Starting phenix.real_space_refine on Fri May 23 02:53:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5kuf_8289/05_2025/5kuf_8289.cif Found real_map, /net/cci-nas-00/data/ceres_data/5kuf_8289/05_2025/5kuf_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5kuf_8289/05_2025/5kuf_8289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5kuf_8289/05_2025/5kuf_8289.map" model { file = "/net/cci-nas-00/data/ceres_data/5kuf_8289/05_2025/5kuf_8289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5kuf_8289/05_2025/5kuf_8289.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 1, 'ARG:plan': 2} 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: {'GLU:plan': 1, 'ARG:plan': 2} 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: 23.40, per 1000 atoms: 0.99 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: 6.53 Conformation dependent library (CDL) restraints added in 3.3 seconds 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: 3.18 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: 8.34 Time building geometry restraints manager: 7.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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 - 16.15: 13970 16.15 - 32.30: 452 32.30 - 48.44: 66 48.44 - 64.59: 6 64.59 - 80.74: 18 Dihedral angle restraints: 14512 sinusoidal: 5812 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 14509 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: 0.12 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: 1.940 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: 0.810 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 63.110 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 : 9.227 80.738 8888 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 29.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.032 0.004 TRP B 265 HIS 0.019 0.004 HIS B 105 PHE 0.040 0.004 PHE A 524 TYR 0.024 0.003 TYR D 412 ARG 0.013 0.002 ARG D 189 Details of bonding type rmsd hydrogen bonds : bond 0.34470 ( 862) hydrogen bonds : angle 11.30937 ( 2472) SS BOND : bond 0.00828 ( 8) SS BOND : angle 1.20665 ( 16) covalent geometry : bond 0.00937 (24240) covalent geometry : angle 1.02262 (32828) Misc. bond : bond 0.88310 ( 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 : 2.657 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: 0.4313 time to fit residues: 268.3097 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 : 2.740 ------------------------------------------------------------------------------- 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 253 optimal weight: 7.9990 chunk 227 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 235 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 272 optimal weight: 30.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 HIS D 477 HIS D 518 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.090207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.080541 restraints weight = 102683.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.080732 restraints weight = 68572.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.080856 restraints weight = 54378.358| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24250 Z= 0.205 Angle : 0.794 11.274 32844 Z= 0.414 Chirality : 0.046 0.179 3716 Planarity : 0.006 0.060 4144 Dihedral : 7.642 54.070 3285 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.31 % Allowed : 6.44 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.13), residues: 2976 helix: -2.51 (0.12), residues: 1254 sheet: -3.24 (0.25), residues: 346 loop : -2.76 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 675 HIS 0.008 0.002 HIS B 105 PHE 0.032 0.003 PHE B 135 TYR 0.033 0.002 TYR D 535 ARG 0.009 0.001 ARG C 189 Details of bonding type rmsd hydrogen bonds : bond 0.07046 ( 862) hydrogen bonds : angle 7.06953 ( 2472) SS BOND : bond 0.00996 ( 8) SS BOND : angle 1.26584 ( 16) covalent geometry : bond 0.00440 (24240) covalent geometry : angle 0.79382 (32828) Misc. bond : bond 0.01005 ( 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 335 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 2.762 Fit side-chains revert: symmetry clash REVERT: A 163 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6896 (ptp-170) REVERT: A 267 MET cc_start: 0.7945 (mtt) cc_final: 0.7695 (mtm) REVERT: A 548 PHE cc_start: 0.6246 (t80) cc_final: 0.5481 (m-80) REVERT: A 690 SER cc_start: 0.8166 (m) cc_final: 0.7893 (t) REVERT: A 704 LEU cc_start: 0.8228 (tp) cc_final: 0.7943 (tt) REVERT: B 518 ASN cc_start: 0.6328 (OUTLIER) cc_final: 0.6120 (m-40) REVERT: B 733 