.537A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.576A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.648A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 924 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.679A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 removed outlier: 3.740A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.832A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C1009 " --> pdb=" O GLN C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.892A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.907A pdb=" N LYS D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 417 through 422 removed outlier: 3.959A pdb=" N TYR D 421 " --> pdb=" O ASN D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 639 removed outlier: 3.977A pdb=" N SER D 637 " --> pdb=" O ARG D 634 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR D 638 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY D 639 " --> pdb=" O TYR D 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 634 through 639' Processing helix chain 'D' and resid 737 through 742 removed outlier: 3.533A pdb=" N ILE D 742 " --> pdb=" O CYS D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 751 removed outlier: 3.966A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 746 through 751' Processing helix chain 'D' and resid 759 through 770 removed outlier: 3.688A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 783 removed outlier: 3.909A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 781 " --> pdb=" O ASN D 777 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 824 removed outlier: 4.095A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 884 removed outlier: 3.637A pdb=" N THR D 881 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 882 " --> pdb=" O LEU D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 removed outlier: 3.720A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 918 removed outlier: 3.925A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 913 through 918' Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.739A pdb=" N THR D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 965 removed outlier: 4.120A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 959 " --> pdb=" O ASN D 955 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 965 " --> pdb=" O THR D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 3.937A pdb=" N GLU D 990 " --> pdb=" O PRO D 986 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE D 993 " --> pdb=" O ALA D 989 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D1033 " --> pdb=" O MET D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.689A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.804A pdb=" N THR A 347 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 351 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 23 removed outlier: 5.577A pdb=" N THR B 22 " --> pdb=" O PHE B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.704A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.658A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.662A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.662A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.444A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.549A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.724A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 400 through 402 removed outlier: 3.659A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.637A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.123A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.412A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.206A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.816A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.882A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.886A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 317 removed outlier: 5.596A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.979A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.998A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.444A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 660 removed outlier: 3.689A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.845A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.845A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.231A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.469A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 28 through 30 removed outlier: 3.692A pdb=" N VAL D 193 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 204 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS D 195 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.539A pdb=" N HIS D 49 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 273 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.912A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY D 103 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 244 through 245 Processing sheet with id=AE1, first strand: chain 'D' and resid 311 through 317 removed outlier: 3.735A pdb=" N THR D 599 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR D 313 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 325 through 328 removed outlier: 3.620A pdb=" N GLY D 550 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY D 548 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.593A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL D 511 " --> pdb=" O ILE D 434 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 434 " --> pdb=" O VAL D 511 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.617A pdb=" N CYS D 361 " --> pdb=" O CYS D 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.520A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 660 removed outlier: 4.959A pdb=" N THR D 696 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN D 658 " --> pdb=" O THR D 696 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 666 " --> pdb=" O ILE D 670 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 664 " --> pdb=" O ALA D 672 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 712 through 728 removed outlier: 6.664A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN D 717 " --> pdb=" O ALA D1070 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 721 " --> pdb=" O THR D1066 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY D1059 " --> pdb=" O ALA D1056 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET D1050 " --> pdb=" O VAL D1065 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.469A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.604A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1094 through 1097 removed outlier: 3.632A pdb=" N VAL D1104 " --> pdb=" O GLN D1113 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2466 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: 11.23 Time building geometry restraints manager: 7.