Starting phenix.real_space_refine on Mon Jul 6 08:45:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xlk_38451/07_2026/8xlk_38451_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xlk_38451/07_2026/8xlk_38451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xlk_38451/07_2026/8xlk_38451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xlk_38451/07_2026/8xlk_38451.map" model { file = "/net/cci-nas-00/data/ceres_data/8xlk_38451/07_2026/8xlk_38451_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xlk_38451/07_2026/8xlk_38451_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 182 5.16 5 C 21720 2.51 5 N 5684 2.21 5 O 6530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34118 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 6322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 6322 Classifications: {'peptide': 800} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 765} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 6279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6279 Classifications: {'peptide': 792} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 762} Chain breaks: 1 Chain: "C" Number of atoms: 6325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 6325 Classifications: {'peptide': 800} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 765} Chain breaks: 1 Chain: "D" Number of atoms: 6260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6260 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 763} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 938 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "F" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 828 Classifications: {'peptide': 110} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1693 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain: "H" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1576 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 202} Chain: "I" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 938 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "J" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 822 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 899 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'7RC': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'7RC': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.07, per 1000 atoms: 0.21 Number of scatterers: 34118 At special positions: 0 Unit cell: (187.425, 207.774, 184.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 182 16.00 P 2 15.00 O 6530 8.00 N 5684 7.00 C 21720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 800 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.04 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 116 " distance=2.03 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 111 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 210 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 42 " - pdb=" SG CYS I 116 " distance=2.04 Simple disulfide: pdb=" SG CYS J 42 " - pdb=" SG CYS J 111 " distance=2.04 Simple disulfide: pdb=" SG CYS K 42 " - pdb=" SG CYS K 116 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Links applied ALPHA1-4 " NAG M 2 " - " MAN M 3 " " NAG O 2 " - " MAN O 3 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1001 " - " ASN A 61 " " NAG A1002 " - " ASN A 203 " " NAG A1003 " - " ASN A 239 " " NAG A1004 " - " ASN A 276 " " NAG A1005 " - " ASN A 300 " " NAG A1006 " - " ASN A 350 " " NAG A1007 " - " ASN A 471 " " NAG B1501 " - " ASN B 541 " " NAG B1502 " - " ASN B 340 " " NAG B1503 " - " ASN B 380 " " NAG C1001 " - " ASN C 61 " " NAG C1002 " - " ASN C 203 " " NAG C1003 " - " ASN C 239 " " NAG C1004 " - " ASN C 276 " " NAG C1005 " - " ASN C 300 " " NAG C1006 " - " ASN C 350 " " NAG C1007 " - " ASN C 471 " " NAG D1501 " - " ASN D 542 " " NAG D1502 " - " ASN D 341 " " NAG D1503 " - " ASN D 688 " " NAG M 1 " - " ASN A 771 " " NAG N 1 " - " ASN B 687 " " NAG O 1 " - " ASN C 771 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7994 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 50 sheets defined 33.4% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 35 through 54 Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 103 through 113 removed outlier: 3.873A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.619A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.248A pdb=" N GLN A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.502A pdb=" N LEU A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.812A pdb=" N ALA A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.595A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 327 removed outlier: 4.138A pdb=" N LEU A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.871A pdb=" N SER A 507 " --> pdb=" O GLY A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 559 through 580 removed outlier: 3.724A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 584 removed outlier: 3.654A pdb=" N SER A 584 " --> pdb=" O ASP A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 584' Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 626 through 658 Processing helix chain 'A' and resid 669 through 674 removed outlier: 3.947A pdb=" N ARG A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 696 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.622A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.690A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 744 removed outlier: 4.239A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 813 through 839 removed outlier: 3.595A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 94 removed outlier: 3.538A pdb=" N ARG B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.658A pdb=" N GLN B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 150 through 165 Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.895A pdb=" N THR B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.859A pdb=" N LEU B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 4.043A pdb=" N SER B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 311 Processing helix chain 'B' and resid 330 through 338 removed outlier: 4.090A pdb=" N LEU B 334 " --> pdb=" O PRO B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.697A pdb=" N TYR B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 522 removed outlier: 4.240A pdb=" N VAL B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 554 through 579 removed outlier: 4.072A pdb=" N