Starting phenix.real_space_refine on Fri Feb 6 17:51:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ooo_70667/02_2026/9ooo_70667.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ooo_70667/02_2026/9ooo_70667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ooo_70667/02_2026/9ooo_70667.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ooo_70667/02_2026/9ooo_70667.map" model { file = "/net/cci-nas-00/data/ceres_data/9ooo_70667/02_2026/9ooo_70667.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ooo_70667/02_2026/9ooo_70667.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.034 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 156 5.16 5 C 16868 2.51 5 N 4520 2.21 5 O 4968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26512 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6628 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 808} Chain: "B" Number of atoms: 6628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6628 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 808} Chain: "C" Number of atoms: 6628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6628 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 808} Chain: "D" Number of atoms: 6628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6628 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 808} Time building chain proxies: 6.46, per 1000 atoms: 0.24 Number of scatterers: 26512 At special positions: 0 Unit cell: (165.36, 171.72, 184.44, 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 156 16.00 O 4968 8.00 N 4520 7.00 C 16868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 756 " - pdb=" SG CYS A 811 " distance=2.03 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 355 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 756 " - pdb=" SG CYS B 811 " distance=2.03 Simple disulfide: pdb=" SG CYS C 83 " - pdb=" SG CYS C 355 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 756 " - pdb=" SG CYS C 811 " distance=2.03 Simple disulfide: pdb=" SG CYS D 83 " - pdb=" SG CYS D 355 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 298 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 756 " - pdb=" SG CYS D 811 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6192 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 31 sheets defined 47.6% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 37 through 51 removed outlier: 3.630A pdb=" N ASP A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.723A pdb=" N GLN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.697A pdb=" N LEU A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 151 through 163 removed outlier: 4.479A pdb=" N LEU A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 216 through 227 removed outlier: 4.156A pdb=" N ARG A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP A 225 " --> pdb=" O ASN A 221 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 249 removed outlier: 3.998A pdb=" N SER A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.842A pdb=" N GLU A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.570A pdb=" N ARG A 297 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 316 through 320 removed outlier: 4.261A pdb=" N MET A 320 " --> pdb=" O ALA A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 344 removed outlier: 3.746A pdb=" N ASN A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.988A pdb=" N GLU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 removed outlier: 4.256A pdb=" N TYR A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 566 through 591 removed outlier: 3.859A pdb=" N VAL A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 removed outlier: 3.770A pdb=" N PHE A 616 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 659 removed outlier: 3.799A pdb=" N ILE A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 703 through 713 Processing helix chain 'A' and resid 724 through 735 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.698A pdb=" N TYR A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 795 removed outlier: 3.572A pdb=" N SER A 785 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 805 removed outlier: 3.865A pdb=" N LEU A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 860 removed outlier: 5.005A pdb=" N GLY A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE A 835 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG A 858 " --> pdb=" O TRP A 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 52 Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.578A pdb=" N GLU B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 101 through 109 removed outlier: 3.745A pdb=" N LEU B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.683A pdb=" N GLY B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.956A pdb=" N ILE B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 180 Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.999A pdb=" N ASP B 186 " --> pdb=" O GLN B 182 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 removed outlier: 3.766A pdb=" N MET B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.956A pdb=" N ASN B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 248 removed outlier: 3.541A pdb=" N LYS B 240 " --> pdb=" O PRO B 236 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N SER B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 removed outlier: 3.916A pdb=" N GLN B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 removed outlier: 3.742A pdb=" N ARG B 297 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 314 through 319 Processing helix chain 'B' and resid 322 through 335 removed outlier: 3.554A pdb=" N TYR B 326 " --> pdb=" O ILE B 322 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 374 removed outlier: 4.805A pdb=" N GLU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 removed outlier: 4.309A pdb=" N TYR B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 removed outlier: 3.802A pdb=" N LEU B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 removed outlier: 4.004A pdb=" N ASN B 532 " --> pdb=" O PRO B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 563 removed outlier: 4.116A pdb=" N LEU B 562 " --> pdb=" O PHE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 591 removed outlier: 3.790A pdb=" N ALA B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 removed outlier: 4.290A pdb=" N VAL B 612 " --> pdb=" O SER B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 627 through 658 Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.841A pdb=" N SER B 663 " --> pdb=" O ARG B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 702 through 713 removed outlier: 3.563A pdb=" N MET B 711 " --> pdb=" O GLN B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 734 Processing helix chain 'B' and resid 743 through 753 Processing helix chain 'B' and resid 779 through 794 removed outlier: 3.577A pdb=" N VAL B 783 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 785 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLN B 786 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG B 787 " --> pdb=" O VAL B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 805 Processing helix chain 'B' and resid 827 through 832 Processing helix chain 'B' and resid 832 through 860 removed outlier: 3.679A pdb=" N GLY B 841 " --> pdb=" O ILE B 837 