Starting phenix.real_space_refine on Sun Sep 13 13:32:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5kuf_8289/09_2026/5kuf_8289.cif Found real_map, /net/cci-nas-00/data/ceres_data/5kuf_8289/09_2026/5kuf_8289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5kuf_8289/09_2026/5kuf_8289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5kuf_8289/09_2026/5kuf_8289.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5kuf_8289/09_2026/5kuf_8289.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5kuf_8289/09_2026/5kuf_8289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5kuf_8289/09_2026/5kuf_8289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5kuf_8289/09_2026/5kuf_8289.map" } resolution = 3.8 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= -0.000 sd= 0.007 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 124 5.16 5 C 15232 2.51 5 N 3944 2.21 5 O 4428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23728 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5921 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 24, 'TRANS': 720} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5921 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 24, 'TRANS': 720} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'SYM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'SYM': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, D Time building chain proxies: 11.33, per 1000 atoms: 0.48 Number of scatterers: 23728 At special positions: 0 Unit cell: (136.372, 131.076, 182.712, 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 124 16.00 O 4428 8.00 N 3944 7.00 C 15232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 316 " distance=2.04 Simple disulfide: pdb=" SG CYS A 719 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 719 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 316 " distance=2.04 Simple disulfide: pdb=" SG CYS C 719 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 316 " distance=2.03 Simple disulfide: pdb=" SG CYS D 719 " - pdb=" SG CYS D 773 " distance=2.02 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 892.1 milliseconds 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5600 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 47.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 20 through 36 removed outlier: 4.709A pdb=" N ALA A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 69 removed outlier: 4.102A pdb=" N LYS A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 4.646A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 148 through 154 removed outlier: 4.158A pdb=" N ILE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.768A pdb=" N LEU A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 removed outlier: 4.287A pdb=" N LYS A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.564A pdb=" N PHE A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.662A pdb=" N ARG A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 240' Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.599A pdb=" N GLU A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 305 removed outlier: 3.744A pdb=" N MET A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.664A pdb=" N MET A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 removed outlier: 4.186A pdb=" N SER A 396 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 397' Processing helix chain 'A' and resid 423 through 426 Processing helix chain 'A' and resid 432 through 444 removed outlier: 3.607A pdb=" N ARG A 437 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 477 Processing helix chain 'A' and resid 532 through 545 removed outlier: 3.722A pdb=" N LEU A 537 " --> pdb=" O TRP A 533 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 539 " --> pdb=" O TYR A 535 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 544 " --> pdb=" O TYR A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 600 through 629 removed outlier: 3.965A pdb=" N VAL A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 627 " --> pdb=" O ASN A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 633 removed outlier: 3.610A pdb=" N MET A 633 " --> pdb=" O VAL A 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 633' Processing helix chain 'A' and resid 639 through 646 removed outlier: 3.746A pdb=" N LEU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 665 Processing helix chain 'A' and resid 668 through 680 Processing helix chain 'A' and resid 681 through 686 Processing helix chain 'A' and resid 689 through 700 removed outlier: 3.631A pdb=" N VAL A 697 " --> pdb=" O GLY A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.790A pdb=" N GLN A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 757 removed outlier: 3.566A pdb=" N GLN A 753 " --> pdb=" O ILE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 768 Processing helix chain 'A' and resid 789 through 796 removed outlier: 3.858A pdb=" N PHE A 793 " --> pdb=" O ILE A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 803 removed outlier: 4.054A pdb=" N LEU A 800 " --> pdb=" O LEU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 removed outlier: 3.664A pdb=" N ALA A 807 " --> pdb=" O VAL A 804 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 808 " --> pdb=" O PHE A 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 804 through 808' Processing helix chain 'B' and resid 20 through 33 removed outlier: 3.945A pdb=" N PHE B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 57 through 70 removed outlier: 3.934A pdb=" N LEU B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 removed outlier: 3.777A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 137 removed outlier: 4.007A pdb=" N ARG B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 removed outlier: 5.947A pdb=" N GLU B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 191 removed outlier: 3.653A pdb=" N GLU B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 214 removed outlier: 3.524A pdb=" N ALA B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.819A pdb=" N PHE B 231 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 removed outlier: 3.674A pdb=" N GLU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 304 removed outlier: 3.942A pdb=" N MET B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 333 removed outlier: 4.074A pdb=" N SER B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS B 333 " --> pdb=" O MET B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.690A pdb=" N ARG B 427 " --> pdb=" O GLY B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 443 removed outlier: 4.060A pdb=" N GLU B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 477 removed outlier: 3.849A pdb=" N GLU B 473 " --> pdb=" O GLY B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 496 Processing helix chain 'B' and resid 520 through 525 removed outlier: 4.029A pdb=" N PHE B 524 " --> pdb=" O GLY B 520 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 525 " --> pdb=" O VAL B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 525' Processing helix chain 'B' and resid 529 through 551 removed outlier: 4.512A pdb=" N LEU B 537 " --> pdb=" O TRP B 533 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 544 " --> pdb=" O TYR B 540 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 549 " --> pdb=" O VAL B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 634 removed outlier: 4.569A pdb=" N ILE B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 612 " --> pdb=" O ILE B 608 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 634 " --> pdb=" O VAL B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 645 Processing helix chain 'B' and resid 657 through 665 Processing helix chain 'B' and resid 670 through 679 removed outlier: 3.642A pdb=" N MET B 678 " --> pdb=" O