TYR B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 614 removed outlier: 4.072A pdb=" N ILE B 605 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 653 removed outlier: 3.867A pdb=" N MET B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.758A pdb=" N GLN B 671 " --> pdb=" O ASP B 667 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 672 " --> pdb=" O LYS B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 672' Processing helix chain 'B' and resid 673 through 676 removed outlier: 3.619A pdb=" N TYR B 676 " --> pdb=" O PRO B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 676' Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 732 through 742 Processing helix chain 'B' and resid 743 through 745 No H-bonds generated for 'chain 'B' and resid 743 through 745' Processing helix chain 'B' and resid 771 through 786 removed outlier: 3.644A pdb=" N GLY B 786 " --> pdb=" O PHE B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'B' and resid 817 through 841 removed outlier: 4.351A pdb=" N PHE B 821 " --> pdb=" O MET B 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'C' and resid 71 through 81 Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.980A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.679A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 159 removed outlier: 4.060A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 removed outlier: 4.133A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.582A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 277 through 297 Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.553A pdb=" N GLY C 384 " --> pdb=" O TRP C 381 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 385' Processing helix chain 'C' and resid 457 through 470 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.088A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 580 removed outlier: 4.128A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 580 " --> pdb=" O MET C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.941A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 657 removed outlier: 4.174A pdb=" N ILE C 631 " --> pdb=" O PHE C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.570A pdb=" N TYR C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 744 removed outlier: 3.959A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 743 " --> pdb=" O GLU C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 782 Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 810 through 828 removed outlier: 4.443A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY C 822 " --> pdb=" O MET C 818 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 824 " --> pdb=" O VAL C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 838 removed outlier: 3.905A pdb=" N GLU C 834 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 835 " --> pdb=" O ILE C 831 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.858A pdb=" N ILE D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 179 through 192 Processing helix chain 'D' and resid 211 through 221 removed outlier: 4.549A pdb=" N ASN D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 3.759A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 4.075A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.752A pdb=" N ASN D 333 " --> pdb=" O ILE D 329 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET D 334 " --> pdb=" O TYR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 555 through 578 removed outlier: 4.237A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 628 through 653 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 771 through 787 removed outlier: 4.443A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 4.277A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 842 removed outlier: 3.906A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.528A pdb=" N THR G 92 " --> pdb=" O THR G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 204 removed outlier: 3.734A pdb=" N GLU G 203 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 183 through 189 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.595A pdb=" N LEU I 84 " --> pdb=" O ASN I 81 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS I 85 " --> pdb=" O PRO I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 85' Processing helix chain 'I' and resid 120 through 124 removed outlier: 3.549A pdb=" N PHE I 123 " --> pdb=" O TYR I 120 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR I 124 " --> pdb=" O TYR I 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 120 through 124' Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 66 removed outlier: 6.182A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N TYR A 88 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ASN A 28 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE A 90 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY A 30 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL A 92 " --> pdb=" O GLY A 30 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL A 32 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.397A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 362 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.354A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.694A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.705A pdb=" N VAL A 490 " --> pdb=" O LYS A 495 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.607A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 538 " --> pdb=" O PHE A 754 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE A 754 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 10.162A pdb=" N ILE A 540 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N LEU A 752 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 10.480A pdb=" N VAL A 542 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N GLY A 750 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 74 removed outlier: 6.486A pdb=" N ILE B 36 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU B 72 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL B 38 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET B 74 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU B 40 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 41 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 205 removed outlier: 7.904A pdb=" N PHE B 170 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASN B 202 