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5779 1.33 - 1.46: 10962 1.46 - 1.60: 13319 1.60 - 1.73: 0 1.73 - 1.86: 194 Bond restraints: 30254 Sorted by residual: bond pdb=" CA THR C 581 " pdb=" C THR C 581 " ideal model delta sigma weight residual 1.533 1.466 0.068 5.60e-03 3.19e+04 1.45e+02 bond pdb=" CA ALA B 989 " pdb=" C ALA B 989 " ideal model delta sigma weight residual 1.524 1.415 0.109 1.27e-02 6.20e+03 7.32e+01 bond pdb=" CA TYR D 380 " pdb=" C TYR D 380 " ideal model delta sigma weight residual 1.523 1.428 0.096 1.34e-02 5.57e+03 5.08e+01 bond pdb=" N ILE C 584 " pdb=" CA ILE C 584 " ideal model delta sigma weight residual 1.459 1.379 0.080 1.15e-02 7.56e+03 4.82e+01 bond pdb=" N ILE D 980 " pdb=" CA ILE D 980 " ideal model delta sigma weight residual 1.461 1.386 0.075 1.17e-02 7.31e+03 4.10e+01 ... (remaining 30249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 40196 2.50 - 5.01: 831 5.01 - 7.51: 77 7.51 - 10.02: 26 10.02 - 12.52: 4 Bond angle restraints: 41134 Sorted by residual: angle pdb=" CA ASP C 578 " pdb=" C ASP C 578 " pdb=" N PRO C 579 " ideal model delta sigma weight residual 119.27 110.11 9.16 1.13e+00 7.83e-01 6.57e+01 angle pdb=" N ALA B 989 " pdb=" CA ALA B 989 " pdb=" C ALA B 989 " ideal model delta sigma weight residual 111.07 102.61 8.46 1.07e+00 8.73e-01 6.24e+01 angle pdb=" C THR C 581 " pdb=" CA THR C 581 " pdb=" CB THR C 581 " ideal model delta sigma weight residual 117.07 106.24 10.83 1.44e+00 4.82e-01 5.65e+01 angle pdb=" N ILE D 980 " pdb=" CA ILE D 980 " pdb=" C ILE D 980 " ideal model delta sigma weight residual 110.42 103.77 6.65 9.60e-01 1.09e+00 4.80e+01 angle pdb=" N PHE D 981 " pdb=" CA PHE D 981 " pdb=" C PHE D 981 " ideal model delta sigma weight residual 111.28 118.78 -7.50 1.09e+00 8.42e-01 4.74e+01 ... (remaining 41129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16048 17.95 - 35.91: 1586 35.91 - 53.86: 306 53.86 - 71.81: 69 71.81 - 89.77: 26 Dihedral angle restraints: 18035 sinusoidal: 7115 harmonic: 10920 Sorted by residual: dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -5.42 -80.58 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CB CYS D 538 " pdb=" SG CYS D 538 " pdb=" SG CYS D 590 " pdb=" CB CYS D 590 " ideal model delta sinusoidal sigma weight residual 93.00 169.16 -76.16 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -20.80 -65.20 1 1.00e+01 1.00e-02 5.57e+01 ... (remaining 18032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4077 0.088 - 0.176: 452 0.176 - 0.264: 55 0.264 - 0.351: 9 0.351 - 0.439: 1 Chirality restraints: 4594 Sorted by residual: chirality pdb=" CA PHE D 981 " pdb=" N PHE D 981 " pdb=" C PHE D 981 " pdb=" CB PHE D 981 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA SER D 982 " pdb=" N SER D 982 " pdb=" C SER D 982 " pdb=" CB SER D 982 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA GLU B 990 " pdb=" N GLU B 990 " pdb=" C GLU B 990 " pdb=" CB GLU B 990 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 4591 not shown) Planarity restraints: 5319 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 578 " -0.027 2.00e-02 2.50e+03 5.84e-02 3.41e+01 pdb=" C ASP C 578 " 0.101 2.00e-02 2.50e+03 pdb=" O ASP C 578 " -0.040 2.00e-02 2.50e+03 pdb=" N PRO C 579 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D 986 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO D 987 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO D 987 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 987 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.066 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO C 987 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.056 5.00e-02 4.00e+02 ... (remaining 5316 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 10080 2.85 - 3.36: 22721 3.36 - 3.88: 48642 3.88 - 4.39: 52644 4.39 - 4.90: 91942 Nonbonded interactions: 226029 Sorted by model distance: nonbonded pdb=" O GLN B 957 " pdb=" OG1 THR B 961 " model vdw 2.338 3.040 nonbonded pdb=" O LEU A 156 " pdb=" OH TYR A 252 " model vdw 2.341 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.352 3.040 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.356 3.040 nonbonded pdb=" O ASP D 290 " pdb=" OG SER D 297 " model vdw 2.357 3.040 ... (remaining 226024 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 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) selection = (chain 'D' and (resid 14 through 631 or resid 641 through 1147)) } 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: 10.420 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: 0.990 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 61.780 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.100 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 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 : 0.005 0.109 30296 Z= 0.295 Angle : 0.862 12.523 41218 Z= 0.514 Chirality : 0.055 0.439 4594 Planarity : 0.007 0.109 5319 Dihedral : 14.662 89.768 10875 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.44 % Favored : 96.40 % Rotamer: Outliers : 0.49 % Allowed : 8.50 % Favored : 91.01 % Cbeta Deviations : 0.06 % 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: -4.28 (0.10), residues: 3693 helix: -5.04 (0.04), residues: 853 sheet: -1.22 (0.18), residues: 641 loop : -2.49 (0.10), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 275 HIS 0.005 0.001 HIS A 378 PHE 0.034 0.001 PHE B 377 TYR 0.021 0.001 TYR A 385 ARG 0.003 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.30909 ( 875) hydrogen bonds : angle 11.19840 ( 2466) SS BOND : bond 0.00596 ( 42) SS BOND : angle 1.48214 ( 84) covalent geometry : bond 0.00511 (30254) covalent geometry : angle 0.86015 (41134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 605 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: -0.0669 (tmm) cc_final: -0.0909 (tmm) REVERT: A 383 MET cc_start: 0.3120 (mtp) cc_final: 0.2344 (tpp) REVERT: B 40 ASP cc_start: 0.8699 (p0) cc_final: 0.8476 (p0) REVERT: B 201 PHE cc_start: 0.6278 (m-80) cc_final: 0.6012 (m-80) REVERT: B 308 VAL cc_start: 0.8421 (t) cc_final: 0.8100 (t) REVERT: B 921 LYS cc_start: 0.7127 (mmtp) cc_final: 0.6920 (tttp) REVERT: B 970 PHE cc_start: 0.8374 (m-80) cc_final: 0.7810 (m-80) REVERT: B 1139 ASP cc_start: 0.7026 (t0) cc_final: 0.6727 (p0) REVERT: C 351 TYR cc_start: 0.7649 (p90) cc_final: 0.7311 (p90) REVERT: C 377 PHE cc_start: 0.4885 (p90) cc_final: 0.4310 (p90) REVERT: C 740 MET cc_start: 0.7370 (tpt) cc_final: 0.6989 (tpp) REVERT: D 153 MET cc_start: -0.2134 (ttp) cc_final: -0.2865 (mtm) REVERT: D 436 TRP cc_start: 0.3595 (t60) cc_final: 0.3126 (t-100) REVERT: D 452 LEU cc_start: 0.5650 (mt) cc_final: 0.5320 (mt) REVERT: D 710 ASN cc_start: 0.6396 (p0) cc_final: 0.6146 (p0) REVERT: D 752 LEU cc_start: 0.7923 (mt) cc_final: 0.7670 (mp) REVERT: D 898 PHE cc_start: 0.5868 (m-10) cc_final: 0.5592 (m-80) REVERT: D 950 ASP cc_start: 0.6489 (p0) cc_final: 0.6184 (p0) outliers start: 16 outliers final: 6 residues processed: 619 average time/residue: 0.4586 time to fit residues: 456.3051 Evaluate side-chains 376 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 370 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 407 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 10.0000 chunk 281 optimal weight: 0.7980 chunk 156 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 337 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 241 HIS ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN B 542 ASN B 641 ASN B 824 ASN B 949 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS C 134 GLN C 394 ASN C 448 ASN C 505 HIS C 563 GLN C 717 ASN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 914 ASN C 935 GLN C 955 ASN C 960 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN D 61 ASN D 66 HIS D 239 GLN D 394 ASN D 690 GLN D 751 ASN D 777 ASN D 784 GLN D 901 GLN D 914 ASN D 925 ASN D 926 GLN D 935 GLN D 957 GLN D1010 GLN D1036 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.149825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.121744 restraints weight = 113240.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.123932 restraints weight = 68169.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.124300 restraints weight = 41623.207| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30296 Z= 0.163 Angle : 0.612 13.165 41218 Z= 0.322 Chirality : 0.044 0.175 4594 Planarity : 0.005 0.068 5319 Dihedral : 4.386 47.097 4023 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.22 % Allowed : 14.53 % Favored : 83.24 % 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: -2.85 (0.11), residues: 3693 helix: -2.77 (0.12), residues: 901 sheet: -0.35 (0.19), residues: 592 loop : -2.00 (0.11), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 886 HIS 0.008 0.001 HIS C 49 PHE 0.025 0.002 PHE C 55 TYR 0.022 0.002 TYR D 380 ARG 0.006 0.001 ARG B 498 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 875) hydrogen bonds : angle 6.25731 ( 2466) SS BOND : bond 0.00447 ( 42) SS BOND : angle 1.54803 ( 84) covalent geometry : bond 0.00329 (30254) covalent geometry : angle 0.60866 (41134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 384 time to evaluate : 3.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: -0.5033 (ptm) cc_final: -0.5237 (mtp) REVERT: A 190 MET cc_start: 0.0058 (tmm) cc_final: -0.0306 (tmm) REVERT: A 478 TRP cc_start: 0.3200 (p-90) cc_final: 0.2233 (p-90) REVERT: B 308 VAL cc_start: 0.8580 (t) cc_final: 0.8364 (t) REVERT: B 970 PHE cc_start: 0.8531 (m-80) cc_final: 0.7887 (m-80) REVERT: B 982 SER cc_start: 0.8424 (t) cc_final: 0.8169 (p) REVERT: B 988 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7774 (mp0) REVERT: B 1088 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.5891 (t-90) REVERT: B 1139 ASP cc_start: 0.7470 (t0) cc_final: 0.6695 (p0) REVERT: C 377 PHE cc_start: 0.5026 (p90) cc_final: 0.4390 (p90) REVERT: C 636 TYR cc_start: 0.6142 (m-80) cc_final: 0.5883 (m-80) REVERT: C 725 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8272 (tm-30) REVERT: C 740 MET cc_start: 0.7676 (tpt) cc_final: 0.7050 (tpp) REVERT: D 90 VAL cc_start: 0.8573 (t) cc_final: 0.8329 (m) REVERT: D 153 MET cc_start: -0.2353 (ttp) cc_final: -0.2970 (mtm) REVERT: D 202 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8291 (tptt) REVERT: D 436 TRP cc_start: 0.3371 (t60) cc_final: 0.3110 (t-100) REVERT: D 710 ASN cc_start: 0.6841 (p0) cc_final: 0.6493 (p0) REVERT: D 725 GLU cc_start: 0.7158 (tt0) cc_final: 0.6917 (tt0) REVERT: D 965 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7837 (tp-100) REVERT: D 1029 MET cc_start: 0.7907 (mmm) cc_final: 0.7658 (tpt) REVERT: D 1036 GLN cc_start: 0.5674 (OUTLIER) cc_final: 0.5452 (tt0) outliers start: 73 outliers final: 45 residues processed: 421 average time/residue: 0.4023 time to fit residues: 277.9290 Evaluate side-chains 364 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1088 HIS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 1036 GLN Chi-restraints excluded: chain D residue 1049 LEU Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 260 optimal weight: 0.9980 chunk 214 optimal weight: 7.9990 chunk 333 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 278 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 chunk 272 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 368 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 141 optimal weight: 0.4980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 586 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN B 564 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 505 HIS C 506 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN C 787 GLN C 957 GLN C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 GLN D 955 ASN ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1036 GLN D1135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.148114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.119569 restraints weight = 111188.