MET B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 689 through 700 removed outlier: 3.508A pdb=" N ARG B 696 " --> pdb=" O GLU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 717 removed outlier: 3.611A pdb=" N ILE B 711 " --> pdb=" O GLU B 707 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU B 712 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE B 713 " --> pdb=" O THR B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 758 removed outlier: 3.634A pdb=" N ILE B 747 " --> pdb=" O TYR B 743 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 749 " --> pdb=" O ASP B 745 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 751 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 753 " --> pdb=" O ILE B 749 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU B 754 " --> pdb=" O ALA B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 805 removed outlier: 3.533A pdb=" N GLY B 799 " --> pdb=" O VAL B 795 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 800 " --> pdb=" O LEU B 796 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL B 801 " --> pdb=" O ALA B 797 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 804 " --> pdb=" O LEU B 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 36 removed outlier: 4.709A pdb=" N ALA C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL C 30 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 69 removed outlier: 4.102A pdb=" N LYS C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 92 removed outlier: 4.647A pdb=" N ALA C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 92 " --> pdb=" O GLN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 121 through 136 Processing helix chain 'C' and resid 148 through 154 removed outlier: 4.158A pdb=" N ILE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.768A pdb=" N LEU C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 214 removed outlier: 4.287A pdb=" N LYS C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 4.564A pdb=" N PHE C 231 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 240 removed outlier: 3.661A pdb=" N ARG C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 240' Processing helix chain 'C' and resid 255 through 270 removed outlier: 3.599A pdb=" N GLU C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 305 removed outlier: 3.744A pdb=" N MET C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 294 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS C 297 " --> pdb=" O TYR C 293 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C 305 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.664A pdb=" N MET C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 330 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 removed outlier: 4.186A pdb=" N SER C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 397 " --> pdb=" O ILE C 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 392 through 397' Processing helix chain 'C' and resid 423 through 426 Processing helix chain 'C' and resid 432 through 444 removed outlier: 3.607A pdb=" N ARG C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 477 Processing helix chain 'C' and resid 532 through 545 removed outlier: 3.722A pdb=" N LEU C 537 " --> pdb=" O TRP C 533 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 539 " --> pdb=" O TYR C 535 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER C 544 " --> pdb=" O TYR C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 551 Processing helix chain 'C' and resid 600 through 629 removed outlier: 3.965A pdb=" N VAL C 605 " --> pdb=" O SER C 601 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE C 615 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 616 " --> pdb=" O PHE C 612 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 617 " --> pdb=" O THR C 613 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE C 627 " --> pdb=" O ASN C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 633 removed outlier: 3.610A pdb=" N MET C 633 " --> pdb=" O VAL C 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 630 through 633' Processing helix chain 'C' and resid 639 through 646 removed outlier: 3.745A pdb=" N LEU C 643 " --> pdb=" O SER C 639 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 646 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 665 Processing helix chain 'C' and resid 668 through 680 Processing helix chain 'C' and resid 681 through 686 Processing helix chain 'C' and resid 689 through 700 removed outlier: 3.632A pdb=" N VAL C 697 " --> pdb=" O GLY C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 718 removed outlier: 3.789A pdb=" N GLN C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 717 " --> pdb=" O PHE C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 757 removed outlier: 3.565A pdb=" N GLN C 753 " --> pdb=" O ILE C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 768 Processing helix chain 'C' and resid 789 through 796 removed outlier: 3.858A pdb=" N PHE C 793 " --> pdb=" O ILE C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 803 removed outlier: 4.054A pdb=" N LEU C 800 " --> pdb=" O LEU C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 808 removed outlier: 3.665A pdb=" N ALA C 807 " --> pdb=" O VAL C 804 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 808 " --> pdb=" O PHE C 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 804 through 808' Processing helix chain 'D' and resid 20 through 33 removed outlier: 3.944A pdb=" N PHE D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 57 through 70 removed outlier: 3.934A pdb=" N LEU D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 94 removed outlier: 3.777A pdb=" N ALA D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 137 removed outlier: 4.007A pdb=" N ARG D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 159 removed outlier: 5.948A pdb=" N GLU D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.653A pdb=" N GLU D 186 " --> pdb=" O PRO D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 214 removed outlier: 3.524A pdb=" N ALA D 204 " --> pdb=" O SER D 200 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 206 " --> pdb=" O GLU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 removed outlier: 3.819A pdb=" N PHE D 231 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 270 removed outlier: 3.674A pdb=" N GLU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU D 270 " --> pdb=" O SER D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 304 removed outlier: 3.943A pdb=" N MET D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 333 removed outlier: 4.074A pdb=" N SER D 330 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU D 331 " --> pdb=" O ARG D 327 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS D 333 " --> pdb=" O MET D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 387 Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.690A pdb=" N ARG D 427 " --> pdb=" O GLY D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 443 removed outlier: 4.059A pdb=" N GLU D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 477 removed outlier: 3.850A pdb=" N GLU D 473 " --> pdb=" O GLY D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 496 Processing helix chain 'D' and resid 520 through 525 removed outlier: 4.030A pdb=" N PHE D 524 " --> pdb=" O GLY D 520 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 525 " --> pdb=" O VAL D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 525' Processing helix chain 'D' and resid 529 through 551 removed outlier: 4.512A pdb=" N LEU D 537 " --> pdb=" O TRP D 533 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 538 " --> pdb=" O MET D 534 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER D 544 " --> pdb=" O TYR D 540 