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 859 " --> pdb=" O TRP B 855 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 74 through 89 Processing helix chain 'C' and resid 98 through 113 removed outlier: 4.287A pdb=" N SER C 104 " --> pdb=" O THR C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.956A pdb=" N GLY C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.751A pdb=" N VAL C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 159 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 180 Processing helix chain 'C' and resid 181 through 192 removed outlier: 3.575A pdb=" N GLN C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 216 through 227 Processing helix chain 'C' and resid 235 through 249 Processing helix chain 'C' and resid 266 through 277 Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.112A pdb=" N CYS C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 314 through 320 removed outlier: 3.740A pdb=" N GLN C 318 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 344 removed outlier: 3.607A pdb=" N LEU C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 375 removed outlier: 4.192A pdb=" N ARG C 367 " --> pdb=" O TRP C 363 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET C 369 " --> pdb=" O GLY C 365 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS C 375 " --> pdb=" O GLU C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 463 Processing helix chain 'C' and resid 469 through 483 removed outlier: 3.779A pdb=" N TYR C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 514 removed outlier: 3.562A pdb=" N GLU C 511 " --> pdb=" O GLY C 507 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 590 removed outlier: 3.687A pdb=" N LEU C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 579 " --> pdb=" O GLY C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 617 Processing helix chain 'C' and resid 627 through 659 removed outlier: 3.721A pdb=" N THR C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 674 removed outlier: 3.859A pdb=" N GLN C 674 " --> pdb=" O ASP C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.595A pdb=" N ASN C 697 " --> pdb=" O MET C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 713 removed outlier: 4.224A pdb=" N TRP C 710 " --> pdb=" O SER C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 724 through 734 removed outlier: 4.074A pdb=" N GLY C 728 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN C 730 " --> pdb=" O GLN C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.804A pdb=" N TYR C 748 " --> pdb=" O ALA C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 794 removed outlier: 3.573A pdb=" N LEU C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 795 through 800 Processing helix chain 'C' and resid 827 through 856 removed outlier: 5.302A pdb=" N GLY C 833 " --> pdb=" O LYS C 829 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL C 834 " --> pdb=" O SER C 830 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE C 835 " --> pdb=" O PHE C 831 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 838 " --> pdb=" O VAL C 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 52 removed outlier: 3.666A pdb=" N ASP D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 89 Processing helix chain 'D' and resid 98 through 113 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 151 through 164 removed outlier: 3.865A pdb=" N VAL D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 Processing helix chain 'D' and resid 203 through 215 removed outlier: 3.575A pdb=" N MET D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 227 Processing helix chain 'D' and resid 235 through 250 Processing helix chain 'D' and resid 266 through 277 Processing helix chain 'D' and resid 293 through 297 Processing helix chain 'D' and resid 306 through 311 removed outlier: 4.002A pdb=" N ASP D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 321 through 344 removed outlier: 3.904A pdb=" N LEU D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 376 removed outlier: 3.627A pdb=" N ARG D 367 " --> pdb=" O TRP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 483 Processing helix chain 'D' and resid 506 through 514 removed outlier: 4.070A pdb=" N LEU D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 532 Processing helix chain 'D' and resid 552 through 556 removed outlier: 3.835A pdb=" N THR D 555 " --> pdb=" O ALA D 552 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL D 556 " --> pdb=" O GLU D 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 552 through 556' Processing helix chain 'D' and resid 557 through 562 removed outlier: 3.829A pdb=" N ALA D 560 " --> pdb=" O ASP D 557 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS D 561 " --> pdb=" O MET D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 591 removed outlier: 3.709A pdb=" N VAL D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D 578 " --> pdb=" O ALA D 574 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU D 579 " --> pdb=" O GLY D 575 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL D 580 " --> pdb=" O THR D 576 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY D 581 " --> pdb=" O VAL D 577 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU D 582 " --> pdb=" O LEU D 578 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 617 removed outlier: 3.716A pdb=" N TRP D 610 " --> pdb=" O TYR D 606 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 659 removed outlier: 3.889A pdb=" N ALA D 636 " --> pdb=" O MET D 632 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 639 " --> pdb=" O GLY D 635 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 703 through 713 removed outlier: 4.232A pdb=" N MET D 711 " --> pdb=" O GLN D 707 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 719 removed outlier: 3.632A pdb=" N GLU D 719 " --> pdb=" O SER D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 734 Processing helix chain 'D' and resid 743 through 753 Processing helix chain 'D' and resid 780 through 794 Processing helix chain 'D' and resid 795 through 803 removed outlier: 4.062A pdb=" N ILE D 799 " --> pdb=" O GLY D 795 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU D 800 " --> pdb=" O ASP D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 830 Processing helix chain 'D' and resid 831 through 860 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 70 removed outlier: 6.561A pdb=" N ILE A 29 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N THR A 68 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA A 31 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 70 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE A 33 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 34 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.555A pdb=" N LEU A 144 " --> pdb=" O HIS A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 196 through 199 removed outlier: 3.677A pdb=" N TYR A 172 " --> pdb=" O GLN A 198 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 230 " --> pdb=" O HIS A 257 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TRP A 258 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 282 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 281 " --> pdb=" O THR A 403 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR A 403 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A 