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.120978 restraints weight = 68539.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.122052 restraints weight = 47796.114| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30296 Z= 0.128 Angle : 0.547 11.745 41218 Z= 0.282 Chirality : 0.043 0.163 4594 Planarity : 0.004 0.051 5319 Dihedral : 4.107 32.739 4020 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.50 % Allowed : 16.36 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.12), residues: 3693 helix: -1.21 (0.16), residues: 891 sheet: -0.21 (0.19), residues: 589 loop : -1.74 (0.11), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 886 HIS 0.009 0.001 HIS C 505 PHE 0.018 0.001 PHE A 315 TYR 0.018 0.001 TYR B 707 ARG 0.008 0.000 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.03941 ( 875) hydrogen bonds : angle 5.64134 ( 2466) SS BOND : bond 0.00427 ( 42) SS BOND : angle 1.42115 ( 84) covalent geometry : bond 0.00283 (30254) covalent geometry : angle 0.54397 (41134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 341 time to evaluate : 3.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: -0.0048 (tmm) cc_final: -0.0641 (tmm) REVERT: B 301 CYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7227 (t) REVERT: B 564 GLN cc_start: 0.6697 (mm110) cc_final: 0.6043 (mm110) REVERT: B 868 GLU cc_start: 0.7829 (mp0) cc_final: 0.7522 (tm-30) REVERT: B 959 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8715 (mt) REVERT: B 978 ASN cc_start: 0.7573 (p0) cc_final: 0.6794 (p0) REVERT: B 1139 ASP cc_start: 0.7380 (t0) cc_final: 0.6592 (p0) REVERT: C 377 PHE cc_start: 0.5311 (p90) cc_final: 0.4719 (p90) REVERT: C 480 CYS cc_start: 0.1517 (OUTLIER) cc_final: 0.0516 (t) REVERT: C 725 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 740 MET cc_start: 0.7656 (tpt) cc_final: 0.7211 (tpp) REVERT: D 90 VAL cc_start: 0.8648 (t) cc_final: 0.8383 (m) REVERT: D 153 MET cc_start: -0.2549 (ttp) cc_final: -0.3147 (mtm) REVERT: D 202 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8244 (tptt) REVERT: D 436 TRP cc_start: 0.3457 (t60) cc_final: 0.3235 (t-100) REVERT: D 710 ASN cc_start: 0.6971 (p0) cc_final: 0.6592 (p0) REVERT: D 725 GLU cc_start: 0.7242 (tt0) cc_final: 0.7019 (tt0) REVERT: D 767 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7291 (mm) REVERT: D 965 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7907 (tp-100) REVERT: D 1011 GLN cc_start: 0.8233 (tp-100) cc_final: 0.8014 (mm-40) REVERT: D 1036 GLN cc_start: 0.5942 (OUTLIER) cc_final: 0.5251 (tt0) outliers start: 82 outliers final: 44 residues processed: 401 average time/residue: 0.3792 time to fit residues: 251.9199 Evaluate side-chains 351 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 302 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 747 THR Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 918 GLU Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 1036 GLN Chi-restraints excluded: chain D residue 1076 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 281 optimal weight: 8.9990 chunk 294 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 199 optimal weight: 0.0980 chunk 337 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 253 optimal weight: 0.9980 chunk 167 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 GLN D1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.147588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.118646 restraints weight = 113469.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.120397 restraints weight = 67261.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.120846 restraints weight = 48211.915| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30296 Z= 0.115 Angle : 0.540 11.902 41218 Z= 0.275 Chirality : 0.043 0.207 4594 Planarity : 0.004 0.049 5319 Dihedral : 4.051 32.976 4020 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.71 % Allowed : 17.40 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3693 helix: -0.50 (0.17), residues: 894 sheet: -0.08 (0.19), residues: 592 loop : -1.55 (0.12), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 886 HIS 0.007 0.001 HIS C 49 PHE 0.033 0.001 PHE C1121 TYR 0.020 0.001 TYR D1007 ARG 0.004 0.000 ARG B 905 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 875) hydrogen bonds : angle 5.30102 ( 2466) SS BOND : bond 0.00585 ( 42) SS BOND : angle 1.52861 ( 84) covalent geometry : bond 0.00256 (30254) covalent geometry : angle 0.53623 (41134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 345 time to evaluate : 4.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: -0.0293 (tmm) cc_final: -0.0843 (tmm) REVERT: A 266 LEU cc_start: -0.0024 (OUTLIER) cc_final: -0.0388 (pp) REVERT: B 564 GLN cc_start: 0.6496 (OUTLIER) cc_final: 0.5914 (mm110) REVERT: B 567 ARG cc_start: 0.7653 (ttp-110) cc_final: 0.7165 (ttp-110) REVERT: B 725 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7499 (tm-30) REVERT: B 1139 ASP cc_start: 0.7242 (t0) cc_final: 0.6615 (p0) REVERT: C 351 TYR cc_start: 0.7541 (p90) cc_final: 0.7253 (p90) REVERT: C 377 PHE cc_start: 0.5326 (p90) cc_final: 0.4736 (p90) REVERT: C 480 CYS cc_start: 0.1569 (OUTLIER) cc_final: 0.0546 (t) REVERT: C 582 LEU cc_start: 0.8175 (tp) cc_final: 0.7873 (pt) REVERT: C 740 MET cc_start: 0.7734 (tpt) cc_final: 0.7313 (tpp) REVERT: D 90 VAL cc_start: 0.8645 (t) cc_final: 0.8416 (m) REVERT: D 153 MET cc_start: -0.2481 (ttp) cc_final: -0.2960 (mtm) REVERT: D 436 TRP cc_start: 0.3679 (t60) cc_final: 0.3419 (t-100) REVERT: D 697 MET cc_start: 0.7411 (ppp) cc_final: 0.7172 (ppp) REVERT: D 710 ASN cc_start: 0.7154 (p0) cc_final: 0.6866 (p0) REVERT: D 725 GLU cc_start: 0.7295 (tt0) cc_final: 0.7048 (tt0) REVERT: D 965 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7947 (tp-100) REVERT: D 1011 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8144 (mm-40) REVERT: D 1017 GLU cc_start: 0.7459 (tp30) cc_final: 0.7241 (tp30) REVERT: D 1036 GLN cc_start: 0.6211 (OUTLIER) cc_final: 0.5782 (tt0) outliers start: 89 outliers final: 59 residues processed: 403 average time/residue: 0.6438 time to fit residues: 441.4046 Evaluate side-chains 362 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 299 time to evaluate : 8.