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 549 " --> pdb=" O VAL D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 634 removed outlier: 4.571A pdb=" N ILE D 608 " --> pdb=" O ILE D 604 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE D 612 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 616 " --> pdb=" O PHE D 612 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL D 630 " --> pdb=" O ALA D 626 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 634 " --> pdb=" O VAL D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 645 Processing helix chain 'D' and resid 657 through 665 Processing helix chain 'D' and resid 670 through 679 removed outlier: 3.643A pdb=" N MET D 678 " --> pdb=" O MET D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 686 Processing helix chain 'D' and resid 689 through 700 removed outlier: 3.509A pdb=" N ARG D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 717 removed outlier: 3.612A pdb=" N ILE D 711 " --> pdb=" O GLU D 707 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU D 712 " --> pdb=" O SER D 708 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE D 713 " --> pdb=" O THR D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 758 removed outlier: 3.635A pdb=" N ILE D 747 " --> pdb=" O TYR D 743 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 749 " --> pdb=" O ASP D 745 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 751 " --> pdb=" O ILE D 747 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN D 753 " --> pdb=" O ILE D 749 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU D 754 " --> pdb=" O ALA D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 768 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 805 removed outlier: 3.533A pdb=" N GLY D 799 " --> pdb=" O VAL D 795 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 800 " --> pdb=" O LEU D 796 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL D 801 " --> pdb=" O ALA D 797 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 13 removed outlier: 5.754A pdb=" N PHE A 7 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN A 50 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY A 9 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE A 52 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N PHE A 11 " --> pdb=" O ILE A 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.297A pdb=" N ILE A 75 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS A 98 " --> pdb=" O VAL A 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 172 removed outlier: 7.907A pdb=" N ILE A 196 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR A 142 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASP A 198 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 144 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 195 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE A 248 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N MET A 245 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 363 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY A 247 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 249 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A 359 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N SER A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS A 370 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 337 through 339 removed outlier: 3.553A pdb=" N TRP A 337 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 446 through 451 Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 498 Processing sheet with id=AA8, first strand: chain 'A' and resid 509 through 512 removed outlier: 3.933A pdb=" N ILE A 509 " --> pdb=" O ILE A 724 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 650 through 652 removed outlier: 6.604A pdb=" N GLU A 650 " --> pdb=" O ALA A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 44 through 47 removed outlier: 5.448A pdb=" N LEU B 5 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N PHE B 76 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 8 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 75 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU B 118 " --> pdb=" O HIS B 98 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLN B 100 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ARG B 353 " --> pdb=" O TYR B 115 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N SER B 117 " --> pdb=" O ARG B 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 167 through 172 removed outlier: 4.099A pdb=" N VAL B 141 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE B 196 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR B 142 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 195 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR B 223 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N MET B 245 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS B 370 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS B 364 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 338 through 339 Processing sheet with id=AB4, first strand: chain 'B' and resid 402 through 406 removed outlier: 6.767A pdb=" N LEU B 402 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ARG B 450 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 404 " --> pdb=" O ARG B 450 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 482 through 483 Processing sheet with id=AB6, first strand: chain 'B' and resid 503 through 505 removed outlier: 4.057A pdb=" N MET B 503 " --> pdb=" O TYR B 733 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 704 through 706 removed outlier: 3.690A pdb=" N ILE B 509 " --> pdb=" O ILE B 724 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 6 through 13 removed outlier: 5.753A pdb=" N PHE C 7 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN C 50 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLY C 9 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE C 52 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N PHE C 11 " --> pdb=" O ILE C 52 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.297A pdb=" N ILE C 75 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 167 through 172 removed outlier: 7.908A pdb=" N ILE C 196 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR C 142 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP C 198 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL C 144 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 195 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N PHE C 248 " --> pdb=" O PHE C 225 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N MET C 245 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 363 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C 247 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 249 " --> pdb=" O ASP C 359 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 359 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N LYS C 370 " --> pdb=" O SER C 362 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 337 through 339 removed outlier: 3.553A pdb=" N TRP C 337 " --> pdb=" O ILE C 344 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 446 through 451 Processing sheet with id=AC4, first strand: chain 'C' and resid 414 through 415 Processing sheet with id=AC5, first strand: chain 'C' and resid 496 through 498 Processing sheet with id=AC6, first strand: chain 'C' and resid 509 through 512 removed outlier: 3.933A pdb=" N ILE C 509 " --> pdb=" O ILE C 724 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 650 through 652 removed outlier: 6.604A pdb=" N GLU C 650 " --> pdb=" O ALA C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 44 through 47 removed outlier: 5.448A pdb=" N LEU D 5 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N PHE D 76 " --> pdb=" O ARG D 6 