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 169 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 228 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER B 171 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N TYR B 230 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL B 173 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TRP B 255 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL B 279 " --> pdb=" O TRP B 255 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL B 257 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL B 365 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS B 374 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB3, first strand: chain 'B' and resid 409 through 410 removed outlier: 3.610A pdb=" N THR B 410 " --> pdb=" O TYR B 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB5, first strand: chain 'B' and resid 682 through 684 removed outlier: 6.574A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 682 through 684 removed outlier: 6.574A pdb=" N GLY B 683 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N ASP B 731 " --> pdb=" O GLY B 683 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE B 533 " --> pdb=" O ALA B 757 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 757 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 62 removed outlier: 8.993A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 119 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 92 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 197 Processing sheet with id=AB9, first strand: chain 'C' and resid 267 through 268 removed outlier: 3.968A pdb=" N GLY C 365 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 410 through 413 removed outlier: 7.986A pdb=" N ILE C 435 " --> pdb=" O TYR C 474 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL C 476 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 478 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 401 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 489 Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.710A pdb=" N ALA C 682 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE C 730 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 11.058A pdb=" N LYS C 534 " --> pdb=" O ARG C 755 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N ARG C 755 " --> pdb=" O LYS C 534 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N GLN C 536 " --> pdb=" O PHE C 753 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N PHE C 753 " --> pdb=" O GLN C 536 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 73 removed outlier: 5.971A pdb=" N GLY D 36 " --> pdb=" O GLY D 96 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL D 98 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 205 removed outlier: 8.116A pdb=" N PHE D 169 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL D 202 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE D 171 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU D 204 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR D 173 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE D 168 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU D 229 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 343 through 344 removed outlier: 4.058A pdb=" N PHE D 344 " --> pdb=" O ARG D 347 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 419 through 421 removed outlier: 5.836A pdb=" N LEU D 478 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 437 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 480 " --> pdb=" O GLN D 437 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG D 439 " --> pdb=" O LEU D 480 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N GLY D 511 " --> pdb=" O ALA D 765 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA D 765 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU D 513 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 524 through 525 removed outlier: 5.235A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 23 through 27 Processing sheet with id=AD1, first strand: chain 'E' and resid 78 through 80 removed outlier: 6.243A pdb=" N LEU E 66 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N PHE E 61 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TRP E 68 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG E 59 " --> pdb=" O TRP E 68 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY E 70 " --> pdb=" O TRP E 57 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 23 through 26 Processing sheet with id=AD3, first strand: chain 'F' and resid 68 through 72 removed outlier: 5.656A pdb=" N LEU F 69 " --> pdb=" O GLN F 60 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN F 60 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AD5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.589A pdb=" N ALA G 51 " --> pdb=" O TRP G 38 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG G 40 " --> pdb=" O TRP G 49 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TRP G 49 " --> pdb=" O ARG G 40 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AD7, first strand: chain 'G' and resid 130 through 132 Processing sheet with id=AD8, first strand: chain 'G' and resid 210 through 214 Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.640A pdb=" N CYS H 23 " --> pdb=" O TYR H 71 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.882A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ALA H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU H 33 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.965A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN H 160 " --> pdb=" O THR H 178 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 145 through 150 Processing sheet with id=AE4, first strand: chain 'I' and resid 23 through 27 Processing sheet with id=AE5, first strand: chain 'I' and resid 78 through 79 removed outlier: 6.072A pdb=" N TRP I 68 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG I 59 " --> pdb=" O TRP I 68 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 23 through 26 Processing sheet with id=AE7, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AE8, first strand: chain 'J' and resid 68 through 71 removed outlier: 6.612A pdb=" N TRP J 58 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 23 through 27 removed outlier: 3.744A pdb=" N LEU K 38 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU K 101 " --> pdb=" O LEU K 40 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N CYS K 42 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU K 99 " --> pdb=" O CYS K 42 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 57 through 59 Processing sheet with id=AF2, first strand: chain 'K' and resid 113 through 114 Processing sheet with id=AF3, first strand: chain 'K' and resid 117 through 118 removed outlier: 4.338A pdb=" N VAL K 131 " --> pdb=" O ARG K 118 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 38 through 44 Processing sheet with id=AF5, first strand: chain 'L' and resid 65 through 66 removed outlier: 3.659A pdb=" N THR L 121 " --> pdb=" O TYR L 106 " (cutoff:3.500A) 1352 hydrogen bonds defined for protein. 