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 898 PHE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1036 GLN Chi-restraints excluded: chain D residue 1049 LEU Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 124 optimal weight: 4.9990 chunk 344 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 350 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 275 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 GLN D1005 GLN D1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.147323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.118539 restraints weight = 112016.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.120404 restraints weight = 64726.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.120767 restraints weight = 45812.290| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 30296 Z= 0.105 Angle : 0.535 11.068 41218 Z= 0.270 Chirality : 0.043 0.187 4594 Planarity : 0.004 0.047 5319 Dihedral : 3.956 32.891 4018 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.74 % Allowed : 18.40 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3693 helix: -0.13 (0.18), residues: 889 sheet: -0.06 (0.19), residues: 607 loop : -1.40 (0.12), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 886 HIS 0.006 0.001 HIS D1064 PHE 0.027 0.001 PHE B 817 TYR 0.022 0.001 TYR D1007 ARG 0.003 0.000 ARG B 983 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 875) hydrogen bonds : angle 5.12017 ( 2466) SS BOND : bond 0.00381 ( 42) SS BOND : angle 1.42836 ( 84) covalent geometry : bond 0.00235 (30254) covalent geometry : angle 0.53128 (41134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 324 time to evaluate : 7.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: -0.0011 (OUTLIER) cc_final: -0.0365 (pp) REVERT: A 297 MET cc_start: -0.3121 (ptm) cc_final: -0.3567 (ptm) REVERT: A 302 TRP cc_start: 0.2085 (OUTLIER) cc_final: -0.1553 (m-10) REVERT: A 557 MET cc_start: -0.0998 (mmp) cc_final: -0.1219 (mmp) REVERT: B 301 CYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7423 (t) REVERT: B 564 GLN cc_start: 0.6505 (OUTLIER) cc_final: 0.6034 (mm110) REVERT: B 868 GLU cc_start: 0.7877 (mp0) cc_final: 0.7349 (tm-30) REVERT: B 902 MET cc_start: 0.7122 (mmp) cc_final: 0.6823 (mmt) REVERT: B 960 ASN cc_start: 0.8466 (p0) cc_final: 0.7226 (p0) REVERT: B 1139 ASP cc_start: 0.7253 (t0) cc_final: 0.6661 (p0) REVERT: C 377 PHE cc_start: 0.5372 (p90) cc_final: 0.4762 (p90) REVERT: C 480 CYS cc_start: 0.0916 (OUTLIER) cc_final: -0.0080 (t) REVERT: C 954 HIS cc_start: 0.6813 (OUTLIER) cc_final: 0.6421 (m-70) REVERT: D 90 VAL cc_start: 0.8685 (t) cc_final: 0.8453 (m) REVERT: D 153 MET cc_start: -0.2786 (ttp) cc_final: -0.3150 (mtm) REVERT: D 436 TRP cc_start: 0.3805 (t60) cc_final: 0.3534 (t-100) REVERT: D 710 ASN cc_start: 0.7201 (p0) cc_final: 0.6853 (p0) REVERT: D 725 GLU cc_start: 0.7256 (tt0) cc_final: 0.7018 (tt0) REVERT: D 864 LEU cc_start: 0.8478 (tt) cc_final: 0.8018 (tp) REVERT: D 917 TYR cc_start: 0.6982 (m-80) cc_final: 0.6554 (m-80) REVERT: D 965 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7907 (tp-100) REVERT: D 1011 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8140 (mm-40) REVERT: D 1017 GLU cc_start: 0.7603 (tp30) cc_final: 0.7328 (tp30) REVERT: D 1036 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.6063 (tt0) outliers start: 90 outliers final: 57 residues processed: 384 average time/residue: 0.6437 time to fit residues: 428.7434 Evaluate side-chains 363 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 299 time to evaluate : 7.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1036 GLN Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 296 optimal weight: 0.9980 chunk 307 optimal weight: 0.9980 chunk 116 optimal weight: 0.0370 chunk 71 optimal weight: 9.9990 chunk 354 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 208 optimal weight: 0.9980 chunk 357 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 121 ASN B 245 HIS B 487 ASN B 935 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1036 GLN D 519 HIS D 784 GLN D 935 GLN D 955 ASN D 957 GLN D1036 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.146992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.118282 restraints weight = 112582.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.120387 restraints weight = 67674.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.120464 restraints weight = 44206.466| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30296 Z= 0.103 Angle : 0.533 10.761 41218 Z= 0.268 Chirality : 0.043 0.204 4594 Planarity : 0.003 0.047 5319 Dihedral : 3.899 33.280 4018 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.83 % Allowed : 18.34 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 3693 helix: 0.11 (0.18), residues: 881 sheet: -0.04 (0.20), residues: 590 loop : -1.30 (0.12), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 886 HIS 0.012 0.001 HIS D 519 PHE 0.018 0.001 PHE B 817 TYR 0.024 0.001 TYR D1007 ARG 0.006 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 875) hydrogen bonds : angle 5.01221 ( 2466) SS BOND : bond 0.00349 ( 42) SS BOND : angle 1.29536 ( 84) covalent geometry : bond 0.00225 (30254) covalent geometry : angle 0.53008 (41134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 323 time to evaluate : 7.