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLY D 8 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE D 75 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS D 98 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N LEU D 118 " --> pdb=" O HIS D 98 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLN D 100 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ARG D 353 " --> pdb=" O TYR D 115 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N SER D 117 " --> pdb=" O ARG D 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 167 through 172 removed outlier: 4.099A pdb=" N VAL D 141 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE D 196 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N THR D 142 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL D 195 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR D 223 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N MET D 245 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N SER D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS D 370 " --> pdb=" O SER D 362 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS D 364 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU D 368 " --> pdb=" O LYS D 364 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY D 379 " --> pdb=" O ASP D 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 338 through 339 Processing sheet with id=AD2, first strand: chain 'D' and resid 402 through 406 removed outlier: 6.767A pdb=" N LEU D 402 " --> pdb=" O GLU D 448 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ARG D 450 " --> pdb=" O LEU D 402 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL D 404 " --> pdb=" O ARG D 450 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 482 through 483 Processing sheet with id=AD4, first strand: chain 'D' and resid 503 through 505 removed outlier: 4.057A pdb=" N MET D 503 " --> pdb=" O TYR D 733 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 704 through 706 removed outlier: 3.690A pdb=" N ILE D 509 " --> pdb=" O ILE D 724 " (cutoff:3.500A) 862 hydrogen bonds defined for protein. 2472 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: 4.50 Time building geometry restraints manager: 2.60 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: 7511 1.34 - 1.46: 5278 1.46 - 1.58: 11231 1.58 - 1.70: 0 1.70 - 1.82: 220 Bond restraints: 24240 Sorted by residual: bond pdb=" C GLN B 271 " pdb=" N ALA B 272 " ideal model delta sigma weight residual 1.331 1.391 -0.060 2.07e-02 2.33e+03 8.51e+00 bond pdb=" C GLN D 271 " pdb=" N ALA D 272 " ideal model delta sigma weight residual 1.331 1.391 -0.060 2.07e-02 2.33e+03 8.50e+00 bond pdb=" C SER C 162 " pdb=" N ARG C 163 " ideal model delta sigma weight residual 1.332 1.298 0.035 1.40e-02 5.10e+03 6.14e+00 bond pdb=" C SER A 162 " pdb=" N ARG A 163 " ideal model delta sigma weight residual 1.332 1.298 0.034 1.40e-02 5.10e+03 5.88e+00 bond pdb=" CB TRP C 265 " pdb=" CG TRP C 265 " ideal model delta sigma weight residual 1.498 1.432 0.066 3.10e-02 1.04e+03 4.55e+00 ... (remaining 24235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 31487 2.26 - 4.53: 1131 4.53 - 6.79: 166 6.79 - 9.05: 30 9.05 - 11.32: 14 Bond angle restraints: 32828 Sorted by residual: angle pdb=" C LYS A 513 " pdb=" N PRO A 514 " pdb=" CD PRO A 514 " ideal model delta sigma weight residual 120.60 109.37 11.23 2.20e+00 2.07e-01 2.61e+01 angle pdb=" C LYS C 513 " pdb=" N PRO C 514 " pdb=" CD PRO C 514 " ideal model delta sigma weight residual 120.60 109.40 11.20 2.20e+00 2.07e-01 2.59e+01 angle pdb=" N VAL C 549 " pdb=" CA VAL C 549 " pdb=" C VAL C 549 " ideal model delta sigma weight residual 112.96 108.14 4.82 1.00e+00 1.00e+00 2.32e+01 angle pdb=" N VAL A 549 " pdb=" CA VAL A 549 " pdb=" C VAL A 549 " ideal model delta sigma weight residual 112.96 108.19 4.77 1.00e+00 1.00e+00 2.28e+01 angle pdb=" C LYS C 513 " pdb=" N PRO C 514 " pdb=" CA PRO C 514 " ideal model delta sigma weight residual 127.00 138.32 -11.32 2.40e+00 1.74e-01 2.22e+01 ... (remaining 32823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.85: 13785 14.85 - 29.69: 587 29.69 - 44.54: 74 44.54 - 59.39: 2 59.39 - 74.24: 16 Dihedral angle restraints: 14464 sinusoidal: 5764 harmonic: 8700 Sorted by residual: dihedral pdb=" CA ARG B 35 " pdb=" C ARG B 35 " pdb=" N ASN B 36 " pdb=" CA ASN B 36 " ideal model delta harmonic sigma weight residual 180.00 143.40 36.60 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA ARG D 35 " pdb=" C ARG D 35 " pdb=" N ASN D 36 " pdb=" CA ASN D 36 " ideal model delta harmonic sigma weight residual 180.00 143.40 36.60 0 5.00e+00 4.00e-02 5.36e+01 dihedral pdb=" CA HIS C 80 " pdb=" C HIS C 80 " pdb=" N SER C 81 " pdb=" CA SER C 81 " ideal model delta harmonic sigma weight residual 180.00 -147.81 -32.19 0 5.00e+00 4.00e-02 4.14e+01 ... (remaining 14461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2026 0.037 - 0.074: 1141 0.074 - 0.111: 404 0.111 - 0.148: 117 0.148 - 0.185: 28 Chirality restraints: 3716 Sorted by residual: chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA SYM D 901 " pdb=" N SYM D 901 " pdb=" C SYM D 901 " pdb=" CB SYM D 901 " both_signs ideal model delta sigma weight residual False 2.48 2.66 -0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 3713 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 513 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.05e+00 pdb=" N PRO B 514 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 513 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO D 514 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 514 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 514 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 524 " -0.030 2.00e-02 2.50e+03 1.97e-02 6.77e+00 pdb=" CG PHE A 524 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 524 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 524 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 524 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 524 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 524 " -0.008 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 523 2.60 - 3.17: 24534 3.17 - 3.75: 36729 3.75 - 4.32: 55021 4.32 - 4.90: 82236 Nonbonded interactions: 199043 Sorted by model distance: nonbonded pdb=" OE1 GLU B 634 " pdb=" OG SER B 635 " model vdw 2.021 3.040 nonbonded pdb=" OE1 GLU D 634 " pdb=" OG SER D 635 " model vdw 2.022 3.040 nonbonded pdb=" O PHE C 677 " pdb=" OG SER C 680 " model vdw 2.056 3.040 nonbonded pdb=" O PHE A 677 " pdb=" OG SER A 680 " model vdw 2.057 3.040 nonbonded pdb=" O SER A 69 " pdb=" OG SER A 313 " model vdw 2.080 3.040 ... (remaining 199038 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.770 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 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 : 0.012 0.886 24250 Z= 0.909 Angle : 1.023 11.319 32844 Z= 0.540 Chirality : 0.052 0.185 3716 Planarity : 0.006 0.066 4144 Dihedral : 8.871 74.073 8840 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 29.