398 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N CYS A 418 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE A 400 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 380 removed outlier: 3.709A pdb=" N LEU A 385 " --> pdb=" O VAL A 378 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 485 through 490 removed outlier: 8.466A pdb=" N ILE A 519 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ARG A 444 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 460 removed outlier: 7.375A pdb=" N VAL A 456 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N TYR A 467 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU A 458 " --> pdb=" O LYS A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 removed outlier: 3.811A pdb=" N MET A 541 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 739 through 742 removed outlier: 3.625A pdb=" N PHE A 739 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 545 " --> pdb=" O ASN A 763 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 64 through 70 removed outlier: 3.559A pdb=" N ASP B 34 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU B 93 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 194 through 196 removed outlier: 3.619A pdb=" N ILE B 231 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 261 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY B 417 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN B 420 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 300 removed outlier: 3.655A pdb=" N HIS B 303 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 378 through 380 Processing sheet with id=AB5, first strand: chain 'B' and resid 485 through 490 removed outlier: 5.047A pdb=" N SER B 522 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY B 771 " --> pdb=" O SER B 522 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 524 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY B 769 " --> pdb=" O LEU B 524 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 485 through 490 removed outlier: 5.047A pdb=" N SER B 522 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY B 771 " --> pdb=" O SER B 522 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 524 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY B 769 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR B 543 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE B 739 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY B 680 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N ASP B 742 " --> pdb=" O GLY B 680 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 455 through 460 removed outlier: 6.189A pdb=" N LYS B 466 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 459 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 65 through 70 removed outlier: 4.012A pdb=" N ALA C 31 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY C 30 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER C 96 " --> pdb=" O GLY C 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE C 32 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU C 93 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE C 119 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N SER C 95 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS C 116 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 194 through 200 removed outlier: 4.723A pdb=" N ARG C 229 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 173 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA C 230 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N TRP C 258 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ILE C 284 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 260 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLN C 286 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU C 281 " --> pdb=" O THR C 403 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR C 403 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N PHE C 398 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N CYS C 418 " --> pdb=" O PHE C 398 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE C 400 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 299 through 300 Processing sheet with id=AC2, first strand: chain 'C' and resid 378 through 380 Processing sheet with id=AC3, first strand: chain 'C' and resid 485 through 490 removed outlier: 3.546A pdb=" N TYR C 489 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 447 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE C 519 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 521 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 520 " --> pdb=" O ALA C 773 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 455 through 456 Processing sheet with id=AC5, first strand: chain 'C' and resid 541 through 542 removed outlier: 3.942A pdb=" N MET C 541 " --> pdb=" O TYR C 770 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 679 through 680 removed outlier: 6.975A pdb=" N GLY C 680 " --> pdb=" O VAL C 740 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N ASP C 742 " --> pdb=" O GLY C 680 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE C 739 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 29 through 33 removed outlier: 6.614A pdb=" N LEU D 93 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N HIS D 116 " --> pdb=" O LEU D 144 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 194 through 200 removed outlier: 3.640A pdb=" N PHE D 168 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 172 " --> pdb=" O GLN D 198 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG D 229 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP D 173 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 230 " --> pdb=" O HIS D 257 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE D 261 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU D 281 " --> pdb=" O THR D 403 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLY D 402 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LYS D 415 " --> pdb=" O GLY D 402 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS D 418 " --> pdb=" O ASN D 426 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 299 through 300 Processing sheet with id=AD1, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AD2, first strand: chain 'D' and resid 485 through 490 removed outlier: 6.378A pdb=" N TYR D 770 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG D 539 " --> pdb=" O TYR D 770 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ILE D 772 " --> pdb=" O THR D 537 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 455 through 460 removed outlier: 6.632A pdb=" N VAL D 456 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR D 467 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU D 458 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 679 through 681 removed outlier: 6.876A pdb=" N GLY D 680 " --> pdb=" O VAL D 740 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N ASP D 742 " --> pdb=" O GLY D 680 " (cutoff:3.500A) 1177 hydrogen bonds defined for protein. 