3813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.97 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5582 1.31 - 1.44: 9606 1.44 - 1.58: 19397 1.58 - 1.72: 2 1.72 - 1.85: 305 Bond restraints: 34892 Sorted by residual: bond pdb=" CA ASP E 52 " pdb=" CB ASP E 52 " ideal model delta sigma weight residual 1.530 1.342 0.189 1.52e-02 4.33e+03 1.54e+02 bond pdb=" CA ASP E 52 " pdb=" C ASP E 52 " ideal model delta sigma weight residual 1.526 1.368 0.158 1.37e-02 5.33e+03 1.33e+02 bond pdb=" CA SER E 51 " pdb=" C SER E 51 " ideal model delta sigma weight residual 1.523 1.670 -0.147 1.34e-02 5.57e+03 1.21e+02 bond pdb=" C ASP E 52 " pdb=" N TYR E 53 " ideal model delta sigma weight residual 1.332 1.460 -0.128 1.40e-02 5.10e+03 8.34e+01 bond pdb=" CA TYR J 109 " pdb=" C TYR J 109 " ideal model delta sigma weight residual 1.523 1.633 -0.110 1.34e-02 5.57e+03 6.69e+01 ... (remaining 34887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.90: 47186 4.90 - 9.81: 134 9.81 - 14.71: 8 14.71 - 19.61: 5 19.61 - 24.51: 1 Bond angle restraints: 47334 Sorted by residual: angle pdb=" N ASP E 52 " pdb=" CA ASP E 52 " pdb=" CB ASP E 52 " ideal model delta sigma weight residual 110.60 86.09 24.51 1.52e+00 4.33e-01 2.60e+02 angle pdb=" N TYR E 74 " pdb=" CA TYR E 74 " pdb=" C TYR E 74 " ideal model delta sigma weight residual 113.41 95.82 17.59 1.22e+00 6.72e-01 2.08e+02 angle pdb=" CA ASP E 52 " pdb=" C ASP E 52 " pdb=" O ASP E 52 " ideal model delta sigma weight residual 121.73 103.83 17.90 1.35e+00 5.49e-01 1.76e+02 angle pdb=" N TYR J 110 " pdb=" CA TYR J 110 " pdb=" C TYR J 110 " ideal model delta sigma weight residual 109.59 125.63 -16.04 1.61e+00 3.86e-01 9.92e+01 angle pdb=" O ALA J 107 " pdb=" C ALA J 107 " pdb=" N THR J 108 " ideal model delta sigma weight residual 123.04 112.74 10.30 1.04e+00 9.25e-01 9.81e+01 ... (remaining 47329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.69: 19784 22.69 - 45.38: 1224 45.38 - 68.07: 113 68.07 - 90.76: 44 90.76 - 113.45: 15 Dihedral angle restraints: 21180 sinusoidal: 8728 harmonic: 12452 Sorted by residual: dihedral pdb=" N ASP E 52 " pdb=" C ASP E 52 " pdb=" CA ASP E 52 " pdb=" CB ASP E 52 " ideal model delta harmonic sigma weight residual 122.80 88.42 34.38 0 2.50e+00 1.60e-01 1.89e+02 dihedral pdb=" C ASP E 52 " pdb=" N ASP E 52 " pdb=" CA ASP E 52 " pdb=" CB ASP E 52 " ideal model delta harmonic sigma weight residual -122.60 -94.09 -28.51 0 2.50e+00 1.60e-01 1.30e+02 dihedral pdb=" N TYR J 110 " pdb=" C TYR J 110 " pdb=" CA TYR J 110 " pdb=" CB TYR J 110 " ideal model delta harmonic sigma weight residual 122.80 149.89 -27.09 0 2.50e+00 1.60e-01 1.17e+02 ... (remaining 21177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 5340 0.239 - 0.479: 7 0.479 - 0.718: 1 0.718 - 0.957: 0 0.957 - 1.197: 1 Chirality restraints: 5349 Sorted by residual: chirality pdb=" CA TYR J 110 " pdb=" N TYR J 110 " pdb=" C TYR J 110 " pdb=" CB TYR J 110 " both_signs ideal model delta sigma weight residual False 2.51 1.31 1.20 2.00e-01 2.50e+01 3.58e+01 chirality pdb=" CA TYR J 109 " pdb=" N TYR J 109 " pdb=" C TYR J 109 " pdb=" CB TYR J 109 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" C1 NAG C1005 " pdb=" ND2 ASN C 300 " pdb=" C2 NAG C1005 " pdb=" O5 NAG C1005 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 5346 not shown) Planarity restraints: 6022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 471 " 0.139 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" CG ASN A 471 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN A 471 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 471 " -0.196 2.00e-02 2.50e+03 pdb=" C1 NAG A1007 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 203 " 0.091 2.00e-02 2.50e+03 1.28e-01 2.04e+02 pdb=" CG ASN A 203 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 203 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 203 " -0.226 2.00e-02 2.50e+03 pdb=" C1 NAG A1002 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 688 " -0.025 2.00e-02 2.50e+03 8.36e-02 8.74e+01 pdb=" CG ASN D 688 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN D 688 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN D 688 " 0.150 2.00e-02 2.50e+03 pdb=" C1 NAG D1503 " -0.090 2.00e-02 2.50e+03 ... (remaining 6019 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 642 2.63 - 3.20: 32953 3.20 - 3.77: 54887 3.77 - 4.33: 72558 4.33 - 4.90: 113921 Nonbonded interactions: 274961 Sorted by model distance: nonbonded pdb=" O PHE K 129 " pdb=" OH TYR L 56 " model vdw 2.066 3.040 nonbonded pdb=" OH TYR L 70 " pdb=" OH TYR L 111 " model vdw 2.090 3.040 nonbonded pdb=" O MET B 135 " pdb=" OH TYR B 355 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR L 105 " pdb=" O THR L 121 " model vdw 2.141 3.040 nonbonded pdb=" O ASP C 198 " pdb=" OG1 THR C 201 " model vdw 2.173 3.040 ... (remaining 274956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 25 through 817 or (resid 818 and (name N or name CA or nam \ e C or name O or name CB )) or resid 819 through 1007)) } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = (chain 'F' and (resid 21 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O or name CB )) or resid 122 through 130)) selection = chain 'J' } ncs_group { reference = chain 'M' selection = chain 'O' } 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: 2.210 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 30.180 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.009 0.872 34950 Z= 0.856 Angle : 0.820 41.090 47468 Z= 0.435 Chirality : 0.052 1.197 5349 Planarity : 0.005 0.075 5999 Dihedral : 14.458 113.449 13111 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.52 % Favored : 93.23 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.46 