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.52 % Favored : 84.41 % Rotamer: Outliers : 0.08 % Allowed : 0.62 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -5.82 (0.11), residues: 2976 helix: -4.24 (0.09), residues: 1098 sheet: -3.30 (0.23), residues: 388 loop : -3.74 (0.13), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 189 TYR 0.024 0.003 TYR D 412 PHE 0.040 0.004 PHE A 524 TRP 0.032 0.004 TRP B 265 HIS 0.019 0.004 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00937 / 0.43 (24240) covalent geometry : angle 1.02262 / 0.54 (32828) SS BOND : bond 0.00828 / 0.53 ( 8) SS BOND : angle 1.20665 / 0.80 ( 16) hydrogen bonds : bond 0.34470 / 23.18 ( 862) hydrogen bonds : angle 11.30937 / 7.91 ( 2472) Misc. bond : bond 0.88310 / 44.33 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 423 time to evaluate : 0.979 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 214 MET cc_start: 0.7703 (mmt) cc_final: 0.7491 (mmm) REVERT: A 329 MET cc_start: 0.8244 (tpt) cc_final: 0.7924 (tpp) REVERT: A 548 PHE cc_start: 0.6500 (t80) cc_final: 0.5572 (m-80) REVERT: A 682 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8029 (mtp85) REVERT: A 690 SER cc_start: 0.8377 (m) cc_final: 0.8063 (t) REVERT: B 14 VAL cc_start: 0.5372 (t) cc_final: 0.5156 (p) REVERT: B 203 MET cc_start: 0.8125 (mmm) cc_final: 0.7139 (mmt) REVERT: B 217 MET cc_start: 0.8675 (mmm) cc_final: 0.8400 (mmm) REVERT: B 220 TYR cc_start: 0.7922 (m-80) cc_final: 0.7252 (m-80) REVERT: B 223 TYR cc_start: 0.8704 (m-80) cc_final: 0.8311 (m-80) REVERT: B 624 LEU cc_start: 0.9262 (tp) cc_final: 0.9027 (tt) REVERT: C 214 MET cc_start: 0.7694 (mmt) cc_final: 0.7482 (mmm) REVERT: C 329 MET cc_start: 0.8244 (tpt) cc_final: 0.7912 (tpp) REVERT: C 548 PHE cc_start: 0.6565 (t80) cc_final: 0.5581 (m-80) REVERT: C 615 ILE cc_start: 0.9082 (mm) cc_final: 0.8753 (mt) REVERT: C 682 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8052 (mtp85) REVERT: C 690 SER cc_start: 0.8373 (m) cc_final: 0.8055 (t) REVERT: D 14 VAL cc_start: 0.5384 (t) cc_final: 0.5162 (p) REVERT: D 203 MET cc_start: 0.8142 (mmm) cc_final: 0.7201 (mmt) REVERT: D 217 MET cc_start: 0.8628 (mmm) cc_final: 0.8380 (mmm) REVERT: D 220 TYR cc_start: 0.7937 (m-80) cc_final: 0.7673 (m-80) REVERT: D 223 TYR cc_start: 0.8669 (m-80) cc_final: 0.8264 (m-80) outliers start: 2 outliers final: 2 residues processed: 423 average time/residue: 0.1891 time to fit residues: 118.8663 Evaluate side-chains 239 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 237 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain C residue 505 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 92 ASN B 319 HIS B 477 HIS B 518 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN D 92 ASN D 319 HIS D 477 HIS D 518 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.090603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.080691 restraints weight = 103369.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.081298 restraints weight = 75030.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.081540 restraints weight = 55220.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.081706 restraints weight = 47733.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.081708 restraints weight = 46289.230| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24250 Z= 0.188 Angle : 0.790 11.592 32844 Z= 0.410 Chirality : 0.046 0.173 3716 Planarity : 0.006 0.061 4144 Dihedral : 6.932 54.543 3237 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.46 % Allowed : 6.55 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -4.01 (0.13), residues: 2976 helix: -2.38 (0.12), residues: 1242 sheet: -3.21 (0.25), residues: 346 loop : -2.70 (0.15), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 189 TYR 0.035 0.002 TYR B 535 PHE 0.030 0.003 PHE B 135 TRP 0.022 0.002 TRP C 675 HIS 0.008 0.002 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 (24240) covalent geometry : angle 0.79036 / 0.41 (32828) SS BOND : bond 0.00524 / 0.23 ( 8) SS BOND : angle 1.00362 / 0.67 ( 16) hydrogen bonds : bond 0.06148 / 4.15 ( 862) hydrogen bonds : angle 6.92845 / 4.90 ( 2472) Misc. bond : bond 0.00205 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 308 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6747 (ptp-170) REVERT: A 470 MET cc_start: 0.7239 (mtm) cc_final: 0.7015 (mtm) REVERT: A 548 PHE cc_start: 0.6198 (t80) cc_final: 0.5470 (m-80) REVERT: A 690 SER cc_start: 0.8137 (m) cc_final: 0.7873 (t) REVERT: A 704 LEU cc_start: 0.8170 (tp) cc_final: 0.7873 (tt) REVERT: B 518 ASN cc_start: 0.6225 (OUTLIER) cc_final: 0.6021 (m-40) REVERT: B 733 TYR cc_start: 0.3905 (m-80) cc_final: 0.3655 (m-80) REVERT: B 796 LEU cc_start: 0.5278 (OUTLIER) cc_final: 0.4956 (tp) REVERT: C 548 PHE cc_start: 0.6289 (t80) cc_final: 0.5476 (m-80) REVERT: C 690 SER cc_start: 0.8143 (m) cc_final: 0.7865 (t) REVERT: C 704 LEU cc_start: 0.8185 (tp) cc_final: 0.7886 (tt) REVERT: D 733 TYR cc_start: 0.3919 (m-80) cc_final: 0.3652 (m-80) REVERT: D 796 LEU cc_start: 0.5156 (OUTLIER) cc_final: 0.4892 (tp) outliers start: 38 outliers final: 18 residues processed: 331 average time/residue: 0.1458 time to fit residues: 77.9377 Evaluate side-chains 240 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 743 TYR Chi-restraints excluded: chain D residue 13 TYR Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 51 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 280 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 135 optimal weight: 20.0000 chunk 219 optimal weight: 0.4980 chunk 187 optimal weight: 7.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.089739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.079761 restraints weight = 103971.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.080102 restraints weight = 73335.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.080442 restraints weight = 56216.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.080615 restraints weight = 47331.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.080642 restraints weight = 44251.849| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24250 Z= 0.213 Angle : 0.724 9.670 32844 Z= 0.373 Chirality : 0.044 0.161 3716 Planarity : 0.005 0.062 4144 Dihedral : 6.515 57.395 3237 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 1.89 % Allowed : 8.94 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.15 (0.14), residues: 2976 helix: -1.53 (0.13), residues: 1252 sheet: -2.86 (0.27), residues: 320 loop : -2.37 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 744 TYR 0.014 0.002 TYR C 145 PHE 0.038 0.002 PHE B 135 TRP 0.019 0.002 TRP A 675 HIS 0.008 0.002 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (24240) covalent geometry : angle 0.72421 / 0.37 (32828) SS BOND : bond 0.00495 / 0.22 ( 8) SS BOND : angle 0.89403 / 0.60 ( 16) hydrogen bonds : bond 0.04925 / 3.33 ( 862) hydrogen bonds : angle 6.31682 / 4.45 ( 2472) Misc. bond : bond 0.00226 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 628 LEU cc_start: 0.8397 (mt) cc_final: 0.7897 (tp) REVERT: A 645 LYS cc_start: 0.8588 (pttt) cc_final: 0.8072 (mmtp) REVERT: A 690 SER cc_start: 0.7960 (m) cc_final: 0.7740 (t) REVERT: B 14 VAL cc_start: 0.5998 (t) cc_final: 0.5751 (p) REVERT: B 198 ASP cc_start: 0.5465 (t0) cc_final: 0.5261 (t70) REVERT: C 628 LEU cc_start: 0.8410 (mt) cc_final: 0.7956 (tp) REVERT: C 645 LYS cc_start: 0.8573 (pttt) cc_final: 0.8072 (mmtp) REVERT: C 690 SER cc_start: 0.7968 (m) cc_final: 0.7746 (t) REVERT: D 660 MET cc_start: 0.7462 (tmm) cc_final: 0.7214 (tmm) outliers start: 49 outliers final: 33 residues processed: 260 average time/residue: 0.1499 time to fit residues: 65.0396 Evaluate side-chains 230 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 723 GLN Chi-restraints excluded: chain C residue 743 TYR Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain D residue 13 TYR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 206 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 259 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 267 optimal weight: 20.0000 chunk 44 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN D 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.090604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.080729 restraints weight = 103695.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.080994 restraints weight = 73255.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.081240 restraints weight = 53842.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.081398 restraints weight = 48028.