TYR cc_start: 0.4066 (m-80) cc_final: 0.3791 (m-80) REVERT: B 763 MET cc_start: 0.6510 (ttm) cc_final: 0.6283 (ttm) REVERT: B 796 LEU cc_start: 0.5359 (OUTLIER) cc_final: 0.5056 (tp) REVERT: C 267 MET cc_start: 0.7950 (mtt) cc_final: 0.7699 (mtm) REVERT: C 548 PHE cc_start: 0.6330 (t80) cc_final: 0.5471 (m-80) REVERT: C 690 SER cc_start: 0.8161 (m) cc_final: 0.7878 (t) REVERT: C 704 LEU cc_start: 0.8237 (tp) cc_final: 0.8008 (tt) REVERT: D 733 TYR cc_start: 0.4096 (m-80) cc_final: 0.3802 (m-80) REVERT: D 763 MET cc_start: 0.6487 (ttm) cc_final: 0.6285 (ttm) REVERT: D 796 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.5018 (tp) outliers start: 34 outliers final: 18 residues processed: 320 average time/residue: 0.3407 time to fit residues: 172.8818 Evaluate side-chains 229 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 2.610 ------------------------------------------------------------------------------- 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 115 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 267 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 47 optimal weight: 0.3980 chunk 273 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS B 92 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 HIS D 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.091287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.081109 restraints weight = 102781.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.081347 restraints weight = 75665.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.081768 restraints weight = 53603.201| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24250 Z= 0.151 Angle : 0.677 11.294 32844 Z= 0.346 Chirality : 0.042 0.158 3716 Planarity : 0.005 0.061 4144 Dihedral : 6.562 58.786 3285 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.35 % Allowed : 8.59 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.14), residues: 2976 helix: -1.29 (0.13), residues: 1256 sheet: -2.87 (0.26), residues: 346 loop : -2.21 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 675 HIS 0.006 0.001 HIS B 105 PHE 0.038 0.002 PHE B 135 TYR 0.025 0.002 TYR D 535 ARG 0.004 0.001 ARG C 249 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 862) hydrogen bonds : angle 6.11874 ( 2472) SS BOND : bond 0.00447 ( 8) SS BOND : angle 0.90251 ( 16) covalent geometry : bond 0.00315 (24240) covalent geometry : angle 0.67670 (32828) Misc. bond : bond 0.00138 ( 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 307 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 272 time to evaluate : 2.614 Fit side-chains revert: symmetry clash REVERT: A 436 LEU cc_start: 0.8925 (tp) cc_final: 0.8648 (tp) REVERT: A 510 LEU cc_start: 0.8370 (tp) cc_final: 0.8037 (tt) REVERT: A 548 PHE cc_start: 0.6221 (t80) cc_final: 0.5418 (m-80) REVERT: A 628 LEU cc_start: 0.8128 (mt) cc_final: 0.7706 (tp) REVERT: A 645 LYS cc_start: 0.8397 (pttt) cc_final: 0.8017 (mmtp) REVERT: A 690 SER cc_start: 0.8194 (m) cc_final: 0.7948 (t) REVERT: A 704 LEU cc_start: 0.8299 (tp) cc_final: 0.8056 (tt) REVERT: B 157 LEU cc_start: 0.8645 (tp) cc_final: 0.8408 (tp) REVERT: B 470 MET cc_start: 0.6946 (ttm) cc_final: 0.6740 (ttt) REVERT: C 436 LEU cc_start: 0.8899 (tp) cc_final: 0.8624 (tp) REVERT: C 548 PHE cc_start: 0.6046 (t80) cc_final: 0.5055 (m-80) REVERT: C 628 LEU cc_start: 0.8166 (mt) cc_final: 0.7816 (tp) REVERT: C 645 LYS cc_start: 0.8391 (pttt) cc_final: 0.8029 (mmtp) REVERT: C 690 SER cc_start: 0.7961 (m) cc_final: 0.7718 (t) REVERT: C 704 LEU cc_start: 0.8356 (tp) cc_final: 0.7891 (tt) REVERT: C 739 MET cc_start: 0.6989 (tpt) cc_final: 0.6534 (tpp) REVERT: D 660 MET cc_start: 0.7352 (tmm) cc_final: 0.7070 (tmm) outliers start: 35 outliers final: 11 residues processed: 301 average time/residue: 0.2961 time to fit residues: 147.1328 Evaluate side-chains 216 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 205 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain C residue 298 VAL 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 795 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 129 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 262 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 108 optimal weight: 0.0570 chunk 242 optimal weight: 0.0670 chunk 297 optimal weight: 20.0000 overall best weight: 3.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.090042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.080482 restraints weight = 104686.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.080532 restraints weight = 73514.