3372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8702 1.34 - 1.46: 6089 1.46 - 1.58: 12033 1.58 - 1.70: 0 1.70 - 1.82: 256 Bond restraints: 27080 Sorted by residual: bond pdb=" C ALA D 563 " pdb=" N PRO D 564 " ideal model delta sigma weight residual 1.335 1.360 -0.026 1.19e-02 7.06e+03 4.63e+00 bond pdb=" N ARG C 660 " pdb=" CA ARG C 660 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.43e+00 bond pdb=" C GLU A 451 " pdb=" N PRO A 452 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.35e+00 bond pdb=" CA MET B 600 " pdb=" C MET B 600 " ideal model delta sigma weight residual 1.518 1.564 -0.046 4.01e-02 6.22e+02 1.31e+00 bond pdb=" CB VAL C 246 " pdb=" CG1 VAL C 246 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.29e+00 ... (remaining 27075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.68: 36712 5.68 - 11.37: 15 11.37 - 17.05: 0 17.05 - 22.73: 0 22.73 - 28.42: 1 Bond angle restraints: 36728 Sorted by residual: angle pdb=" C GLU A 451 " pdb=" N PRO A 452 " pdb=" CD PRO A 452 " ideal model delta sigma weight residual 125.00 96.58 28.42 4.10e+00 5.95e-02 4.80e+01 angle pdb=" N ARG C 660 " pdb=" CA ARG C 660 " pdb=" C ARG C 660 " ideal model delta sigma weight residual 110.80 121.84 -11.04 2.13e+00 2.20e-01 2.68e+01 angle pdb=" C THR C 659 " pdb=" N ARG C 660 " pdb=" CA ARG C 660 " ideal model delta sigma weight residual 121.54 130.38 -8.84 1.91e+00 2.74e-01 2.14e+01 angle pdb=" C ALA A 766 " pdb=" N ASP A 767 " pdb=" CA ASP A 767 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" N ALA C 563 " pdb=" CA ALA C 563 " pdb=" C ALA C 563 " ideal model delta sigma weight residual 109.81 117.01 -7.20 2.21e+00 2.05e-01 1.06e+01 ... (remaining 36723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 14937 17.47 - 34.93: 981 34.93 - 52.40: 135 52.40 - 69.86: 41 69.86 - 87.33: 30 Dihedral angle restraints: 16124 sinusoidal: 6468 harmonic: 9656 Sorted by residual: dihedral pdb=" CA GLU A 451 " pdb=" C GLU A 451 " pdb=" N PRO A 452 " pdb=" CA PRO A 452 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA ARG C 660 " pdb=" C ARG C 660 " pdb=" N ILE C 661 " pdb=" CA ILE C 661 " ideal model delta harmonic sigma weight residual 180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ARG A 660 " pdb=" C ARG A 660 " pdb=" N ILE A 661 " pdb=" CA ILE A 661 " ideal model delta harmonic sigma weight residual -180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 16121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3571 0.067 - 0.134: 500 0.134 - 0.201: 19 0.201 - 0.268: 1 0.268 - 0.335: 1 Chirality restraints: 4092 Sorted by residual: chirality pdb=" CA PRO A 452 " pdb=" N PRO A 452 " pdb=" C PRO A 452 " pdb=" CB PRO A 452 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA ARG C 660 " pdb=" N ARG C 660 " pdb=" C ARG C 660 " pdb=" CB ARG C 660 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB ILE B 521 " pdb=" CA ILE B 521 " pdb=" CG1 ILE B 521 " pdb=" CG2 ILE B 521 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.29e-01 ... (remaining 4089 not shown) Planarity restraints: 4720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 451 " -0.132 5.00e-02 4.00e+02 2.07e-01 6.86e+01 pdb=" N PRO A 452 " 0.358 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " -0.133 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 481 " 0.001 2.00e-02 2.50e+03 2.45e-02 1.20e+01 pdb=" CG TYR D 481 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR D 481 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR D 481 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 481 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR D 481 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR D 481 " -0.035 2.00e-02 2.50e+03 pdb=" OH TYR D 481 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 185 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C LEU B 185 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU B 185 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP B 186 " 0.021 2.00e-02 2.50e+03 ... (remaining 4717 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 690 2.70 - 3.25: 27170 3.25 - 3.80: 39402 3.80 - 4.35: 52039 4.35 - 4.90: 85539 Nonbonded interactions: 204840 Sorted by model distance: nonbonded pdb=" O GLU A 56 " pdb=" NE2 GLN A 59 " model vdw 2.156 3.120 nonbonded pdb=" OD1 ASP D 267 " pdb=" NH1 ARG D 285 " model vdw 2.225 3.120 nonbonded pdb=" O GLY D 279 " pdb=" OH TYR D 405 " model vdw 2.227 3.040 nonbonded pdb=" NH2 ARG C 147 " pdb=" OE1 GLU C 263 " model vdw 2.231 3.120 nonbonded pdb=" OG1 THR B 627 " pdb=" OG1 THR B 630 " model vdw 2.245 3.040 ... (remaining 204835 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 24.920 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 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 : 0.002 0.046 27096 Z= 0.131 Angle : 0.662 28.416 36760 Z= 0.383 Chirality : 0.045 0.335 4092 Planarity : 0.008 0.207 4720 Dihedral : 12.748 87.328 9884 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.88 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.13), residues: 3336 helix: -1.48 (0.11), residues: 1442 sheet: -1.19 (0.24), residues: 402 loop : -1.33 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.003 ARG A 228 TYR 0.042 0.004 TYR B 585 PHE 0.042 0.001 PHE B 536 TRP 0.034 0.002 TRP B 710 HIS 0.007 0.001 HIS D 397 Details of bonding type rmsd covalent geometry : bond 0.00244 (27080) covalent geometry : angle 0.66214 (36728) SS BOND : bond 0.00178 ( 16) SS BOND : angle 0.93029 ( 32) hydrogen bonds : bond 0.16141 ( 1167) hydrogen bonds : angle 7.46180 ( 3372) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 471 time to evaluate : 0.940 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: A 320 MET cc_start: 0.7364 (mtp) cc_final: 0.7087 (mtm) REVERT: A 432 LYS cc_start: 0.6381 (tmmt) cc_final: 0.5350 (tptt) REVERT: B 207 MET cc_start: 0.7639 (ttp) cc_final: 0.7372 (ttt) REVERT: B 630 THR cc_start: 0.7584 (p) cc_final: 0.6547 (p) REVERT: B 780 TYR cc_start: 0.5957 (m-10) cc_final: 0.5254 (m-10) REVERT: C 112 MET cc_start: 0.1699 (mmm) cc_final: 0.1182 (mmm) REVERT: D 40 ASP cc_start: 0.0838 (m-30) cc_final: 0.0567 (m-30) REVERT: D 106 GLN cc_start: 0.4520 (tt0) cc_final: 0.3907 (pp30) REVERT: D 147 ARG cc_start: 0.0966 (mtp180) cc_final: -0.0047 (tmt170) REVERT: D 637 TRP cc_start: 0.7950 (t-100) cc_final: 0.7305 (t-100) REVERT: D 781 ARG cc_start: 0.0762 (ttt180) cc_final: -0.1102 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 471 average time/residue: 0.1778 time to fit residues: 129.7906 Evaluate side-chains 273 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 30.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 607 ASN A 651 ASN A 669 GLN B 324 ASN B 404 ASN B 480 ASN B 588 ASN C 690 HIS D 404 ASN D 651 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.233824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.211337 restraints weight = 45688.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.208669 restraints weight = 60362.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.205512 restraints weight = 56093.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.205392 restraints weight = 48516.