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.081454 restraints weight = 46023.347| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24250 Z= 0.157 Angle : 0.652 9.933 32844 Z= 0.336 Chirality : 0.042 0.166 3716 Planarity : 0.005 0.058 4144 Dihedral : 6.034 58.048 3237 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.70 % Allowed : 9.71 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.48 (0.14), residues: 2976 helix: -0.96 (0.14), residues: 1258 sheet: -2.59 (0.29), residues: 308 loop : -2.01 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 163 TYR 0.018 0.001 TYR B 115 PHE 0.026 0.002 PHE B 135 TRP 0.018 0.002 TRP B 675 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (24240) covalent geometry : angle 0.65238 / 0.34 (32828) SS BOND : bond 0.00365 / 0.16 ( 8) SS BOND : angle 0.69588 / 0.50 ( 16) hydrogen bonds : bond 0.04030 / 2.72 ( 862) hydrogen bonds : angle 5.83509 / 4.10 ( 2472) Misc. bond : bond 0.00101 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 LEU cc_start: 0.8947 (tp) cc_final: 0.8682 (tp) REVERT: A 483 VAL cc_start: 0.8635 (p) cc_final: 0.8101 (p) REVERT: A 645 LYS cc_start: 0.8462 (pttt) cc_final: 0.8070 (mmtp) REVERT: A 690 SER cc_start: 0.7974 (m) cc_final: 0.7757 (t) REVERT: A 704 LEU cc_start: 0.8412 (tp) cc_final: 0.8053 (tt) REVERT: A 739 MET cc_start: 0.7013 (tpt) cc_final: 0.6620 (tpp) REVERT: B 14 VAL cc_start: 0.5968 (t) cc_final: 0.5725 (p) REVERT: C 436 LEU cc_start: 0.8877 (tp) cc_final: 0.8560 (tp) REVERT: C 645 LYS cc_start: 0.8441 (pttt) cc_final: 0.8034 (mmtp) REVERT: C 690 SER cc_start: 0.7973 (m) cc_final: 0.7760 (t) REVERT: C 704 LEU cc_start: 0.8422 (tp) cc_final: 0.8046 (tt) REVERT: C 739 MET cc_start: 0.7090 (tpt) cc_final: 0.6677 (tpp) outliers start: 44 outliers final: 37 residues processed: 268 average time/residue: 0.1439 time to fit residues: 64.4783 Evaluate side-chains 238 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 743 TYR Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain D residue 13 TYR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 615 ILE Chi-restraints excluded: chain D residue 633 MET Chi-restraints excluded: chain D residue 678 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 226 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 106 optimal weight: 0.0570 chunk 264 optimal weight: 0.0270 chunk 217 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 291 optimal weight: 6.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 HIS ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.092161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.082569 restraints weight = 102424.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.082684 restraints weight = 70187.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.082747 restraints weight = 53351.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.082955 restraints weight = 50384.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.083090 restraints weight = 47593.905| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24250 Z= 0.118 Angle : 0.619 12.157 32844 Z= 0.315 Chirality : 0.041 0.180 3716 Planarity : 0.004 0.056 4144 Dihedral : 5.477 59.477 3237 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.00 % Allowed : 11.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -1.90 (0.15), residues: 2976 helix: -0.35 (0.14), residues: 1266 sheet: -2.36 (0.28), residues: 334 loop : -1.80 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 769 TYR 0.025 0.001 TYR D 431 PHE 0.021 0.001 PHE B 611 TRP 0.017 0.001 TRP D 675 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (24240) covalent geometry : angle 0.61917 / 0.32 (32828) SS BOND : bond 0.00289 / 0.11 ( 8) SS BOND : angle 0.78010 / 0.55 ( 16) hydrogen bonds : bond 0.03441 / 2.31 ( 862) hydrogen bonds : angle 5.42889 / 3.80 ( 2472) Misc. bond : bond 0.00074 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TYR cc_start: 0.5135 (OUTLIER) cc_final: 0.3783 (m-10) REVERT: A 436 LEU cc_start: 0.8792 (tp) cc_final: 0.8447 (tp) REVERT: A 510 LEU cc_start: 0.8202 (tp) cc_final: 0.7994 (tt) REVERT: A 548 PHE cc_start: 0.6055 (t80) cc_final: 0.5063 (m-80) REVERT: A 645 LYS cc_start: 0.8495 (pttt) cc_final: 0.8048 (mmtp) REVERT: A 739 MET cc_start: 0.6850 (tpt) cc_final: 0.6559 (tpt) REVERT: B 528 LEU cc_start: 0.8291 (mt) cc_final: 0.8090 (tt) REVERT: C 240 TYR cc_start: 0.5088 (OUTLIER) cc_final: 0.3784 (m-10) REVERT: C 436 LEU cc_start: 0.8860 (tp) cc_final: 0.8521 (tp) REVERT: C 510 LEU cc_start: 0.8197 (tp) cc_final: 0.7984 (tt) REVERT: C 548 PHE cc_start: 0.5838 (t80) cc_final: 0.4951 (m-80) REVERT: C 645 LYS cc_start: 0.8439 (pttt) cc_final: 0.8009 (mmtp) REVERT: C 739 MET cc_start: 0.6886 (tpt) cc_final: 0.6578 (tpt) REVERT: D 528 LEU cc_start: 0.8165 (mt) cc_final: 0.7963 (tt) REVERT: D 733 TYR cc_start: 0.3587 (m-10) cc_final: 0.3320 (m-80) outliers start: 52 outliers final: 28 residues processed: 289 average time/residue: 0.1554 time to fit residues: 73.3470 Evaluate side-chains 234 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 743 TYR Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 548 PHE Chi-restraints excluded: chain D residue 633 MET Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 84 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 239 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 282 optimal weight: 9.9990 chunk 80 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.090788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.081061 restraints weight = 104101.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.081538 restraints weight = 73878.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.081823 restraints weight = 53319.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.081936 restraints weight = 53066.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.082017 restraints weight = 47244.674| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24250 Z= 0.148 Angle : 0.629 10.059 32844 Z= 0.319 Chirality : 0.041 0.159 3716 Planarity : 0.004 0.054 4144 Dihedral : 5.273 28.027 3233 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.12 % Allowed : 12.37 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -1.63 (0.15), residues: 2976 helix: -0.14 (0.14), residues: 1266 sheet: -2.30 (0.27), residues: 344 loop : -1.59 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 323 TYR 0.017 0.001 TYR B 431 PHE 0.018 0.002 PHE B 548 TRP 0.018 0.001 TRP D 675 HIS 0.004 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (24240) covalent geometry : angle 0.62881 / 0.32 (32828) SS BOND : bond 0.00242 / 0.10 ( 8) SS BOND : angle 0.57697 / 0.42 ( 16) hydrogen bonds : bond 0.03427 / 2.32 ( 862) hydrogen bonds : angle 5.31708 / 3.73 ( 2472) Misc. bond : bond 0.00114 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TYR cc_start: 0.5266 (OUTLIER) cc_final: 0.3856 (m-10) REVERT: A 436 LEU cc_start: 0.8868 (tp) cc_final: 0.8545 (tp) REVERT: A 483 VAL cc_start: 0.8065 (p) cc_final: 0.7673 (m) REVERT: A 503 MET cc_start: 0.5230 (mtt) cc_final: 0.4508 (mtt) REVERT: A 510 LEU cc_start: 0.8255 (tp) cc_final: 0.7955 (tt) REVERT: A 628 LEU cc_start: 0.8368 (mt) cc_final: 0.7919 (tp) REVERT: A 645 LYS cc_start: 0.8476 (pttt) cc_final: 0.8068 (mmtp) REVERT: A 739 MET cc_start: 0.6987 (tpt) cc_final: 0.6669 (tpt) REVERT: B 14 VAL cc_start: 0.5994 (t) cc_final: 0.5755 (p) REVERT: B 528 LEU cc_start: 0.8172 (mt) cc_final: 0.7953 (tt) REVERT: B 706 MET cc_start: 0.7218 (mmm) cc_final: 0.6949 (mmm) REVERT: C 240 TYR cc_start: 0.5271 (OUTLIER) cc_final: 0.3858 (m-10) REVERT: C 329 MET cc_start: 0.7503 (ttm) cc_final: 0.7288 (ttm) REVERT: C 436 LEU cc_start: 0.8848 (tp) cc_final: 0.8525 (tp) REVERT: C 503 MET cc_start: 0.5246 (mtt) cc_final: 0.4451 (mtt) REVERT: C 510 LEU cc_start: 0.8246 (tp) cc_final: 0.7957 (tt) REVERT: C 628 LEU cc_start: 0.8418 (mt) cc_final: 0.8006 (tp) REVERT: C 645 LYS cc_start: 0.8500 (pttt) cc_final: 0.8131 (mmtp) REVERT: C 739 MET cc_start: 0.7012 (tpt) cc_final: 0.6725 (tpt) REVERT: D 528 LEU cc_start: 0.8113 (mt) cc_final: 0.7911 (tt) REVERT: D 706 MET cc_start: 0.7256 (mmm) cc_final: 0.6988 (mmm) outliers start: 55 outliers final: 43 residues processed: 242 average time/residue: 0.1513 time to fit residues: 60.8837 Evaluate side-chains 234 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 723 GLN Chi-restraints excluded: chain C residue 743 TYR Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 548 PHE Chi-restraints excluded: chain D residue 615 ILE Chi-restraints excluded: chain D residue 633 MET Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 284 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 299 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.090175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.080450 restraints weight = 103797.