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.13), residues: 4267 helix: 0.36 (0.15), residues: 1253 sheet: -1.26 (0.18), residues: 824 loop : -1.63 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 37 TYR 0.040 0.001 TYR J 109 PHE 0.028 0.001 PHE G 225 TRP 0.023 0.002 TRP I 57 HIS 0.006 0.001 HIS J 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.22 (34892) covalent geometry : angle 0.77640 / 0.43 (47334) SS BOND : bond 0.00350 / 0.18 ( 25) SS BOND : angle 1.47425 / 0.96 ( 50) hydrogen bonds : bond 0.15738 / 10.73 ( 1340) hydrogen bonds : angle 7.13032 / 5.10 ( 3813) Misc. bond : bond 0.68947 / 37.82 ( 5) link_ALPHA1-4 : bond 0.00530 / 0.27 ( 2) link_ALPHA1-4 : angle 1.70402 / 0.78 ( 6) link_BETA1-4 : bond 0.00325 / 0.17 ( 3) link_BETA1-4 : angle 3.02487 / 1.54 ( 9) link_NAG-ASN : bond 0.04044 / 1.65 ( 23) link_NAG-ASN : angle 6.76844 / 4.65 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 469 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 MET cc_start: 0.8759 (mmp) cc_final: 0.8413 (mmm) REVERT: B 90 MET cc_start: 0.5054 (ppp) cc_final: 0.4330 (ppp) REVERT: B 114 ASP cc_start: 0.8791 (m-30) cc_final: 0.8569 (m-30) REVERT: B 172 LEU cc_start: 0.9127 (tp) cc_final: 0.8907 (tp) REVERT: B 180 TYR cc_start: 0.7328 (p90) cc_final: 0.6315 (p90) REVERT: B 450 MET cc_start: 0.7446 (pmm) cc_final: 0.7244 (pmm) REVERT: B 653 MET cc_start: 0.7660 (ppp) cc_final: 0.7197 (ppp) REVERT: B 763 ILE cc_start: 0.8328 (mt) cc_final: 0.8127 (mt) REVERT: B 803 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7234 (tm-30) REVERT: C 137 PHE cc_start: 0.8119 (t80) cc_final: 0.7836 (t80) REVERT: C 321 PHE cc_start: 0.8008 (t80) cc_final: 0.7700 (t80) REVERT: C 616 ASN cc_start: 0.8986 (t0) cc_final: 0.8779 (t0) REVERT: D 218 ASN cc_start: 0.8720 (t0) cc_final: 0.8477 (m-40) REVERT: D 240 ILE cc_start: 0.8089 (tp) cc_final: 0.7871 (pt) REVERT: D 792 LEU cc_start: 0.8953 (mt) cc_final: 0.8752 (mt) REVERT: G 215 GLN cc_start: 0.2864 (pm20) cc_final: 0.2097 (mp10) REVERT: H 142 ARG cc_start: 0.9153 (pmt-80) cc_final: 0.7937 (tpt170) REVERT: I 69 MET cc_start: 0.7628 (mmp) cc_final: 0.7067 (mmm) REVERT: I 74 TYR cc_start: 0.8254 (p90) cc_final: 0.8023 (p90) REVERT: J 69 LEU cc_start: 0.7625 (tp) cc_final: 0.7245 (tp) REVERT: J 70 LEU cc_start: 0.7513 (mt) cc_final: 0.7157 (mt) REVERT: K 113 MET cc_start: 0.2383 (ttt) cc_final: 0.1963 (ptp) REVERT: L 24 MET cc_start: 0.5959 (mtm) cc_final: 0.4856 (mtp) outliers start: 2 outliers final: 2 residues processed: 471 average time/residue: 0.2066 time to fit residues: 161.8061 Evaluate side-chains 367 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 365 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN A 146 HIS ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 GLN B 697 ASN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 ASN ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN J 112 GLN K 97 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.104123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.087142 restraints weight = 195913.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.085571 restraints weight = 209492.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.086086 restraints weight = 180340.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.086299 restraints weight = 128994.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.086554 restraints weight = 131727.612| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34950 Z= 0.184 Angle : 0.689 14.458 47468 Z= 0.357 Chirality : 0.047 0.355 5349 Planarity : 0.005 0.079 5999 Dihedral : 9.148 107.298 5258 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.73 % Favored : 93.09 % Rotamer: Outliers : 0.19 % Allowed : 4.93 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 4267 helix: 0.44 (0.14), residues: 1299 sheet: -1.35 (0.18), residues: 848 loop : -1.60 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 84 TYR 0.035 0.002 TYR E 53 PHE 0.030 0.002 PHE G 155 TRP 0.017 0.001 TRP I 68 HIS 0.010 0.001 HIS C 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (34892) covalent geometry : angle 0.67394 / 0.35 (47334) SS BOND : bond 0.00259 / 0.17 ( 25) SS BOND : angle 0.99442 / 0.65 ( 50) hydrogen bonds : bond 0.04525 / 3.09 ( 1340) hydrogen bonds : angle 6.15007 / 4.40 ( 3813) Misc. bond : bond 0.00617 / 0.33 ( 5) link_ALPHA1-4 : bond 0.01042 / 0.52 ( 2) link_ALPHA1-4 : angle 2.05825 / 0.96 ( 6) link_BETA1-4 : bond 0.00144 / 0.07 ( 3) link_BETA1-4 : angle 2.53871 / 1.22 ( 9) link_NAG-ASN : bond 0.00534 / 0.35 ( 23) link_NAG-ASN : angle 3.60841 / 2.53 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 442 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8972 (mm) cc_final: 0.8427 (pp) REVERT: A 240 MET cc_start: 0.8975 (mmp) cc_final: 0.8394 (mmm) REVERT: B 114 ASP cc_start: 0.9024 (m-30) cc_final: 0.8809 (m-30) REVERT: B 154 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8458 (mp10) REVERT: B 180 TYR cc_start: 0.7213 (p90) cc_final: 0.6823 (p90) REVERT: B 306 MET cc_start: 0.8154 (tpt) cc_final: 0.7900 (ptp) REVERT: B 653 MET cc_start: 0.7823 (ppp) cc_final: 0.6813 (ppp) REVERT: B 705 MET cc_start: 0.7702 (mmm) cc_final: 0.7257 (mmm) REVERT: B 803 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7178 (tm-30) REVERT: C 321 PHE cc_start: 0.8215 (t80) cc_final: 0.7936 (t80) REVERT: C 398 LEU cc_start: 0.8747 (mp) cc_final: 0.8505 (mp) REVERT: C 616 ASN cc_start: 0.8851 (t0) cc_final: 0.8496 (t0) REVERT: D 101 ASP cc_start: 0.8431 (p0) cc_final: 0.7336 (p0) REVERT: D 240 ILE cc_start: 0.8052 (tp) cc_final: 0.7833 (pt) REVERT: D 538 VAL cc_start: 0.8759 (t) cc_final: 0.8552 (t) REVERT: G 95 TYR cc_start: 0.7839 (m-80) cc_final: 0.7077 (m-80) REVERT: I 69 MET cc_start: 0.7640 (mmp) cc_final: 0.6973 (mmm) REVERT: I 128 TYR cc_start: 0.7757 (m-10) cc_final: 0.7523 (m-10) REVERT: J 69 LEU cc_start: 0.7516 (tp) cc_final: 0.7102 (tp) REVERT: J 70 LEU cc_start: 0.7319 (mt) cc_final: 0.7090 (mt) REVERT: J 109 TYR cc_start: 0.6761 (m-80) cc_final: 0.5979 (m-80) REVERT: K 113 MET cc_start: 0.2188 (ttt) cc_final: 0.1796 (tpt) REVERT: L 24 MET cc_start: 0.5051 (mtm) cc_final: 0.3889 (mtp) outliers start: 7 outliers final: 4 residues processed: 448 average time/residue: 0.2013 time to fit residues: 150.7163 Evaluate side-chains 352 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 347 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 174 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 chunk 341 optimal weight: 0.5980 chunk 328 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 265 optimal weight: 20.0000 chunk 338 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.104644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.087790 restraints weight = 195232.