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: -0.0115 (OUTLIER) cc_final: -0.0462 (pp) REVERT: A 302 TRP cc_start: 0.2133 (OUTLIER) cc_final: -0.0503 (m100) REVERT: B 121 ASN cc_start: 0.1595 (OUTLIER) cc_final: 0.0226 (m-40) REVERT: B 301 CYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7489 (t) REVERT: B 564 GLN cc_start: 0.6489 (OUTLIER) cc_final: 0.5957 (mm110) REVERT: B 868 GLU cc_start: 0.8081 (mp0) cc_final: 0.7422 (tm-30) REVERT: B 960 ASN cc_start: 0.8448 (p0) cc_final: 0.7615 (p0) REVERT: B 1139 ASP cc_start: 0.7415 (t0) cc_final: 0.6723 (p0) REVERT: C 271 GLN cc_start: 0.7494 (mm-40) cc_final: 0.6977 (tm-30) REVERT: C 377 PHE cc_start: 0.5360 (p90) cc_final: 0.4764 (p90) REVERT: C 480 CYS cc_start: 0.0921 (OUTLIER) cc_final: -0.0085 (t) REVERT: C 954 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.6554 (m-70) REVERT: C 1120 THR cc_start: 0.7673 (p) cc_final: 0.7316 (t) REVERT: D 90 VAL cc_start: 0.8731 (t) cc_final: 0.8491 (m) REVERT: D 153 MET cc_start: -0.2681 (ttp) cc_final: -0.2975 (mtm) REVERT: D 436 TRP cc_start: 0.3803 (t60) cc_final: 0.3525 (t-100) REVERT: D 710 ASN cc_start: 0.7327 (p0) cc_final: 0.6942 (p0) REVERT: D 725 GLU cc_start: 0.7374 (tt0) cc_final: 0.7073 (tt0) REVERT: D 965 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8055 (tp-100) REVERT: D 1011 GLN cc_start: 0.8485 (tp-100) cc_final: 0.8179 (mm-40) REVERT: D 1017 GLU cc_start: 0.7813 (tp30) cc_final: 0.7497 (tp30) REVERT: D 1036 GLN cc_start: 0.6449 (OUTLIER) cc_final: 0.6054 (tt0) outliers start: 93 outliers final: 68 residues processed: 383 average time/residue: 0.3843 time to fit residues: 254.7478 Evaluate side-chains 376 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 300 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 392 PHE Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 519 HIS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1032 CYS Chi-restraints excluded: chain D residue 1036 GLN Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 363 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 85 optimal weight: 0.7980 chunk 303 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 207 optimal weight: 0.4980 chunk 188 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 GLN D 955 ASN D 957 GLN D1036 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.146084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.117834 restraints weight = 113031.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.118525 restraints weight = 75511.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.119386 restraints weight = 50210.081| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30296 Z= 0.117 Angle : 0.552 10.760 41218 Z= 0.276 Chirality : 0.044 0.215 4594 Planarity : 0.004 0.047 5319 Dihedral : 3.929 33.958 4018 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.93 % Allowed : 19.41 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 3693 helix: 0.25 (0.18), residues: 879 sheet: -0.02 (0.20), residues: 610 loop : -1.28 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 886 HIS 0.033 0.001 HIS D 519 PHE 0.016 0.001 PHE B 375 TYR 0.025 0.001 TYR D1007 ARG 0.004 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 875) hydrogen bonds : angle 5.00697 ( 2466) SS BOND : bond 0.00355 ( 42) SS BOND : angle 1.32795 ( 84) covalent geometry : bond 0.00260 (30254) covalent geometry : angle 0.54895 (41134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 322 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: -0.0259 (OUTLIER) cc_final: -0.0565 (pp) REVERT: A 302 TRP cc_start: 0.2057 (OUTLIER) cc_final: -0.0560 (m100) REVERT: B 301 CYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7532 (t) REVERT: B 564 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6024 (mm110) REVERT: B 868 GLU cc_start: 0.7772 (mp0) cc_final: 0.7320 (tm-30) REVERT: B 960 ASN cc_start: 0.8339 (p0) cc_final: 0.7738 (p0) REVERT: B 1139 ASP cc_start: 0.7372 (t0) cc_final: 0.6747 (p0) REVERT: C 271 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7044 (tm-30) REVERT: C 480 CYS cc_start: 0.0945 (OUTLIER) cc_final: -0.0100 (t) REVERT: C 954 HIS cc_start: 0.6879 (OUTLIER) cc_final: 0.6481 (m-70) REVERT: C 1002 GLN cc_start: 0.7164 (mt0) cc_final: 0.6943 (mt0) REVERT: D 90 VAL cc_start: 0.8716 (t) cc_final: 0.8454 (m) REVERT: D 153 MET cc_start: -0.2764 (ttp) cc_final: -0.3025 (mtm) REVERT: D 436 TRP cc_start: 0.3663 (t60) cc_final: 0.3428 (t-100) REVERT: D 664 ILE cc_start: 0.8012 (mt) cc_final: 0.7713 (tt) REVERT: D 710 ASN cc_start: 0.7446 (p0) cc_final: 0.7052 (p0) REVERT: D 725 GLU cc_start: 0.7610 (tt0) cc_final: 0.7224 (tt0) REVERT: D 864 LEU cc_start: 0.8499 (tt) cc_final: 0.8064 (tp) REVERT: D 965 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8008 (tp-100) REVERT: D 1011 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8107 (mm-40) REVERT: D 1017 GLU cc_start: 0.7406 (tp30) cc_final: 0.7118 (tp30) REVERT: D 1036 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.6115 (tt0) outliers start: 96 outliers final: 70 residues processed: 378 average time/residue: 0.3530 time to fit residues: 223.8348 Evaluate side-chains 380 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 303 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1036 GLN Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 73 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 267 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 ASN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 ASN ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 GLN D 955 ASN ** D1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.144184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.115582 restraints weight = 113783.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.116357 restraints weight = 80317.