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.080543 restraints weight = 60213.650| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24250 Z= 0.185 Angle : 0.685 13.164 32844 Z= 0.347 Chirality : 0.042 0.154 3716 Planarity : 0.005 0.061 4144 Dihedral : 6.250 35.342 3281 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.39 % Allowed : 9.60 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.14), residues: 2976 helix: -0.88 (0.14), residues: 1254 sheet: -2.67 (0.26), residues: 344 loop : -2.01 (0.16), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 675 HIS 0.006 0.001 HIS D 105 PHE 0.024 0.002 PHE B 135 TYR 0.017 0.002 TYR B 115 ARG 0.005 0.001 ARG A 717 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 862) hydrogen bonds : angle 5.83732 ( 2472) SS BOND : bond 0.00379 ( 8) SS BOND : angle 0.71826 ( 16) covalent geometry : bond 0.00417 (24240) covalent geometry : angle 0.68531 (32828) Misc. bond : bond 0.00066 ( 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 271 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 2.583 Fit side-chains revert: symmetry clash REVERT: A 436 LEU cc_start: 0.8908 (tp) cc_final: 0.8553 (tp) REVERT: A 548 PHE cc_start: 0.6486 (t80) cc_final: 0.5505 (m-80) REVERT: A 645 LYS cc_start: 0.8435 (pttt) cc_final: 0.8076 (mmtp) REVERT: A 690 SER cc_start: 0.8277 (m) cc_final: 0.7955 (t) REVERT: A 704 LEU cc_start: 0.8508 (tp) cc_final: 0.8149 (tt) REVERT: A 739 MET cc_start: 0.7035 (tpt) cc_final: 0.6602 (tpp) REVERT: B 14 VAL cc_start: 0.5992 (t) cc_final: 0.5761 (p) REVERT: C 436 LEU cc_start: 0.8873 (tp) cc_final: 0.8513 (tp) REVERT: C 510 LEU cc_start: 0.8338 (tp) cc_final: 0.8046 (tt) REVERT: C 645 LYS cc_start: 0.8446 (pttt) cc_final: 0.8037 (mmtp) REVERT: C 739 MET cc_start: 0.7056 (tpt) cc_final: 0.6642 (tpp) REVERT: D 14 VAL cc_start: 0.6046 (t) cc_final: 0.5823 (p) REVERT: D 216 MET cc_start: 0.7934 (mtt) cc_final: 0.7659 (mtt) REVERT: D 518 ASN cc_start: 0.6228 (m-40) cc_final: 0.6018 (m-40) outliers start: 62 outliers final: 49 residues processed: 258 average time/residue: 0.2822 time to fit residues: 123.2855 Evaluate side-chains 239 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 GLU 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 643 LEU 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 116 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 360 VAL 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 615 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 256 THR 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 643 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 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 116 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 360 VAL 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 614 LEU Chi-restraints excluded: chain D residue 615 ILE Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 795 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 180 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 297 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN ** D 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.089379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.080100 restraints weight = 104587.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.080102 restraints weight = 77719.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.080288 restraints weight = 65983.017| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24250 Z= 0.225 Angle : 0.702 10.874 32844 Z= 0.359 Chirality : 0.043 0.150 3716 Planarity : 0.005 0.055 4144 Dihedral : 6.280 33.573 3281 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.81 % Allowed : 10.17 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.15), residues: 2976 helix: -0.83 (0.14), residues: 1258 sheet: -2.57 (0.29), residues: 308 loop : -1.95 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 675 HIS 0.007 0.002 HIS C 105 PHE 0.024 0.002 PHE B 135 TYR 0.014 0.002 TYR C 145 ARG 0.005 0.001 ARG D 189 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 862) hydrogen bonds : angle 5.84696 ( 2472) SS BOND : bond 0.00350 ( 8) SS BOND : angle 0.73894 ( 16) covalent geometry : bond 0.00505 (24240) covalent geometry : angle 0.70182 (32828) Misc. bond : bond 0.00130 ( 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 267 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 194 time to evaluate : 2.610 Fit side-chains revert: symmetry clash REVERT: A 240 TYR cc_start: 0.5520 (OUTLIER) cc_final: 0.4088 (m-10) REVERT: A 436 LEU cc_start: 0.8950 (tp) cc_final: 0.8622 (tp) REVERT: A 645 LYS cc_start: 0.8458 (pttt) cc_final: 0.8093 (mmtp) REVERT: A 739 MET cc_start: 0.7159 (tpt) cc_final: 0.6750 (tpp) REVERT: B 14 VAL cc_start: 0.5982 (t) cc_final: 0.5761 (p) REVERT: C 240 TYR cc_start: 0.5478 (OUTLIER) cc_final: 0.4040 (m-10) REVERT: C 436 LEU cc_start: 0.8929 (tp) cc_final: 0.8599 (tp) REVERT: C 628 LEU cc_start: 0.8404 (mt) cc_final: 0.7792 (tp) REVERT: C 645 LYS cc_start: 0.8486 (pttt) cc_final: 0.8134 (mmtp) REVERT: C 739 MET cc_start: 0.7167 (tpt) cc_final: 0.6761 (tpp) REVERT: D 14 VAL cc_start: 0.6017 (t) cc_final: 0.5792 (p) outliers start: 73 outliers final: 59 residues processed: 252 average time/residue: 0.2995 time to fit residues: 125.4669 Evaluate side-chains 236 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 GLU 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 298 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 505 LEU 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 748 THR 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 116 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 360 VAL 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 615 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 108 SER 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 270 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 643 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 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 116 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 360 VAL 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 795 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 114 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 646 GLN ** 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 = 0.3886 r_free = 0.3886 target = 0.090279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.081096 restraints weight = 103211.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.081003 restraints weight = 75222.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.081252 restraints weight = 64406.863| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24250 Z= 0.146 Angle : 0.627 9.965 32844 Z= 0.321 Chirality : 0.041 0.150 3716 Planarity : 0.005 0.053 4144 Dihedral : 5.896 33.954 3281 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.31 % Allowed : 11.48 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.15), residues: 2976 helix: -0.49 (0.14), residues: 1272 sheet: -2.34 (0.30), residues: 304 loop : -1.81 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 675 HIS 0.004 0.001 HIS D 105 PHE 0.021 0.002 PHE B 135 TYR 0.021 0.001 TYR D 115 ARG 0.015 0.001 ARG C 318 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 862) hydrogen bonds : angle 5.56486 ( 2472) SS BOND : bond 0.00295 ( 8) SS BOND : angle 0.62362 ( 16) covalent geometry : bond 0.00329 (24240) covalent geometry : angle 0.62696 (32828) Misc. bond : bond 0.00126 ( 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 262 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 202 time to evaluate : 2.585 Fit side-chains REVERT: A 240 TYR cc_start: 0.5413 (OUTLIER) cc_final: 0.3929 (m-10) REVERT: A 436 LEU cc_start: 0.8934 (tp) cc_final: 0.8612 (tp) REVERT: A 645 LYS cc_start: 0.8481 (pttt) cc_final: 0.8118 (mmtp) REVERT: A 704 LEU cc_start: 0.8560 (tp) cc_final: 0.8335 (tt) REVERT: A 739 MET cc_start: 0.7121 (tpt) cc_final: 0.6598 (tpp) REVERT: B 14 VAL cc_start: 0.5903 (t) cc_final: 0.5690 (p) REVERT: B 796 LEU cc_start: 0.4937 (OUTLIER) cc_final: 0.4733 (tp) REVERT: C 240 TYR cc_start: 0.5435 (OUTLIER) cc_final: 0.3983 (m-10) REVERT: C 436 LEU cc_start: 0.8909 (tp) cc_final: 0.8578 (tp) REVERT: C 645 LYS cc_start: 0.8438 (pttt) cc_final: 0.8151 (mmtp) REVERT: C 704 LEU cc_start: 0.8503 (tp) cc_final: 0.8280 (tt) REVERT: C 739 MET cc_start: 0.7108 (tpt) cc_final: 0.6601 (tpp) REVERT: D 14 VAL cc_start: 0.5936 (t) cc_final: 0.5722 (p) outliers start: 60 outliers final: 43 residues processed: 250 average time/residue: 0.3005 time to fit residues: 123.9669 Evaluate side-chains 228 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 2.568 ------------------------------------------------------------------------------- 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 298 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 505 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 748 THR Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 360 VAL 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 615 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 796 LEU 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 407 ILE 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 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 116 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 360 VAL 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 795 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN D 646 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.088408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.079239 restraints weight = 104974.