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.087325 restraints weight = 229515.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.087877 restraints weight = 185500.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.088263 restraints weight = 130034.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.088485 restraints weight = 129127.185| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34950 Z= 0.152 Angle : 0.658 10.985 47468 Z= 0.341 Chirality : 0.047 0.360 5349 Planarity : 0.005 0.078 5999 Dihedral : 8.355 103.672 5258 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.89 % Favored : 92.95 % Rotamer: Outliers : 0.11 % Allowed : 4.28 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 4267 helix: 0.47 (0.14), residues: 1297 sheet: -1.25 (0.18), residues: 849 loop : -1.62 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 292 TYR 0.026 0.002 TYR J 110 PHE 0.029 0.002 PHE G 155 TRP 0.012 0.001 TRP I 57 HIS 0.007 0.001 HIS C 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (34892) covalent geometry : angle 0.64461 / 0.34 (47334) SS BOND : bond 0.00402 / 0.25 ( 25) SS BOND : angle 1.19571 / 0.78 ( 50) hydrogen bonds : bond 0.04111 / 2.76 ( 1340) hydrogen bonds : angle 5.96116 / 4.28 ( 3813) Misc. bond : bond 0.00378 / 0.19 ( 5) link_ALPHA1-4 : bond 0.01052 / 0.53 ( 2) link_ALPHA1-4 : angle 2.15410 / 0.99 ( 6) link_BETA1-4 : bond 0.00170 / 0.08 ( 3) link_BETA1-4 : angle 2.51088 / 1.22 ( 9) link_NAG-ASN : bond 0.00507 / 0.34 ( 23) link_NAG-ASN : angle 3.19945 / 2.21 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 449 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8923 (mm) cc_final: 0.8409 (pp) REVERT: A 237 MET cc_start: 0.7816 (mmp) cc_final: 0.7517 (mmm) REVERT: A 240 MET cc_start: 0.9042 (mmp) cc_final: 0.8486 (mmm) REVERT: B 114 ASP cc_start: 0.9008 (m-30) cc_final: 0.8799 (m-30) REVERT: B 180 TYR cc_start: 0.7525 (p90) cc_final: 0.7054 (p90) REVERT: B 536 MET cc_start: 0.7416 (ppp) cc_final: 0.7124 (ppp) REVERT: B 705 MET cc_start: 0.7906 (mmm) cc_final: 0.7392 (mmm) REVERT: B 803 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7217 (tm-30) REVERT: C 321 PHE cc_start: 0.8257 (t80) cc_final: 0.8031 (t80) REVERT: C 576 MET cc_start: 0.8807 (ttt) cc_final: 0.8519 (ptm) REVERT: C 616 ASN cc_start: 0.8975 (t0) cc_final: 0.8674 (t0) REVERT: C 668 ASN cc_start: 0.8666 (p0) cc_final: 0.8400 (p0) REVERT: D 52 ASP cc_start: 0.8600 (p0) cc_final: 0.8262 (p0) REVERT: D 101 ASP cc_start: 0.8470 (p0) cc_final: 0.7507 (p0) REVERT: D 240 ILE cc_start: 0.8077 (tp) cc_final: 0.7821 (pt) REVERT: D 538 VAL cc_start: 0.8907 (t) cc_final: 0.8651 (t) REVERT: G 95 TYR cc_start: 0.8111 (m-80) cc_final: 0.7309 (m-80) REVERT: G 96 TYR cc_start: 0.7593 (m-80) cc_final: 0.6904 (m-80) REVERT: H 97 THR cc_start: 0.8553 (m) cc_final: 0.8224 (p) REVERT: H 167 ASP cc_start: 0.8834 (p0) cc_final: 0.8530 (p0) REVERT: H 170 ASP cc_start: 0.8528 (t70) cc_final: 0.8277 (p0) REVERT: I 69 MET cc_start: 0.7698 (mmp) cc_final: 0.7469 (mmm) REVERT: I 128 TYR cc_start: 0.7701 (m-10) cc_final: 0.7479 (m-10) REVERT: J 49 ASP cc_start: 0.6662 (m-30) cc_final: 0.6324 (m-30) REVERT: J 58 TRP cc_start: 0.6545 (t-100) cc_final: 0.6327 (t-100) REVERT: J 69 LEU cc_start: 0.7279 (tp) cc_final: 0.6841 (tp) REVERT: K 113 MET cc_start: 0.2330 (ttt) cc_final: 0.1995 (tpt) outliers start: 4 outliers final: 2 residues processed: 452 average time/residue: 0.1979 time to fit residues: 149.6831 Evaluate side-chains 352 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 350 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 152 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 407 optimal weight: 40.0000 chunk 207 optimal weight: 0.9980 chunk 353 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 140 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS B 697 ASN C 67 HIS ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN G 79 GLN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN I 104 ASN K 97 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.106020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.088954 restraints weight = 193842.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.087883 restraints weight = 195433.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.088460 restraints weight = 162852.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.088963 restraints weight = 115170.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.089224 restraints weight = 108305.412| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34950 Z= 0.122 Angle : 0.642 11.705 47468 Z= 0.329 Chirality : 0.046 0.453 5349 Planarity : 0.005 0.076 5999 Dihedral : 7.580 97.495 5258 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.56 % Favored : 93.30 % Rotamer: Outliers : 0.11 % Allowed : 3.36 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.13), residues: 4267 helix: 0.55 (0.14), residues: 1295 sheet: -1.17 (0.18), residues: 849 loop : -1.56 (0.13), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 695 TYR 0.027 0.001 TYR E 53 PHE 0.027 0.001 PHE G 155 TRP 0.014 0.001 TRP I 57 HIS 0.007 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (34892) covalent geometry : angle 0.62950 / 0.33 (47334) SS BOND : bond 0.00341 / 0.15 ( 25) SS BOND : angle 0.95596 / 0.62 ( 50) hydrogen bonds : bond 0.03738 / 2.54 ( 1340) hydrogen bonds : angle 5.75765 / 4.14 ( 3813) Misc. bond : bond 0.00323 / 0.17 ( 5) link_ALPHA1-4 : bond 0.01284 / 0.65 ( 2) link_ALPHA1-4 : angle 2.51517 / 1.15 ( 6) link_BETA1-4 : bond 0.00114 / 0.06 ( 3) link_BETA1-4 : angle 2.37103 / 1.18 ( 9) link_NAG-ASN : bond 0.00591 / 0.45 ( 23) link_NAG-ASN : angle 3.15292 / 2.15 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 465 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8879 (mm) cc_final: 0.8347 (pp) REVERT: B 112 MET cc_start: 0.7600 (mtt) cc_final: 0.7203 (mmt) REVERT: B 114 ASP cc_start: 0.9017 (m-30) cc_final: 0.8802 (m-30) REVERT: B 180 TYR cc_start: 0.7558 (p90) cc_final: 0.7270 (p90) REVERT: B 561 MET cc_start: 0.8978 (tpp) cc_final: 0.8640 (tmm) REVERT: B 565 LEU cc_start: 0.8936 (mm) cc_final: 0.8109 (mm) REVERT: B 705 MET cc_start: 0.7920 (mmm) cc_final: 0.7468 (mmm) REVERT: C 74 MET cc_start: 0.8214 (mmt) cc_final: 0.8013 (mmt) REVERT: C 398 LEU cc_start: 0.8607 (mp) cc_final: 0.8347 (mp) REVERT: C 501 MET cc_start: 0.8659 (tpt) cc_final: 0.8451 (tpp) REVERT: C 526 TYR cc_start: 0.7160 (m-10) cc_final: 0.6455 (m-10) REVERT: C 576 MET cc_start: 0.8845 (ttt) cc_final: 0.8596 (ptm) REVERT: C 616 ASN cc_start: 0.8874 (t0) cc_final: 0.8588 (t0) REVERT: D 52 ASP cc_start: 0.8536 (p0) cc_final: 0.8169 (p0) REVERT: D 101 ASP cc_start: 0.8343 (p0) cc_final: 0.7612 (p0) REVERT: D 127 HIS cc_start: 0.8176 (t-90) cc_final: 0.7814 (t-170) REVERT: D 240 ILE cc_start: 0.8084 (tp) cc_final: 0.7817 (pt) REVERT: D 561 MET cc_start: 0.8279 (mmp) cc_final: 0.8061 (mmp) REVERT: D 631 MET cc_start: 0.9002 (mmm) cc_final: 0.8802 (mmm) REVERT: E 61 PHE cc_start: 0.6722 (t80) cc_final: 0.6510 (t80) REVERT: E 121 TYR cc_start: 0.6593 (t80) cc_final: 0.6196 (t80) REVERT: G 79 GLN cc_start: 0.6242 (OUTLIER) cc_final: 0.5659 (pp30) REVERT: G 81 PHE cc_start: 0.8842 (m-10) cc_final: 0.8549 (m-80) REVERT: G 91 ASP cc_start: 0.8293 (t0) cc_final: 0.7982 (t0) REVERT: G 96 TYR cc_start: 0.7727 (m-80) cc_final: 0.6948 (m-80) REVERT: H 97 THR cc_start: 0.8494 (m) cc_final: 0.8161 (p) REVERT: H 167 ASP cc_start: 0.8800 (p0) cc_final: 0.8436 (p0) REVERT: I 69 MET cc_start: 0.8196 (mmp) cc_final: 0.7298 (mmm) REVERT: J 49 ASP cc_start: 0.6638 (m-30) cc_final: 0.6387 (m-30) REVERT: J 57 ASN cc_start: 0.8531 (p0) cc_final: 0.7995 (p0) REVERT: K 113 MET cc_start: 0.2421 (ttt) cc_final: 0.2025 (tpt) REVERT: L 24 MET cc_start: 0.4285 (mtm) cc_final: 0.3675 (mtt) outliers start: 4 outliers final: 1 residues processed: 468 average time/residue: 0.1916 time to fit residues: 151.1759 Evaluate side-chains 351 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 349 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 170 optimal weight: 0.0470 chunk 355 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 400 optimal weight: 0.1980 chunk 91 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 406 optimal weight: 0.1980 chunk 389 optimal weight: 8.9990 chunk 319 optimal weight: 20.0000 chunk 202 optimal weight: 0.7980 chunk 398 optimal weight: 7.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN D 649 ASN F 53 ASN F 112 GLN ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 GLN I 104 ASN K 97 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.106540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.088968 restraints weight = 195582.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.087383 restraints weight = 192656.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.088068 restraints weight = 160266.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.088484 restraints weight = 114066.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.088749 restraints weight = 111318.571| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34950 Z= 0.120 Angle : 0.627 10.700 47468 Z= 0.322 Chirality : 0.046 0.421 5349 Planarity : 0.005 0.090 5999 Dihedral : 7.147 91.465 5258 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.19 % Favored : 93.70 % Rotamer: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 4267 helix: 0.58 (0.14), residues: 1296 sheet: -1.14 (0.18), residues: 835 loop : -1.49 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 548 TYR 0.023 0.001 TYR L 115 PHE 0.036 0.001 PHE B 756 TRP 0.016 0.001 TRP I 129 HIS 0.006 0.001 HIS B 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (34892) covalent geometry : angle 0.61487 / 0.32 (47334) SS BOND : bond 0.00267 / 0.15 ( 25) SS BOND : angle 1.32422 / 0.83 ( 50) hydrogen bonds : bond 0.03578 / 2.40 ( 1340) hydrogen bonds : angle 5.67661 / 4.08 ( 3813) Misc. bond : bond 0.00254 / 0.13 ( 5) link_ALPHA1-4 : bond 0.01169 / 0.59 ( 2) link_ALPHA1-4 : angle 2.62376 / 1.22 ( 6) link_BETA1-4 : bond 0.00137 / 0.07 ( 3) link_BETA1-4 : angle 2.29401 / 1.16 ( 9) link_NAG-ASN : bond 0.00532 / 0.39 ( 23) link_NAG-ASN : angle 2.98879 / 2.02 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 467 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8847 (mm) cc_final: 0.8326 (pp) REVERT: A 240 MET cc_start: 0.8629 (mmm) cc_final: 0.8121 (mmm) REVERT: B 90 MET cc_start: 0.5104 (ppp) cc_final: 0.4440 (ppp) REVERT: B 112 MET cc_start: 0.7424 (mtt) cc_final: 0.7098 (mmt) REVERT: B 180 TYR cc_start: 0.7459 (p90) cc_final: 0.7230 (p90) REVERT: B 641 PHE cc_start: 0.7881 (t80) cc_final: 0.7618 (t80) REVERT: B 763 ILE cc_start: 0.8740 (mt) cc_final: 0.8506 (mt) REVERT: C 74 MET cc_start: 0.8277 (mmt) cc_final: 0.8037 (mmt) REVERT: C 137 PHE cc_start: 0.7761 (t80) cc_final: 0.7461 (t80) REVERT: C 321 PHE cc_start: 0.8293 (t80) cc_final: 0.8090 (t80) REVERT: C 512 MET cc_start: 0.7803 (ttm) cc_final: 0.7511 (ttm) REVERT: C 526 TYR cc_start: 0.6552 (m-10) cc_final: 0.5866 (m-80) REVERT: C 576 MET cc_start: 0.8838 (ttt) cc_final: 0.8588 (ptm) REVERT: C 616 ASN cc_start: 0.8663 (t0) cc_final: 0.8329 (t0) REVERT: C 810 PHE cc_start: 0.7605 (t80) cc_final: 0.7386 (t80) REVERT: D 52 ASP cc_start: 0.8542 (p0) cc_final: 0.8159 (p0) REVERT: D 101 ASP cc_start: 0.8388 (p0) cc_final: 0.7832 (p0) REVERT: D 127 HIS cc_start: 0.8191 (t-90) cc_final: 0.7962 (t-170) REVERT: D 240 ILE cc_start: 0.8105 (tp) cc_final: 0.7894 (pt) REVERT: D 561 MET cc_start: 0.8219 (mmp) cc_final: 0.7956 (mmt) REVERT: E 61 PHE cc_start: 0.6804 (t80) cc_final: 0.6538 (t80) REVERT: E 102 GLN cc_start: 0.7874 (mp10) cc_final: 0.7659 (tm-30) REVERT: E 121 TYR cc_start: 0.6314 (t80) cc_final: 0.5670 (t80) REVERT: E 123 PHE cc_start: 0.5526 (t80) cc_final: 0.5173 (t80) REVERT: E 126 MET cc_start: 0.3570 (mtt) cc_final: 0.2820 (tpp) REVERT: G 39 ILE cc_start: 0.7632 (tp) cc_final: 0.7231 (tp) REVERT: G 96 TYR cc_start: 0.7636 (m-80) cc_final: 0.6905 (m-80) REVERT: H 97 THR cc_start: 0.8434 (m) cc_final: 0.8161 (p) REVERT: I 69 MET cc_start: 0.8149 (mmp) cc_final: 0.7274 (mmm) REVERT: J 49 ASP cc_start: 0.6604 (m-30) cc_final: 0.6290 (m-30) REVERT: J 69 LEU cc_start: 0.7251 (tp) cc_final: 0.6771 (tp) REVERT: L 24 MET cc_start: 0.4427 (mtm) cc_final: 0.3611 (mtt) outliers start: 2 outliers final: 2 residues processed: 469 average time/residue: 0.1944 time to fit residues: 153.6965 Evaluate side-chains 357 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 355 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 316 optimal weight: 20.0000 chunk 185 optimal weight: 30.0000 chunk 410 optimal weight: 0.9990 chunk 424 optimal weight: 30.0000 chunk 326 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 235 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 143 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 405 HIS D 486 HIS ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.101945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.085273 restraints weight = 195707.