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.116965 restraints weight = 53552.186| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 30296 Z= 0.145 Angle : 0.590 11.383 41218 Z= 0.297 Chirality : 0.045 0.214 4594 Planarity : 0.004 0.048 5319 Dihedral : 4.118 35.144 4018 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.20 % Allowed : 19.53 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.97 (0.13), residues: 3693 helix: 0.24 (0.18), residues: 886 sheet: -0.07 (0.19), residues: 650 loop : -1.23 (0.13), residues: 2157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 886 HIS 0.010 0.001 HIS D 519 PHE 0.018 0.001 PHE B 888 TYR 0.024 0.001 TYR D1007 ARG 0.006 0.000 ARG D 905 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 875) hydrogen bonds : angle 5.10008 ( 2466) SS BOND : bond 0.00405 ( 42) SS BOND : angle 1.48495 ( 84) covalent geometry : bond 0.00324 (30254) covalent geometry : angle 0.58638 (41134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 316 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: -0.0245 (OUTLIER) cc_final: -0.0522 (pp) REVERT: A 302 TRP cc_start: 0.1863 (OUTLIER) cc_final: -0.1002 (m100) REVERT: B 301 CYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7685 (t) REVERT: B 564 GLN cc_start: 0.6474 (OUTLIER) cc_final: 0.6073 (mm110) REVERT: B 868 GLU cc_start: 0.7864 (mp0) cc_final: 0.7431 (tm-30) REVERT: B 1139 ASP cc_start: 0.7145 (t0) cc_final: 0.6602 (p0) REVERT: C 400 PHE cc_start: 0.3878 (OUTLIER) cc_final: 0.2569 (p90) REVERT: C 425 LEU cc_start: 0.7632 (tt) cc_final: 0.7430 (mm) REVERT: C 480 CYS cc_start: 0.1139 (OUTLIER) cc_final: -0.0055 (t) REVERT: C 954 HIS cc_start: 0.6817 (OUTLIER) cc_final: 0.6316 (m90) REVERT: D 90 VAL cc_start: 0.8763 (t) cc_final: 0.8545 (m) REVERT: D 153 MET cc_start: -0.2790 (ttp) cc_final: -0.3124 (mtm) REVERT: D 436 TRP cc_start: 0.3583 (t60) cc_final: 0.3381 (t-100) REVERT: D 501 TYR cc_start: 0.5326 (OUTLIER) cc_final: 0.4252 (m-80) REVERT: D 725 GLU cc_start: 0.7716 (tt0) cc_final: 0.7320 (tt0) REVERT: D 767 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7510 (mm) REVERT: D 965 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8280 (tp-100) REVERT: D 1011 GLN cc_start: 0.8467 (tp-100) cc_final: 0.8170 (mm-40) REVERT: D 1017 GLU cc_start: 0.7452 (tp30) cc_final: 0.7098 (tp30) REVERT: D 1036 GLN cc_start: 0.5888 (OUTLIER) cc_final: 0.5053 (tt0) outliers start: 105 outliers final: 70 residues processed: 391 average time/residue: 0.3734 time to fit residues: 243.2658 Evaluate side-chains 369 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 289 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1021 SER Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1036 GLN Chi-restraints excluded: chain D residue 1076 THR Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 282 optimal weight: 4.9990 chunk 367 optimal weight: 4.9990 chunk 317 optimal weight: 0.9980 chunk 190 optimal weight: 0.0370 chunk 300 optimal weight: 3.9990 chunk 162 optimal weight: 0.0170 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 250 optimal weight: 0.9980 chunk 231 optimal weight: 0.1980 chunk 112 optimal weight: 10.0000 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1108 ASN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN D 710 ASN D 935 GLN D 955 ASN D 957 GLN D1036 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.145697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.117217 restraints weight = 112156.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.117845 restraints weight = 76160.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.118210 restraints weight = 59624.820| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30296 Z= 0.100 Angle : 0.569 11.357 41218 Z= 0.281 Chirality : 0.044 0.231 4594 Planarity : 0.004 0.048 5319 Dihedral : 3.985 36.516 4018 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.22 % Allowed : 20.75 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.87 (0.13), residues: 3693 helix: 0.40 (0.18), residues: 876 sheet: -0.01 (0.20), residues: 604 loop : -1.18 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 886 HIS 0.027 0.001 HIS C 954 PHE 0.023 0.001 PHE D 981 TYR 0.029 0.001 TYR D1007 ARG 0.004 0.000 ARG B 567 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 875) hydrogen bonds : angle 4.94200 ( 2466) SS BOND : bond 0.00315 ( 42) SS BOND : angle 1.21371 ( 84) covalent geometry : bond 0.00224 (30254) covalent geometry : angle 0.56651 (41134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 323 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ARG cc_start: 0.0759 (OUTLIER) cc_final: -0.1112 (mmm-85) REVERT: A 266 LEU cc_start: -0.0201 (OUTLIER) cc_final: -0.0491 (pp) REVERT: A 302 TRP cc_start: 0.2302 (OUTLIER) cc_final: -0.0425 (m100) REVERT: A 557 MET cc_start: -0.1164 (mmp) cc_final: -0.1426 (mmp) REVERT: B 301 CYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7684 (t) REVERT: B 564 GLN cc_start: 0.6674 (OUTLIER) cc_final: 0.6237 (mm110) REVERT: B 868 GLU cc_start: 0.8034 (mp0) cc_final: 0.7512 (tm-30) REVERT: B 1050 MET cc_start: 0.7869 (ptm) cc_final: 0.7623 (ptm) REVERT: B 1139 ASP cc_start: 0.7278 (t0) cc_final: 0.6619 (p0) REVERT: C 400 PHE cc_start: 0.3714 (OUTLIER) cc_final: 0.2139 (p90) REVERT: C 480 CYS cc_start: 0.1056 (OUTLIER) cc_final: -0.0104 (t) REVERT: C 954 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6542 (m-70) REVERT: C 1120 THR cc_start: 0.7750 (p) cc_final: 0.7445 (t) REVERT: D 90 VAL cc_start: 0.8780 (t) cc_final: 0.8556 (m) REVERT: D 153 MET cc_start: -0.2639 (ttp) cc_final: -0.3138 (mtm) REVERT: D 436 TRP cc_start: 0.3812 (t60) cc_final: 0.3542 (t-100) REVERT: D 501 TYR cc_start: 0.5161 (OUTLIER) cc_final: 0.4246 (m-80) REVERT: D 699 LEU cc_start: 0.7306 (tt) cc_final: 0.6140 (mt) REVERT: D 725 GLU cc_start: 0.7643 (tt0) cc_final: 0.7197 (tt0) REVERT: D 767 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6830 (mm) REVERT: D 864 LEU cc_start: 0.8486 (tt) cc_final: 0.8055 (tp) REVERT: D 965 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8290 (tp-100) REVERT: D 1017 GLU cc_start: 0.7559 (tp30) cc_final: 0.7181 (tp30) outliers start: 73 outliers final: 53 residues processed: 367 average time/residue: 0.3761 time to fit residues: 230.3513 Evaluate side-chains 361 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 298 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 710 ASN Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 935 GLN Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 245 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 365 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 244 optimal weight: 0.0170 chunk 278 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 153 optimal weight: 0.0050 chunk 213 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 overall best weight: 0.5834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 954 HIS C1002 GLN D 710 ASN D 935 GLN D 955 ASN D1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.145686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.116852 restraints weight = 113531.