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.204518 restraints weight = 36369.948| |-----------------------------------------------------------------------------| r_work (final): 0.4616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 27096 Z= 0.161 Angle : 0.662 13.112 36760 Z= 0.349 Chirality : 0.046 0.325 4092 Planarity : 0.005 0.157 4720 Dihedral : 5.825 43.036 3640 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 1.62 % Allowed : 6.27 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3336 helix: 0.26 (0.13), residues: 1465 sheet: -1.17 (0.24), residues: 417 loop : -0.98 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 631 TYR 0.031 0.002 TYR B 543 PHE 0.021 0.002 PHE A 44 TRP 0.045 0.002 TRP C 610 HIS 0.006 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00361 (27080) covalent geometry : angle 0.66155 (36728) SS BOND : bond 0.00224 ( 16) SS BOND : angle 0.96282 ( 32) hydrogen bonds : bond 0.04834 ( 1167) hydrogen bonds : angle 5.40541 ( 3372) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 293 time to evaluate : 0.716 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: A 156 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8371 (tp) REVERT: A 752 ASN cc_start: 0.6860 (m-40) cc_final: 0.6629 (m110) REVERT: B 207 MET cc_start: 0.8376 (ttp) cc_final: 0.7899 (ttm) REVERT: B 215 MET cc_start: 0.6186 (mtt) cc_final: 0.4774 (ttm) REVERT: B 221 ASN cc_start: 0.7626 (t0) cc_final: 0.7404 (t0) REVERT: B 797 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6123 (mtp) REVERT: C 112 MET cc_start: 0.2139 (mmm) cc_final: 0.1732 (mmm) REVERT: C 215 MET cc_start: 0.2897 (mtp) cc_final: 0.2661 (mtp) REVERT: C 711 MET cc_start: 0.8727 (tpp) cc_final: 0.8106 (tpp) REVERT: D 40 ASP cc_start: 0.0700 (m-30) cc_final: 0.0396 (m-30) REVERT: D 86 MET cc_start: 0.1041 (mpp) cc_final: -0.0418 (ptm) REVERT: D 147 ARG cc_start: 0.0958 (mtp180) cc_final: 0.0478 (tmt170) REVERT: D 350 MET cc_start: 0.2709 (mtm) cc_final: 0.2123 (ttm) REVERT: D 438 MET cc_start: 0.3994 (OUTLIER) cc_final: 0.3232 (mtp) REVERT: D 704 MET cc_start: 0.7443 (mmp) cc_final: 0.7056 (mmt) REVERT: D 781 ARG cc_start: 0.0825 (ttt180) cc_final: -0.0809 (ptp-170) REVERT: D 790 GLU cc_start: 0.4300 (tp30) cc_final: 0.2964 (mt-10) REVERT: D 862 ARG cc_start: 0.1645 (mtt180) cc_final: 0.0258 (ptm160) outliers start: 47 outliers final: 20 residues processed: 329 average time/residue: 0.1734 time to fit residues: 89.7147 Evaluate side-chains 270 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 607 ASN Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 106 optimal weight: 0.9990 chunk 249 optimal weight: 0.0670 chunk 94 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 267 optimal weight: 0.4980 chunk 69 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 172 optimal weight: 50.0000 overall best weight: 0.4920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 726 GLN A 730 GLN B 318 GLN ** B 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 588 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.235474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.214391 restraints weight = 46201.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.210460 restraints weight = 55633.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.205933 restraints weight = 54756.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.205884 restraints weight = 54107.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.205080 restraints weight = 39130.626| |-----------------------------------------------------------------------------| r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27096 Z= 0.109 Angle : 0.584 14.365 36760 Z= 0.303 Chirality : 0.043 0.376 4092 Planarity : 0.004 0.161 4720 Dihedral : 5.172 34.450 3640 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 1.34 % Allowed : 7.37 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3336 helix: 0.79 (0.13), residues: 1474 sheet: -0.84 (0.24), residues: 419 loop : -0.87 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 692 TYR 0.021 0.001 TYR A 734 PHE 0.019 0.001 PHE A 655 TRP 0.060 0.001 TRP C 610 HIS 0.007 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00227 (27080) covalent geometry : angle 0.58378 (36728) SS BOND : bond 0.00143 ( 16) SS BOND : angle 0.65554 ( 32) hydrogen bonds : bond 0.03963 ( 1167) hydrogen bonds : angle 4.92955 ( 3372) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 277 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 MET cc_start: 0.8052 (mmt) cc_final: 0.7559 (mmm) REVERT: A 156 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8508 (tp) REVERT: A 175 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7791 (mm-30) REVERT: A 411 ARG cc_start: 0.7386 (mtm110) cc_final: 0.7133 (mtm110) REVERT: A 432 LYS cc_start: 0.5816 (tmmt) cc_final: 0.5109 (tptp) REVERT: A 541 MET cc_start: 0.8148 (tmm) cc_final: 0.7879 (tmm) REVERT: A 752 ASN cc_start: 0.6679 (m-40) cc_final: 0.6428 (m110) REVERT: B 207 MET cc_start: 0.8301 (ttp) cc_final: 0.7684 (ttt) REVERT: B 215 MET cc_start: 0.6342 (OUTLIER) cc_final: 0.5888 (ttm) REVERT: B 221 ASN cc_start: 0.7532 (t0) cc_final: 0.7092 (t0) REVERT: B 673 LYS cc_start: 0.4131 (OUTLIER) cc_final: 0.2929 (ptmm) REVERT: B 797 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6746 (mtt) REVERT: C 112 MET cc_start: 0.2087 (mmm) cc_final: 0.1583 (mmm) REVERT: C 350 MET cc_start: 0.2596 (mtm) cc_final: 0.2299 (ttm) REVERT: C 609 MET cc_start: 0.6529 (ppp) cc_final: 0.6292 (ppp) REVERT: C 711 MET cc_start: 0.8665 (tpp) cc_final: 0.8093 (tpp) REVERT: D 40 ASP cc_start: 0.0716 (m-30) cc_final: 0.0145 (m-30) REVERT: D 45 ARG cc_start: 0.4844 (mtt-85) cc_final: 0.4588 (mtt180) REVERT: D 86 MET cc_start: 0.0918 (mpp) cc_final: -0.0271 (ptm) REVERT: D 147 ARG cc_start: 0.1436 (mtp180) cc_final: 0.0936 (tmt170) REVERT: D 781 ARG cc_start: 0.0840 (ttt180) cc_final: -0.0797 (ptp-170) REVERT: D 790 GLU cc_start: 0.4728 (tp30) cc_final: 0.3250 (mt-10) outliers start: 39 outliers final: 21 residues processed: 302 average time/residue: 0.1535 time to fit residues: 76.7677 Evaluate side-chains 270 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 607 ASN Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 247 optimal weight: 9.9990 chunk 38 optimal weight: 0.0770 chunk 167 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 295 optimal weight: 20.0000 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 HIS B 28 HIS B 302 ASN B 324 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 775 GLN C 190 GLN D 153 HIS D 752 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.232998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.211866 restraints weight = 45501.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.210035 restraints weight = 66268.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.207449 restraints weight = 60818.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.207244 restraints weight = 57897.