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.081063 restraints weight = 74794.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.081383 restraints weight = 53358.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.081465 restraints weight = 46885.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.081491 restraints weight = 43332.414| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24250 Z= 0.174 Angle : 0.651 16.962 32844 Z= 0.331 Chirality : 0.042 0.173 3716 Planarity : 0.005 0.053 4144 Dihedral : 5.323 28.330 3233 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.20 % Allowed : 12.52 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -1.59 (0.15), residues: 2976 helix: -0.11 (0.14), residues: 1286 sheet: -2.24 (0.28), residues: 328 loop : -1.62 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 323 TYR 0.017 0.002 TYR B 431 PHE 0.019 0.002 PHE B 548 TRP 0.018 0.002 TRP B 675 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (24240) covalent geometry : angle 0.65117 / 0.33 (32828) SS BOND : bond 0.00225 / 0.09 ( 8) SS BOND : angle 0.58062 / 0.41 ( 16) hydrogen bonds : bond 0.03504 / 2.38 ( 862) hydrogen bonds : angle 5.30291 / 3.73 ( 2472) Misc. bond : bond 0.00107 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TYR cc_start: 0.5486 (OUTLIER) cc_final: 0.3990 (m-10) REVERT: A 436 LEU cc_start: 0.8867 (tp) cc_final: 0.8521 (tp) REVERT: A 483 VAL cc_start: 0.7917 (p) cc_final: 0.7539 (m) REVERT: A 503 MET cc_start: 0.5257 (mtt) cc_final: 0.4444 (mtt) REVERT: A 510 LEU cc_start: 0.8362 (tp) cc_final: 0.8090 (tt) REVERT: A 645 LYS cc_start: 0.8480 (pttt) cc_final: 0.8154 (mmtp) REVERT: A 739 MET cc_start: 0.7083 (tpt) cc_final: 0.6804 (tpt) REVERT: B 14 VAL cc_start: 0.5934 (t) cc_final: 0.5706 (p) REVERT: B 706 MET cc_start: 0.7383 (mmm) cc_final: 0.7109 (mmm) REVERT: C 240 TYR cc_start: 0.5473 (OUTLIER) cc_final: 0.3983 (m-10) REVERT: C 436 LEU cc_start: 0.8880 (tp) cc_final: 0.8553 (tp) REVERT: C 503 MET cc_start: 0.5255 (mtt) cc_final: 0.4594 (mtt) REVERT: C 510 LEU cc_start: 0.8357 (tp) cc_final: 0.8082 (tt) REVERT: C 645 LYS cc_start: 0.8468 (pttt) cc_final: 0.8108 (mmtp) REVERT: C 739 MET cc_start: 0.7061 (tpt) cc_final: 0.6788 (tpt) REVERT: D 528 LEU cc_start: 0.8286 (mt) cc_final: 0.8037 (tt) REVERT: D 706 MET cc_start: 0.7403 (mmm) cc_final: 0.7124 (mmm) outliers start: 57 outliers final: 50 residues processed: 238 average time/residue: 0.1447 time to fit residues: 57.1812 Evaluate side-chains 235 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 723 GLN Chi-restraints excluded: chain C residue 743 TYR Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 498 PHE Chi-restraints excluded: chain D residue 548 PHE Chi-restraints excluded: chain D residue 615 ILE Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 789 ILE Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 245 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 180 optimal weight: 0.0070 chunk 90 optimal weight: 0.8980 chunk 123 optimal weight: 0.0010 chunk 118 optimal weight: 4.9990 chunk 111 optimal weight: 0.0870 chunk 150 optimal weight: 8.9990 chunk 28 optimal weight: 0.0970 overall best weight: 0.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.092607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.082875 restraints weight = 103541.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.083430 restraints weight = 72322.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.083789 restraints weight = 52485.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.083809 restraints weight = 47146.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.083851 restraints weight = 46054.444| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24250 Z= 0.112 Angle : 0.592 15.440 32844 Z= 0.299 Chirality : 0.040 0.211 3716 Planarity : 0.004 0.053 4144 Dihedral : 4.823 25.157 3233 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.62 % Allowed : 13.22 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -1.20 (0.15), residues: 2976 helix: 0.24 (0.15), residues: 1286 sheet: -2.25 (0.28), residues: 330 loop : -1.38 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 327 TYR 0.022 0.001 TYR B 431 PHE 0.021 0.001 PHE B 611 TRP 0.020 0.001 TRP B 675 HIS 0.003 0.001 HIS C 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (24240) covalent geometry : angle 0.59182 / 0.30 (32828) SS BOND : bond 0.00214 / 0.07 ( 8) SS BOND : angle 0.58614 / 0.43 ( 16) hydrogen bonds : bond 0.03027 / 2.04 ( 862) hydrogen bonds : angle 4.97932 / 3.50 ( 2472) Misc. bond : bond 0.00089 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 234 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TYR cc_start: 0.5104 (OUTLIER) cc_final: 0.3738 (m-10) REVERT: A 436 LEU cc_start: 0.8846 (tp) cc_final: 0.8552 (tp) REVERT: A 503 MET cc_start: 0.5030 (mtt) cc_final: 0.4302 (mtt) REVERT: A 510 LEU cc_start: 0.8189 (tp) cc_final: 0.7756 (tt) REVERT: A 645 LYS cc_start: 0.8431 (pttt) cc_final: 0.8010 (mmtp) REVERT: A 739 MET cc_start: 0.6762 (tpt) cc_final: 0.6458 (tpt) REVERT: B 14 VAL cc_start: 0.5804 (t) cc_final: 0.5576 (p) REVERT: C 240 TYR cc_start: 0.5057 (OUTLIER) cc_final: 0.3670 (m-10) REVERT: C 436 LEU cc_start: 0.8775 (tp) cc_final: 0.8482 (tp) REVERT: C 483 VAL cc_start: 0.7768 (p) cc_final: 0.7421 (m) REVERT: C 503 MET cc_start: 0.5048 (mtt) cc_final: 0.4304 (mtt) REVERT: C 510 LEU cc_start: 0.8241 (tp) cc_final: 0.7843 (tt) REVERT: C 548 PHE cc_start: 0.6005 (t80) cc_final: 0.4909 (m-80) REVERT: C 645 LYS cc_start: 0.8476 (pttt) cc_final: 0.7940 (mttm) REVERT: C 739 MET cc_start: 0.6662 (tpt) cc_final: 0.6399 (tpt) outliers start: 42 outliers final: 27 residues processed: 268 average time/residue: 0.1579 time to fit residues: 68.5880 Evaluate side-chains 224 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 743 TYR Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 548 PHE Chi-restraints excluded: chain D residue 615 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 137 optimal weight: 7.9990 chunk 291 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 293 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 526 ASN B 80 HIS C 34 ASN ** C 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.089558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.079741 restraints weight = 104642.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.080291 restraints weight = 72211.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.080585 restraints weight = 52841.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.080625 restraints weight = 46697.