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.079058 restraints weight = 78893.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.079239 restraints weight = 62115.573| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 24250 Z= 0.248 Angle : 0.733 8.222 32844 Z= 0.375 Chirality : 0.044 0.144 3716 Planarity : 0.006 0.053 4144 Dihedral : 6.356 33.760 3281 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.97 % Allowed : 11.87 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.15), residues: 2976 helix: -0.65 (0.14), residues: 1270 sheet: -2.55 (0.28), residues: 326 loop : -1.83 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 675 HIS 0.007 0.002 HIS C 201 PHE 0.023 0.002 PHE B 135 TYR 0.017 0.002 TYR C 221 ARG 0.008 0.001 ARG A 318 Details of bonding type rmsd hydrogen bonds : bond 0.04157 ( 862) hydrogen bonds : angle 5.72245 ( 2472) SS BOND : bond 0.00320 ( 8) SS BOND : angle 0.65038 ( 16) covalent geometry : bond 0.00554 (24240) covalent geometry : angle 0.73256 (32828) Misc. bond : bond 0.00148 ( 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 266 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 189 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 TYR cc_start: 0.5627 (OUTLIER) cc_final: 0.4019 (m-10) REVERT: A 436 LEU cc_start: 0.8963 (tp) cc_final: 0.8620 (tp) REVERT: A 503 MET cc_start: 0.5503 (mtp) cc_final: 0.5183 (mtp) REVERT: A 645 LYS cc_start: 0.8500 (pttt) cc_final: 0.8183 (mmtp) REVERT: A 704 LEU cc_start: 0.8644 (tp) cc_final: 0.8369 (tt) REVERT: A 739 MET cc_start: 0.7128 (tpt) cc_final: 0.6772 (tpp) REVERT: B 706 MET cc_start: 0.7349 (mmm) cc_final: 0.7058 (mmm) REVERT: B 805 PHE cc_start: 0.5634 (t80) cc_final: 0.5409 (t80) REVERT: C 240 TYR cc_start: 0.5613 (OUTLIER) cc_final: 0.4019 (m-10) REVERT: C 436 LEU cc_start: 0.8937 (tp) cc_final: 0.8598 (tp) REVERT: C 503 MET cc_start: 0.5531 (mtt) cc_final: 0.4727 (mtt) REVERT: C 628 LEU cc_start: 0.8329 (mt) cc_final: 0.7771 (tp) REVERT: C 645 LYS cc_start: 0.8466 (pttt) cc_final: 0.8192 (mmtp) REVERT: C 739 MET cc_start: 0.7222 (tpt) cc_final: 0.6834 (tpp) REVERT: D 285 MET cc_start: 0.7794 (ttt) cc_final: 0.7511 (ttt) outliers start: 77 outliers final: 63 residues processed: 253 average time/residue: 0.2951 time to fit residues: 124.6466 Evaluate side-chains 245 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 180 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 203 MET 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 463 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 706 MET 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 A residue 804 VAL 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 230 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 360 VAL 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 505 LEU Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 789 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 108 SER 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 463 VAL 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 C residue 751 ILE Chi-restraints excluded: chain C residue 804 VAL 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 250 ILE Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 360 VAL 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 505 LEU Chi-restraints excluded: chain D residue 615 ILE Chi-restraints excluded: chain D residue 646 GLN 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 157 optimal weight: 10.0000 chunk 240 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 chunk 228 optimal weight: 0.0060 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.090905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.081197 restraints weight = 103900.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.081813 restraints weight = 73594.