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.206623 restraints weight = 42177.065| |-----------------------------------------------------------------------------| r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 27096 Z= 0.320 Angle : 0.785 17.894 36760 Z= 0.408 Chirality : 0.050 0.332 4092 Planarity : 0.006 0.169 4720 Dihedral : 5.689 38.371 3640 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.02 % Rotamer: Outliers : 2.44 % Allowed : 9.88 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3336 helix: 0.59 (0.13), residues: 1465 sheet: -1.35 (0.24), residues: 407 loop : -1.18 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 411 TYR 0.029 0.003 TYR C 543 PHE 0.037 0.003 PHE B 184 TRP 0.076 0.002 TRP C 610 HIS 0.009 0.002 HIS B 397 Details of bonding type rmsd covalent geometry : bond 0.00775 (27080) covalent geometry : angle 0.78406 (36728) SS BOND : bond 0.00406 ( 16) SS BOND : angle 1.77748 ( 32) hydrogen bonds : bond 0.05482 ( 1167) hydrogen bonds : angle 5.46710 ( 3372) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 266 time to evaluate : 1.251 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 86 MET cc_start: 0.7253 (mtm) cc_final: 0.7034 (mtm) REVERT: A 156 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8625 (tp) REVERT: A 432 LYS cc_start: 0.5666 (tmmt) cc_final: 0.4753 (tptp) REVERT: B 207 MET cc_start: 0.8114 (ttp) cc_final: 0.7887 (ttm) REVERT: B 215 MET cc_start: 0.6681 (OUTLIER) cc_final: 0.5310 (ttm) REVERT: B 221 ASN cc_start: 0.7770 (t0) cc_final: 0.7303 (t0) REVERT: B 797 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6919 (mtt) REVERT: C 86 MET cc_start: 0.1124 (mtm) cc_final: 0.0498 (ttm) REVERT: C 112 MET cc_start: 0.2180 (mmm) cc_final: 0.1799 (mmm) REVERT: C 711 MET cc_start: 0.8703 (tpp) cc_final: 0.8046 (tpp) REVERT: D 40 ASP cc_start: 0.0972 (m-30) cc_final: 0.0567 (m-30) REVERT: D 86 MET cc_start: 0.1229 (mpp) cc_final: -0.0217 (ptm) REVERT: D 106 GLN cc_start: 0.4793 (tt0) cc_final: 0.3799 (pp30) REVERT: D 147 ARG cc_start: 0.0558 (mtp180) cc_final: 0.0202 (tmt170) REVERT: D 234 MET cc_start: 0.3052 (ptt) cc_final: 0.2381 (ptt) REVERT: D 350 MET cc_start: 0.1751 (mtp) cc_final: 0.1371 (mtp) REVERT: D 781 ARG cc_start: 0.0950 (ttt180) cc_final: -0.0106 (mtm180) REVERT: D 790 GLU cc_start: 0.5208 (tp30) cc_final: 0.3518 (mt-10) outliers start: 71 outliers final: 49 residues processed: 316 average time/residue: 0.1557 time to fit residues: 81.2233 Evaluate side-chains 286 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 607 ASN Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 372 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 295 optimal weight: 9.9990 chunk 242 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 chunk 169 optimal weight: 0.0040 chunk 188 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 chunk 260 optimal weight: 50.0000 chunk 156 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 ASN B 106 GLN B 302 ASN B 324 ASN B 690 HIS ** D 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4879 r_free = 0.4879 target = 0.246981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.220661 restraints weight = 48181.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.212601 restraints weight = 38202.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.208184 restraints weight = 48229.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.206475 restraints weight = 51633.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.204430 restraints weight = 51689.098| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27096 Z= 0.110 Angle : 0.582 16.188 36760 Z= 0.298 Chirality : 0.043 0.351 4092 Planarity : 0.004 0.161 4720 Dihedral : 4.978 35.987 3640 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.12 % Favored : 96.85 % Rotamer: Outliers : 1.62 % Allowed : 11.60 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3336 helix: 1.02 (0.14), residues: 1479 sheet: -1.08 (0.25), residues: 417 loop : -1.11 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 631 TYR 0.018 0.001 TYR A 734 PHE 0.034 0.001 PHE A 254 TRP 0.040 0.001 TRP C 610 HIS 0.008 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00241 (27080) covalent geometry : angle 0.58190 (36728) SS BOND : bond 0.00143 ( 16) SS BOND : angle 0.97827 ( 32) hydrogen bonds : bond 0.03894 ( 1167) hydrogen bonds : angle 4.85046 ( 3372) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 257 time to evaluate : 1.014 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: A 432 LYS cc_start: 0.5506 (tmmt) cc_final: 0.4863 (tptp) REVERT: A 747 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6759 (tm-30) REVERT: B 215 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6343 (ttm) REVERT: B 221 ASN cc_start: 0.7869 (t0) cc_final: 0.7418 (t0) REVERT: B 690 HIS cc_start: 0.7931 (t-90) cc_final: 0.7529 (t70) REVERT: C 112 MET cc_start: 0.1734 (mmm) cc_final: 0.1113 (mmm) REVERT: C 711 MET cc_start: 0.8673 (tpp) cc_final: 0.8018 (tpp) REVERT: D 40 ASP cc_start: 0.0814 (m-30) cc_final: 0.0412 (m-30) REVERT: D 86 MET cc_start: 0.1265 (mpp) cc_final: -0.0248 (ptm) REVERT: D 147 ARG cc_start: 0.0103 (mtp180) cc_final: -0.0216 (tmt170) REVERT: D 234 MET cc_start: 0.2442 (ptt) cc_final: 0.1734 (ptt) REVERT: D 438 MET cc_start: 0.4298 (OUTLIER) cc_final: 0.4027 (mmt) REVERT: D 600 MET cc_start: 0.4449 (mmt) cc_final: 0.3767 (tpp) REVERT: D 693 MET cc_start: 0.4284 (mmm) cc_final: 0.4032 (ttt) REVERT: D 781 ARG cc_start: 0.0802 (ttt180) cc_final: -0.0878 (ptp-170) REVERT: D 790 GLU cc_start: 0.5106 (tp30) cc_final: 0.3836 (mt-10) outliers start: 47 outliers final: 27 residues processed: 286 average time/residue: 0.1628 time to fit residues: 76.1522 Evaluate side-chains 269 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 269 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 165 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 HIS C 588 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.238866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.212775 restraints weight = 47035.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.209425 restraints weight = 59260.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.206281 restraints weight = 54797.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.204613 restraints weight = 51494.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.202782 restraints weight = 49738.438| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27096 Z= 0.127 Angle : 0.584 16.370 36760 Z= 0.298 Chirality : 0.043 0.369 4092 Planarity : 0.004 0.162 4720 Dihedral : 4.793 38.801 3640 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 1.72 % Allowed : 12.26 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3336 helix: 1.18 (0.14), residues: 1480 sheet: -0.98 (0.25), residues: 417 loop : -1.13 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 147 TYR 0.015 0.001 TYR B 780 PHE 0.026 0.001 PHE A 254 TRP 0.040 0.001 TRP C 610 HIS 0.008 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00292 (27080) covalent geometry : angle 0.58331 (36728) SS BOND : bond 0.00129 ( 16) SS BOND : angle 1.15071 ( 32) hydrogen bonds : bond 0.03866 ( 1167) hydrogen bonds : angle 4.79011 ( 3372) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 0.703 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 432 LYS cc_start: 0.5542 (tmmt) cc_final: 0.4968 (tptp) REVERT: B 215 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6377 (ttm) REVERT: B 221 ASN cc_start: 0.7980 (t0) cc_final: 0.7528 (t0) REVERT: B 673 LYS cc_start: 0.4848 (OUTLIER) cc_final: 0.3800 (ptmm) REVERT: C 86 MET cc_start: 0.0751 (mtm) cc_final: 0.0257 (ttm) REVERT: C 711 MET cc_start: 0.8454 (tpp) cc_final: 0.7850 (tpp) REVERT: D 86 MET cc_start: 0.1363 (mpp) cc_final: -0.0205 (ptm) REVERT: D 147 ARG cc_start: 0.0097 (mtp180) cc_final: -0.0227 (tmt170) REVERT: D 350 MET cc_start: 0.2783 (mmm) cc_final: 0.2040 (mtp) REVERT: D 600 MET cc_start: 0.4986 (mmt) cc_final: 0.4372 (tpp) REVERT: D 781 ARG cc_start: 0.0633 (ttt180) cc_final: -0.1041 (ptp-170) outliers start: 50 outliers final: 33 residues processed: 281 average time/residue: 0.1604 time to fit residues: 73.7988 Evaluate side-chains 270 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 587 LEU Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 181 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 200 optimal weight: 20.