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.118177 restraints weight = 79708.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.118827 restraints weight = 49260.898| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30296 Z= 0.103 Angle : 0.574 12.456 41218 Z= 0.284 Chirality : 0.044 0.276 4594 Planarity : 0.003 0.047 5319 Dihedral : 3.942 36.465 4018 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.04 % Allowed : 20.99 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.86 (0.13), residues: 3693 helix: 0.35 (0.18), residues: 879 sheet: 0.02 (0.20), residues: 598 loop : -1.15 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 886 HIS 0.011 0.001 HIS D 519 PHE 0.020 0.001 PHE B 375 TYR 0.028 0.001 TYR D1007 ARG 0.005 0.000 ARG D 346 Details of bonding type rmsd hydrogen bonds : bond 0.03175 ( 875) hydrogen bonds : angle 4.91269 ( 2466) SS BOND : bond 0.00313 ( 42) SS BOND : angle 1.22353 ( 84) covalent geometry : bond 0.00232 (30254) covalent geometry : angle 0.57220 (41134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 314 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ARG cc_start: 0.0636 (OUTLIER) cc_final: -0.1235 (mmm-85) REVERT: A 266 LEU cc_start: -0.0225 (OUTLIER) cc_final: -0.0496 (pp) REVERT: A 302 TRP cc_start: 0.2184 (OUTLIER) cc_final: -0.0536 (m100) REVERT: A 557 MET cc_start: -0.0822 (mmp) cc_final: -0.1023 (mmp) REVERT: B 301 CYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7601 (t) REVERT: B 564 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6230 (mm110) REVERT: B 868 GLU cc_start: 0.7816 (mp0) cc_final: 0.7462 (tm-30) REVERT: B 988 GLU cc_start: 0.7942 (mp0) cc_final: 0.7668 (mp0) REVERT: B 1050 MET cc_start: 0.7835 (ptm) cc_final: 0.7600 (ptm) REVERT: B 1139 ASP cc_start: 0.7266 (t0) cc_final: 0.6643 (p0) REVERT: C 400 PHE cc_start: 0.3292 (OUTLIER) cc_final: 0.1696 (p90) REVERT: C 480 CYS cc_start: 0.0836 (OUTLIER) cc_final: -0.0298 (t) REVERT: C 954 HIS cc_start: 0.6640 (OUTLIER) cc_final: 0.6213 (m90) REVERT: C 1120 THR cc_start: 0.7685 (p) cc_final: 0.7389 (t) REVERT: D 90 VAL cc_start: 0.8746 (t) cc_final: 0.8485 (m) REVERT: D 153 MET cc_start: -0.2735 (ttp) cc_final: -0.3153 (mtm) REVERT: D 436 TRP cc_start: 0.3736 (t60) cc_final: 0.3505 (t-100) REVERT: D 501 TYR cc_start: 0.5211 (OUTLIER) cc_final: 0.4203 (m-80) REVERT: D 699 LEU cc_start: 0.7358 (tt) cc_final: 0.6188 (mt) REVERT: D 725 GLU cc_start: 0.7736 (tt0) cc_final: 0.7366 (tt0) REVERT: D 767 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6852 (mm) REVERT: D 864 LEU cc_start: 0.8470 (tt) cc_final: 0.8056 (tp) REVERT: D 965 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8207 (tp-100) REVERT: D 1017 GLU cc_start: 0.7348 (tp30) cc_final: 0.6990 (tp30) outliers start: 67 outliers final: 52 residues processed: 356 average time/residue: 0.3684 time to fit residues: 221.0222 Evaluate side-chains 362 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 300 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 302 TRP Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 530 CYS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 400 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 480 CYS Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 954 HIS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 432 CYS Chi-restraints excluded: chain D residue 501 TYR Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 582 LEU Chi-restraints excluded: chain D residue 633 TRP Chi-restraints excluded: chain D residue 636 TYR Chi-restraints excluded: chain D residue 724 THR Chi-restraints excluded: chain D residue 753 LEU Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 881 THR Chi-restraints excluded: chain D residue 993 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1082 CYS Chi-restraints excluded: chain D residue 1121 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 8.9990 chunk 50 optimal weight: 30.0000 chunk 184 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 205 optimal weight: 0.0070 chunk 57 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 914 ASN C1002 GLN D 957 GLN D1011 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.141329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.112667 restraints weight = 114173.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.113068 restraints weight = 87129.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.113376 restraints weight = 55799.280| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.5460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30296 Z= 0.208 Angle : 0.704 13.213 41218 Z= 0.361 Chirality : 0.047 0.215 4594 Planarity : 0.005 0.060 5319 Dihedral : 4.640 36.205 4017 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.32 % Allowed : 21.12 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3693 helix: 0.14 (0.18), residues: 883 sheet: -0.29 (0.19), residues: 650 loop : -1.30 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 886 HIS 0.065 0.002 HIS C 954 PHE 0.025 0.002 PHE B 888 TYR 0.031 0.002 TYR D1007 ARG 0.006 0.001 ARG B 905 Details of bonding type rmsd hydrogen bonds : bond 0.04015 ( 875) hydrogen bonds : angle 5.46057 ( 2466) SS BOND : bond 0.00530 ( 42) SS BOND : angle 1.86252 ( 84) covalent geometry : bond 0.00461 (30254) covalent geometry : angle 0.69992 (41134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11977.85 seconds wall clock time: 213 minutes 17.13 seconds (12797.13 seconds total)