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.082082 restraints weight = 53201.459| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24250 Z= 0.119 Angle : 0.631 20.539 32844 Z= 0.320 Chirality : 0.041 0.189 3716 Planarity : 0.005 0.052 4144 Dihedral : 5.715 34.815 3281 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.89 % Allowed : 13.29 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.15), residues: 2976 helix: -0.19 (0.14), residues: 1288 sheet: -2.32 (0.28), residues: 332 loop : -1.69 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 675 HIS 0.003 0.001 HIS B 3 PHE 0.022 0.001 PHE B 611 TYR 0.018 0.001 TYR D 431 ARG 0.005 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 862) hydrogen bonds : angle 5.35701 ( 2472) SS BOND : bond 0.00262 ( 8) SS BOND : angle 0.54756 ( 16) covalent geometry : bond 0.00261 (24240) covalent geometry : angle 0.63097 (32828) Misc. bond : bond 0.00123 ( 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 272 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 TYR cc_start: 0.5381 (OUTLIER) cc_final: 0.3873 (m-10) REVERT: A 436 LEU cc_start: 0.8908 (tp) cc_final: 0.8507 (tp) REVERT: A 503 MET cc_start: 0.5124 (mtp) cc_final: 0.4728 (mtp) REVERT: A 645 LYS cc_start: 0.8417 (pttt) cc_final: 0.8041 (mttm) REVERT: A 704 LEU cc_start: 0.8567 (tp) cc_final: 0.8309 (tt) REVERT: A 739 MET cc_start: 0.7076 (tpt) cc_final: 0.6787 (tpt) REVERT: A 792 ILE cc_start: 0.6156 (mm) cc_final: 0.5945 (mm) REVERT: B 14 VAL cc_start: 0.5748 (t) cc_final: 0.5467 (p) REVERT: B 706 MET cc_start: 0.7252 (mmm) cc_final: 0.6988 (mmm) REVERT: C 214 MET cc_start: 0.7445 (OUTLIER) cc_final: 0.7127 (mtp) REVERT: C 240 TYR cc_start: 0.5342 (OUTLIER) cc_final: 0.3864 (m-10) REVERT: C 436 LEU cc_start: 0.8849 (tp) cc_final: 0.8422 (tp) REVERT: C 503 MET cc_start: 0.5095 (mtt) cc_final: 0.4198 (mtt) REVERT: C 645 LYS cc_start: 0.8416 (pttt) cc_final: 0.8042 (mttm) REVERT: C 704 LEU cc_start: 0.8617 (tp) cc_final: 0.8336 (tt) REVERT: C 739 MET cc_start: 0.7028 (tpt) cc_final: 0.6750 (tpt) REVERT: C 792 ILE cc_start: 0.6164 (mm) cc_final: 0.5954 (mm) REVERT: D 14 VAL cc_start: 0.5874 (t) cc_final: 0.5589 (p) outliers start: 49 outliers final: 35 residues processed: 266 average time/residue: 0.3133 time to fit residues: 135.9474 Evaluate side-chains 227 residues out of total 2612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 108 SER 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 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 70 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 170 ILE 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 461 ASP Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain C residue 59 GLU Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 214 MET 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 463 VAL 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 91 CYS Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 170 ILE 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 751 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.3778 > 50: distance: 3 - 27: 36.430 distance: 14 - 35: 32.035 distance: 18 - 43: 32.442 distance: 22 - 27: 35.425 distance: 23 - 50: 35.737 distance: 27 - 28: 44.505 distance: 28 - 29: 43.858 distance: 28 - 31: 17.450 distance: 29 - 30: 40.859 distance: 29 - 35: 69.348 distance: 30 - 59: 41.396 distance: 31 - 32: 38.997 distance: 32 - 33: 57.498 distance: 32 - 34: 40.706 distance: 35 - 36: 39.661 distance: 36 - 37: 38.786 distance: 36 - 39: 40.804 distance: 37 - 38: 41.233 distance: 37 - 43: 41.207 distance: 38 - 70: 39.066 distance: 43 - 44: 56.179 distance: 44 - 45: 55.698 distance: 44 - 47: 41.010 distance: 45 - 46: 41.219 distance: 45 - 50: 39.173 distance: 51 - 52: 40.087 distance: 51 - 54: 56.734 distance: 54 - 55: 40.297 distance: 55 - 56: 38.914 distance: 56 - 57: 30.263 distance: 56 - 58: 15.898 distance: 60 - 61: 39.871 distance: 64 - 66: 68.795 distance: 65 - 67: 41.129 distance: 67 - 69: 25.509 distance: 68 - 69: 42.574 distance: 71 - 72: 40.104 distance: 71 - 74: 38.555 distance: 72 - 81: 39.715 distance: 74 - 75: 40.635 distance: 75 - 76: 39.260 distance: 77 - 79: 39.861 distance: 82 - 85: 39.810 distance: 83 - 84: 40.244 distance: 83 - 90: 40.997 distance: 86 - 87: 55.925 distance: 87 - 88: 39.651 distance: 91 - 92: 39.665 distance: 91 - 94: 39.175 distance: 92 - 93: 56.158 distance: 92 - 104: 39.787 distance: 94 - 95: 17.495 distance: 95 - 96: 44.127 distance: 95 - 97: 16.037 distance: 96 - 98: 39.866 distance: 97 - 99: 55.326 distance: 97 - 100: 56.595 distance: 99 - 101: 39.191 distance: 100 - 102: 39.736 distance: 101 - 103: 32.000 distance: 102 - 103: 40.830 distance: 106 - 113: 39.118 distance: 109 - 110: 38.866 distance: 110 - 111: 57.362 distance: 114 - 115: 40.506 distance: 115 - 120: 33.458 distance: 120 - 154: 3.152