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 HIS B 250 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 HIS D 426 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.239127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.215604 restraints weight = 46744.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.212375 restraints weight = 58603.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.209123 restraints weight = 55762.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.207731 restraints weight = 48388.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.206024 restraints weight = 51490.090| |-----------------------------------------------------------------------------| r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27096 Z= 0.106 Angle : 0.562 13.772 36760 Z= 0.287 Chirality : 0.042 0.319 4092 Planarity : 0.004 0.149 4720 Dihedral : 4.584 37.474 3640 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 1.52 % Allowed : 12.84 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3336 helix: 1.27 (0.14), residues: 1490 sheet: -0.90 (0.25), residues: 416 loop : -1.12 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 147 TYR 0.018 0.001 TYR C 648 PHE 0.051 0.001 PHE C 611 TRP 0.051 0.001 TRP C 610 HIS 0.011 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00232 (27080) covalent geometry : angle 0.56192 (36728) SS BOND : bond 0.00116 ( 16) SS BOND : angle 0.69509 ( 32) hydrogen bonds : bond 0.03577 ( 1167) hydrogen bonds : angle 4.65007 ( 3372) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 1.224 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: A 107 SER cc_start: 0.8758 (p) cc_final: 0.8554 (m) REVERT: A 432 LYS cc_start: 0.5826 (tmmt) cc_final: 0.5308 (tptp) REVERT: B 215 MET cc_start: 0.6973 (OUTLIER) cc_final: 0.6462 (ttm) REVERT: B 221 ASN cc_start: 0.7838 (t0) cc_final: 0.7383 (t0) REVERT: B 673 LYS cc_start: 0.4930 (OUTLIER) cc_final: 0.4116 (ptmm) REVERT: C 86 MET cc_start: 0.0949 (mtm) cc_final: 0.0446 (ttp) REVERT: C 207 MET cc_start: 0.0474 (tpp) cc_final: 0.0182 (tpt) REVERT: C 234 MET cc_start: 0.1067 (ttp) cc_final: 0.0516 (ttp) REVERT: C 711 MET cc_start: 0.8387 (tpp) cc_final: 0.7831 (tpp) REVERT: D 40 ASP cc_start: -0.0555 (m-30) cc_final: -0.1339 (m-30) REVERT: D 86 MET cc_start: 0.1696 (tpp) cc_final: 0.0288 (ptm) REVERT: D 147 ARG cc_start: 0.0234 (mtp180) cc_final: -0.0129 (tmt170) REVERT: D 350 MET cc_start: 0.2661 (mmm) cc_final: 0.1903 (mtp) REVERT: D 600 MET cc_start: 0.4845 (mmt) cc_final: 0.4380 (tpp) REVERT: D 781 ARG cc_start: 0.0163 (ttt180) cc_final: -0.1766 (ptp-170) outliers start: 44 outliers final: 30 residues processed: 274 average time/residue: 0.1704 time to fit residues: 76.3439 Evaluate side-chains 265 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 690 HIS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 633 MET Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 154 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 285 optimal weight: 30.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 ASN B 324 ASN ** B 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN C 420 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.223334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.192306 restraints weight = 43774.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.187397 restraints weight = 63315.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.184178 restraints weight = 52823.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.183811 restraints weight = 46586.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.183207 restraints weight = 35974.580| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 27096 Z= 0.220 Angle : 0.674 20.831 36760 Z= 0.344 Chirality : 0.046 0.345 4092 Planarity : 0.005 0.175 4720 Dihedral : 4.944 42.235 3640 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 1.83 % Allowed : 13.09 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3336 helix: 1.11 (0.14), residues: 1481 sheet: -1.07 (0.25), residues: 418 loop : -1.21 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 411 TYR 0.025 0.002 TYR B 405 PHE 0.027 0.002 PHE B 171 TRP 0.047 0.002 TRP C 610 HIS 0.027 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00532 (27080) covalent geometry : angle 0.67333 (36728) SS BOND : bond 0.00159 ( 16) SS BOND : angle 0.91895 ( 32) hydrogen bonds : bond 0.04432 ( 1167) hydrogen bonds : angle 4.98265 ( 3372) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 0.754 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: A 432 LYS cc_start: 0.6213 (tmmt) cc_final: 0.5390 (tptp) REVERT: B 215 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6545 (ttm) REVERT: B 221 ASN cc_start: 0.8181 (t0) cc_final: 0.7665 (t0) REVERT: B 609 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6414 (ppp) REVERT: C 86 MET cc_start: 0.0537 (mtm) cc_final: -0.0021 (ttt) REVERT: C 207 MET cc_start: 0.0117 (tpp) cc_final: -0.0119 (tpt) REVERT: C 234 MET cc_start: 0.1135 (ttp) cc_final: 0.0850 (ttp) REVERT: C 350 MET cc_start: -0.1025 (tpt) cc_final: -0.2186 (mmt) REVERT: C 369 MET cc_start: -0.0189 (tpt) cc_final: -0.1872 (ptt) REVERT: C 617 VAL cc_start: 0.7698 (m) cc_final: 0.7263 (p) REVERT: C 711 MET cc_start: 0.8761 (tpp) cc_final: 0.8172 (tpp) REVERT: D 86 MET cc_start: 0.2093 (tpp) cc_final: 0.0488 (ptm) REVERT: D 147 ARG cc_start: 0.0122 (mtp180) cc_final: -0.0319 (tmt170) REVERT: D 350 MET cc_start: 0.2500 (mmm) cc_final: 0.1716 (mtp) REVERT: D 438 MET cc_start: 0.5942 (mmt) cc_final: 0.5135 (tpp) REVERT: D 600 MET cc_start: 0.4878 (mmt) cc_final: 0.4310 (tpp) outliers start: 53 outliers final: 40 residues processed: 279 average time/residue: 0.1662 time to fit residues: 76.4555 Evaluate side-chains 267 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 588 ASN Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 609 MET Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 633 MET Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 147 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 276 optimal weight: 0.0980 chunk 216 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 164 optimal weight: 9.9990 chunk 239 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.226323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.196615 restraints weight = 43662.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.191144 restraints weight = 55938.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.186250 restraints weight = 46790.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.185955 restraints weight = 48933.