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.080671 restraints weight = 45367.318| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24250 Z= 0.231 Angle : 0.706 14.294 32844 Z= 0.358 Chirality : 0.044 0.227 3716 Planarity : 0.005 0.051 4144 Dihedral : 5.357 28.006 3233 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.16 % Allowed : 13.56 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -1.45 (0.15), residues: 2976 helix: -0.01 (0.14), residues: 1280 sheet: -2.17 (0.27), residues: 364 loop : -1.48 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 323 TYR 0.022 0.002 TYR B 733 PHE 0.021 0.002 PHE C 58 TRP 0.021 0.002 TRP A 675 HIS 0.007 0.002 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (24240) covalent geometry : angle 0.70624 / 0.36 (32828) SS BOND : bond 0.00195 / 0.08 ( 8) SS BOND : angle 0.68260 / 0.47 ( 16) hydrogen bonds : bond 0.03625 / 2.47 ( 862) hydrogen bonds : angle 5.21478 / 3.68 ( 2472) Misc. bond : bond 0.00110 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.3965 (m-10) REVERT: A 436 LEU cc_start: 0.8809 (tp) cc_final: 0.8500 (tp) REVERT: A 503 MET cc_start: 0.5330 (mtt) cc_final: 0.4651 (mtt) REVERT: A 510 LEU cc_start: 0.8356 (tp) cc_final: 0.7995 (tt) REVERT: A 645 LYS cc_start: 0.8461 (pttt) cc_final: 0.8146 (mmtp) REVERT: A 739 MET cc_start: 0.7195 (tpt) cc_final: 0.6765 (tpp) REVERT: B 115 TYR cc_start: 0.6668 (p90) cc_final: 0.6409 (p90) REVERT: B 329 MET cc_start: 0.7404 (mtt) cc_final: 0.6935 (mtm) REVERT: C 240 TYR cc_start: 0.5560 (OUTLIER) cc_final: 0.3964 (m-10) REVERT: C 436 LEU cc_start: 0.8914 (tp) cc_final: 0.8565 (tp) REVERT: C 503 MET cc_start: 0.5345 (mtt) cc_final: 0.4625 (mtt) REVERT: C 510 LEU cc_start: 0.8371 (tp) cc_final: 0.8007 (tt) REVERT: C 628 LEU cc_start: 0.8472 (mt) cc_final: 0.7942 (tp) REVERT: C 645 LYS cc_start: 0.8417 (pttt) cc_final: 0.8088 (mmtp) REVERT: C 739 MET cc_start: 0.7215 (tpt) cc_final: 0.6778 (tpp) REVERT: D 14 VAL cc_start: 0.5963 (t) cc_final: 0.5658 (p) REVERT: D 329 MET cc_start: 0.6382 (mtt) cc_final: 0.5961 (mtt) outliers start: 56 outliers final: 49 residues processed: 233 average time/residue: 0.1498 time to fit residues: 58.1357 Evaluate side-chains 239 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 723 GLN Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 723 GLN Chi-restraints excluded: chain C residue 743 TYR Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 751 ILE Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 548 PHE Chi-restraints excluded: chain D residue 615 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 32 optimal weight: 7.9990 chunk 137 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 526 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.090498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.081054 restraints weight = 103600.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.081148 restraints weight = 76689.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.081326 restraints weight = 59425.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.081603 restraints weight = 53383.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.081652 restraints weight = 48838.726| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24250 Z= 0.145 Angle : 0.643 15.147 32844 Z= 0.323 Chirality : 0.042 0.222 3716 Planarity : 0.004 0.051 4144 Dihedral : 5.210 27.134 3233 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.77 % Allowed : 14.18 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -1.33 (0.15), residues: 2976 helix: 0.11 (0.15), residues: 1284 sheet: -2.17 (0.27), residues: 344 loop : -1.43 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 323 TYR 0.023 0.002 TYR D 733 PHE 0.018 0.002 PHE B 548 TRP 0.019 0.001 TRP B 675 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (24240) covalent geometry : angle 0.64348 / 0.32 (32828) SS BOND : bond 0.00169 / 0.06 ( 8) SS BOND : angle 0.49278 / 0.37 ( 16) hydrogen bonds : bond 0.03264 / 2.22 ( 862) hydrogen bonds : angle 5.07444 / 3.58 ( 2472) Misc. bond : bond 0.00117 / 0.06 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TYR cc_start: 0.5429 (OUTLIER) cc_final: 0.3858 (m-10) REVERT: A 436 LEU cc_start: 0.8749 (tp) cc_final: 0.8440 (tp) REVERT: A 503 MET cc_start: 0.5606 (mtt) cc_final: 0.5025 (mtt) REVERT: A 645 LYS cc_start: 0.8229 (pttt) cc_final: 0.7894 (mmtp) REVERT: A 739 MET cc_start: 0.7117 (tpt) cc_final: 0.6846 (tpt) REVERT: B 115 TYR cc_start: 0.6627 (p90) cc_final: 0.6395 (p90) REVERT: B 329 MET cc_start: 0.7405 (mtt) cc_final: 0.6948 (mtm) REVERT: B 382 MET cc_start: 0.6960 (mtm) cc_final: 0.6521 (mtt) REVERT: C 240 TYR cc_start: 0.5396 (OUTLIER) cc_final: 0.3873 (m-10) REVERT: C 436 LEU cc_start: 0.8781 (tp) cc_final: 0.8452 (tp) REVERT: C 503 MET cc_start: 0.5618 (mtt) cc_final: 0.5025 (mtt) REVERT: C 510 LEU cc_start: 0.8248 (tp) cc_final: 0.7947 (tt) REVERT: C 624 LEU cc_start: 0.8346 (tt) cc_final: 0.8138 (tp) REVERT: C 628 LEU cc_start: 0.8420 (mt) cc_final: 0.7887 (tp) REVERT: C 645 LYS cc_start: 0.8377 (pttt) cc_final: 0.8031 (mmtp) REVERT: C 739 MET cc_start: 0.7101 (tpt) cc_final: 0.6857 (tpt) REVERT: D 14 VAL cc_start: 0.5848 (t) cc_final: 0.5554 (p) REVERT: D 329 MET cc_start: 0.6380 (mtt) cc_final: 0.5939 (mtt) REVERT: D 382 MET cc_start: 0.6952 (mtm) cc_final: 0.6506 (mtt) outliers start: 46 outliers final: 41 residues processed: 232 average time/residue: 0.1498 time to fit residues: 57.7221 Evaluate side-chains 233 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 743 TYR Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 548 PHE Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 723 GLN Chi-restraints excluded: chain C residue 743 TYR Chi-restraints excluded: chain C residue 748 THR Chi-restraints excluded: chain C residue 806 VAL Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 91 CYS Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 548 PHE Chi-restraints excluded: chain D residue 615 ILE Chi-restraints excluded: chain D residue 751 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 129 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 154 optimal weight: 5.9990 chunk 285 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 275 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 201 optimal weight: 0.0270 chunk 266 optimal weight: 3.9990 overall best weight: 3.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 80 HIS ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.089919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.080058 restraints weight = 104068.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.080536 restraints weight = 75571.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.080821 restraints weight = 55092.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.080984 restraints weight = 48576.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.081036 restraints weight = 44526.063| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24250 Z= 0.189 Angle : 0.682 14.375 32844 Z= 0.344 Chirality : 0.043 0.206 3716 Planarity : 0.005 0.051 4144 Dihedral : 5.344 27.708 3233 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.97 % Allowed : 14.14 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % 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: -1.43 (0.15), residues: 2976 helix: 0.01 (0.14), residues: 1284 sheet: -2.21 (0.27), residues: 344 loop : -1.48 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 323 TYR 0.023 0.002 TYR D 733 PHE 0.027 0.002 PHE D 231 TRP 0.021 0.002 TRP A 675 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (24240) covalent geometry : angle 0.68234 / 0.34 (32828) SS BOND : bond 0.00180 / 0.07 ( 8) SS BOND : angle 0.52053 / 0.38 ( 16) hydrogen bonds : bond 0.03449 / 2.34 ( 862) hydrogen bonds : angle 5.15678 / 3.64 ( 2472) Misc. bond : bond 0.00103 / 0.05 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.62 seconds wall clock time: 60 minutes 52.32 seconds (3652.32 seconds total)