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.185602 restraints weight = 34175.546| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27096 Z= 0.106 Angle : 0.582 13.857 36760 Z= 0.296 Chirality : 0.042 0.201 4092 Planarity : 0.004 0.078 4720 Dihedral : 4.660 59.703 3640 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 1.38 % Allowed : 13.77 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3336 helix: 1.27 (0.14), residues: 1493 sheet: -0.86 (0.26), residues: 410 loop : -1.19 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 631 TYR 0.021 0.001 TYR C 648 PHE 0.023 0.001 PHE C 835 TRP 0.040 0.001 TRP C 610 HIS 0.009 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00233 (27080) covalent geometry : angle 0.58149 (36728) SS BOND : bond 0.00203 ( 16) SS BOND : angle 1.00672 ( 32) hydrogen bonds : bond 0.03648 ( 1167) hydrogen bonds : angle 4.69139 ( 3372) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 LYS cc_start: 0.6047 (tmmt) cc_final: 0.5486 (tptp) REVERT: A 597 MET cc_start: 0.4119 (ttp) cc_final: 0.2339 (mtm) REVERT: A 711 MET cc_start: 0.7923 (ppp) cc_final: 0.7662 (ppp) REVERT: A 747 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6794 (tm-30) REVERT: B 215 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6461 (ttm) REVERT: B 221 ASN cc_start: 0.8086 (t0) cc_final: 0.7695 (t0) REVERT: B 609 MET cc_start: 0.6904 (ppp) cc_final: 0.6319 (ppp) REVERT: B 673 LYS cc_start: 0.5688 (OUTLIER) cc_final: 0.4859 (ptmm) REVERT: C 112 MET cc_start: 0.2944 (mtp) cc_final: 0.2525 (mtp) REVERT: C 234 MET cc_start: 0.1058 (ttp) cc_final: 0.0745 (ttp) REVERT: C 350 MET cc_start: -0.1215 (tpt) cc_final: -0.1984 (mmt) REVERT: C 369 MET cc_start: -0.0325 (tpt) cc_final: -0.1873 (ptt) REVERT: C 450 GLU cc_start: 0.6779 (tp30) cc_final: 0.6492 (tp30) REVERT: C 617 VAL cc_start: 0.7409 (m) cc_final: 0.6999 (p) REVERT: C 711 MET cc_start: 0.8574 (tpp) cc_final: 0.8052 (tpp) REVERT: D 86 MET cc_start: 0.2072 (tpp) cc_final: 0.0475 (ptm) REVERT: D 147 ARG cc_start: 0.0074 (mtp180) cc_final: -0.0300 (tmt170) REVERT: D 350 MET cc_start: 0.2896 (mmm) cc_final: 0.2094 (mtp) REVERT: D 438 MET cc_start: 0.5909 (mmt) cc_final: 0.5318 (tpp) REVERT: D 600 MET cc_start: 0.5190 (mmt) cc_final: 0.4760 (tpp) REVERT: D 632 MET cc_start: 0.7345 (mmm) cc_final: 0.7131 (mmm) REVERT: D 693 MET cc_start: 0.4591 (mmm) cc_final: 0.3997 (ttp) REVERT: D 781 ARG cc_start: 0.0168 (ttt180) cc_final: -0.1347 (ptt180) outliers start: 40 outliers final: 29 residues processed: 272 average time/residue: 0.1677 time to fit residues: 75.0788 Evaluate side-chains 260 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 734 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 704 MET Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 314 optimal weight: 5.9990 chunk 302 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 192 optimal weight: 0.0970 chunk 38 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 268 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.227308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.198030 restraints weight = 43510.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.192756 restraints weight = 55641.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.187756 restraints weight = 45991.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.187466 restraints weight = 48938.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.186960 restraints weight = 33442.223| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27096 Z= 0.140 Angle : 0.608 13.409 36760 Z= 0.309 Chirality : 0.044 0.305 4092 Planarity : 0.004 0.076 4720 Dihedral : 4.665 59.416 3640 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 1.21 % Allowed : 13.98 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3336 helix: 1.25 (0.14), residues: 1493 sheet: -0.88 (0.26), residues: 410 loop : -1.21 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 411 TYR 0.032 0.002 TYR B 705 PHE 0.027 0.001 PHE A 640 TRP 0.045 0.001 TRP C 610 HIS 0.008 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00330 (27080) covalent geometry : angle 0.60753 (36728) SS BOND : bond 0.00181 ( 16) SS BOND : angle 1.01367 ( 32) hydrogen bonds : bond 0.03850 ( 1167) hydrogen bonds : angle 4.73854 ( 3372) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6672 Ramachandran restraints generated. 3336 Oldfield, 0 Emsley, 3336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.801 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: A 281 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 432 LYS cc_start: 0.5708 (tmmt) cc_final: 0.5101 (tptp) REVERT: A 607 ASN cc_start: 0.7057 (OUTLIER) cc_final: 0.5318 (t0) REVERT: A 747 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6903 (tm-30) REVERT: B 211 LEU cc_start: 0.7622 (tp) cc_final: 0.7341 (tp) REVERT: B 215 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6123 (ttm) REVERT: B 221 ASN cc_start: 0.8089 (t0) cc_final: 0.7719 (t0) REVERT: B 609 MET cc_start: 0.6965 (ppp) cc_final: 0.6396 (ppp) REVERT: B 673 LYS cc_start: 0.5571 (OUTLIER) cc_final: 0.4712 (ptmm) REVERT: C 112 MET cc_start: 0.2987 (mtp) cc_final: 0.2607 (mtp) REVERT: C 234 MET cc_start: 0.0933 (ttp) cc_final: 0.0651 (ttp) REVERT: C 350 MET cc_start: -0.1765 (tpt) cc_final: -0.2359 (mmt) REVERT: C 369 MET cc_start: 0.0113 (tpt) cc_final: -0.1379 (ptt) REVERT: C 617 VAL cc_start: 0.7496 (m) cc_final: 0.7062 (p) REVERT: C 711 MET cc_start: 0.8599 (tpp) cc_final: 0.8061 (tpp) REVERT: D 86 MET cc_start: 0.2129 (tpp) cc_final: 0.0479 (ptm) REVERT: D 147 ARG cc_start: 0.0137 (mtp180) cc_final: -0.0288 (tmt170) REVERT: D 350 MET cc_start: 0.3116 (mmm) cc_final: 0.2369 (mtp) REVERT: D 438 MET cc_start: 0.5819 (mmt) cc_final: 0.5310 (tpp) REVERT: D 600 MET cc_start: 0.5233 (mmt) cc_final: 0.4838 (tpp) REVERT: D 693 MET cc_start: 0.4632 (mmm) cc_final: 0.4022 (ttp) outliers start: 35 outliers final: 26 residues processed: 264 average time/residue: 0.1626 time to fit residues: 71.2860 Evaluate side-chains 265 residues out of total 2904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 607 ASN Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 673 LYS Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 772 ILE Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 817 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 196 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 263 optimal weight: 5.9990 chunk 321 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN C 619 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.227101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.198092 restraints weight = 43568.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.192421 restraints weight = 55355.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.187574 restraints weight = 46046.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.187249 restraints weight = 48972.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.186847 restraints weight = 33794.508| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27096 Z= 0.149 Angle : 0.610 13.749 36760 Z= 0.311 Chirality : 0.044 0.217 4092 Planarity : 0.004 0.061 4720 Dihedral : 4.659 57.249 3640 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 1.34 % Allowed : 14.02 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3336 helix: 1.22 (0.14), residues: 1493 sheet: -0.86 (0.26), residues: 410 loop : -1.23 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 411 TYR 0.024 0.002 TYR C 648 PHE 0.027 0.002 PHE A 640 TRP 0.045 0.002 TRP C 610 HIS 0.008 0.001 HIS A 690 Details of bonding type rmsd covalent geometry : bond 0.00356 (27080) covalent geometry : angle 0.60901 (36728) SS BOND : bond 0.00178 ( 16) SS BOND : angle 1.03906 ( 32) hydrogen bonds : bond 0.03886 ( 1167) hydrogen bonds : angle 4.75273 ( 3372) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3749.33 seconds wall clock time: 65 minutes 50.33 seconds (3950.33 seconds total)