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.084255 restraints weight = 240138.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.083357 restraints weight = 168477.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.082918 restraints weight = 142314.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.082851 restraints weight = 154393.929| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 34950 Z= 0.273 Angle : 0.774 10.841 47468 Z= 0.401 Chirality : 0.049 0.380 5349 Planarity : 0.006 0.077 5999 Dihedral : 7.626 94.139 5258 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.09 % Favored : 91.77 % Rotamer: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 4267 helix: 0.31 (0.14), residues: 1298 sheet: -1.30 (0.17), residues: 851 loop : -1.66 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG D 292 TYR 0.028 0.002 TYR H 86 PHE 0.049 0.003 PHE G 134 TRP 0.022 0.002 TRP K 127 HIS 0.010 0.002 HIS G 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.27 (34892) covalent geometry : angle 0.76316 / 0.40 (47334) SS BOND : bond 0.00354 / 0.23 ( 25) SS BOND : angle 1.34265 / 0.87 ( 50) hydrogen bonds : bond 0.04255 / 2.90 ( 1340) hydrogen bonds : angle 6.03747 / 4.31 ( 3813) Misc. bond : bond 0.01051 / 0.86 ( 5) link_ALPHA1-4 : bond 0.01252 / 0.64 ( 2) link_ALPHA1-4 : angle 2.78937 / 1.35 ( 6) link_BETA1-4 : bond 0.00622 / 0.31 ( 3) link_BETA1-4 : angle 2.83159 / 1.37 ( 9) link_NAG-ASN : bond 0.00641 / 0.43 ( 23) link_NAG-ASN : angle 3.12591 / 2.14 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 419 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8985 (mm) cc_final: 0.8367 (pp) REVERT: A 240 MET cc_start: 0.8891 (mmm) cc_final: 0.8261 (mmm) REVERT: A 326 MET cc_start: 0.8433 (ppp) cc_final: 0.8204 (ppp) REVERT: A 770 GLN cc_start: 0.8618 (pm20) cc_final: 0.8382 (pm20) REVERT: B 114 ASP cc_start: 0.9195 (m-30) cc_final: 0.8906 (m-30) REVERT: B 180 TYR cc_start: 0.7731 (p90) cc_final: 0.7308 (p90) REVERT: B 536 MET cc_start: 0.6901 (ppp) cc_final: 0.6439 (ppp) REVERT: B 705 MET cc_start: 0.7426 (mmm) cc_final: 0.6770 (mmm) REVERT: B 808 MET cc_start: 0.8363 (tmm) cc_final: 0.8134 (tmm) REVERT: C 321 PHE cc_start: 0.8585 (t80) cc_final: 0.8338 (t80) REVERT: C 576 MET cc_start: 0.9061 (ttt) cc_final: 0.8745 (ptm) REVERT: C 616 ASN cc_start: 0.9000 (t0) cc_final: 0.8721 (t0) REVERT: C 746 LEU cc_start: 0.7948 (mt) cc_final: 0.7732 (mt) REVERT: C 769 LYS cc_start: 0.9233 (tppp) cc_final: 0.8915 (tppp) REVERT: D 52 ASP cc_start: 0.8583 (p0) cc_final: 0.8246 (p0) REVERT: E 61 PHE cc_start: 0.7100 (t80) cc_final: 0.6732 (t80) REVERT: F 55 TYR cc_start: 0.8597 (m-80) cc_final: 0.8070 (m-10) REVERT: G 39 ILE cc_start: 0.7849 (tp) cc_final: 0.7431 (tp) REVERT: G 96 TYR cc_start: 0.7769 (m-80) cc_final: 0.7069 (m-80) REVERT: I 69 MET cc_start: 0.8196 (mmp) cc_final: 0.7139 (mmm) REVERT: J 49 ASP cc_start: 0.6390 (m-30) cc_final: 0.6102 (m-30) REVERT: J 69 LEU cc_start: 0.7376 (tp) cc_final: 0.6940 (tp) REVERT: L 24 MET cc_start: 0.5081 (mtm) cc_final: 0.4340 (mtp) outliers start: 2 outliers final: 1 residues processed: 421 average time/residue: 0.2073 time to fit residues: 146.0848 Evaluate side-chains 328 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 170 optimal weight: 6.9990 chunk 159 optimal weight: 30.0000 chunk 246 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 295 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 chunk 346 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 316 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 HIS ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 102 GLN I 104 ASN K 97 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.102989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.086207 restraints weight = 195649.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.085323 restraints weight = 224339.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.086035 restraints weight = 181470.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.086385 restraints weight = 126891.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.086519 restraints weight = 128595.777| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34950 Z= 0.190 Angle : 0.702 10.172 47468 Z= 0.362 Chirality : 0.048 0.392 5349 Planarity : 0.005 0.071 5999 Dihedral : 7.533 93.678 5258 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.41 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.13), residues: 4267 helix: 0.36 (0.14), residues: 1297 sheet: -1.32 (0.18), residues: 850 loop : -1.61 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 227 TYR 0.023 0.002 TYR E 53 PHE 0.054 0.002 PHE G 134 TRP 0.035 0.002 TRP I 68 HIS 0.007 0.001 HIS C 780 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (34892) covalent geometry : angle 0.68966 / 0.36 (47334) SS BOND : bond 0.00447 / 0.24 ( 25) SS BOND : angle 1.53062 / 0.99 ( 50) hydrogen bonds : bond 0.03941 / 2.67 ( 1340) hydrogen bonds : angle 5.91088 / 4.23 ( 3813) Misc. bond : bond 0.00318 / 0.21 ( 5) link_ALPHA1-4 : bond 0.01054 / 0.54 ( 2) link_ALPHA1-4 : angle 2.70053 / 1.27 ( 6) link_BETA1-4 : bond 0.00284 / 0.14 ( 3) link_BETA1-4 : angle 2.53653 / 1.31 ( 9) link_NAG-ASN : bond 0.00555 / 0.38 ( 23) link_NAG-ASN : angle 3.06900 / 2.08 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8957 (mm) cc_final: 0.8404 (pp) REVERT: A 237 MET cc_start: 0.7783 (mmp) cc_final: 0.7550 (mmm) REVERT: A 240 MET cc_start: 0.8789 (mmm) cc_final: 0.8057 (mmm) REVERT: A 770 GLN cc_start: 0.8619 (pm20) cc_final: 0.8374 (pm20) REVERT: B 90 MET cc_start: 0.5642 (ppp) cc_final: 0.4943 (ppp) REVERT: B 112 MET cc_start: 0.7845 (mtt) cc_final: 0.7459 (mmt) REVERT: B 180 TYR cc_start: 0.7638 (p90) cc_final: 0.7303 (p90) REVERT: B 536 MET cc_start: 0.6715 (ppp) cc_final: 0.6217 (ppp) REVERT: B 705 MET cc_start: 0.7511 (mmm) cc_final: 0.6885 (mmm) REVERT: B 808 MET cc_start: 0.8253 (tmm) cc_final: 0.7938 (tmm) REVERT: B 823 MET cc_start: 0.6237 (mmp) cc_final: 0.5941 (mmm) REVERT: C 321 PHE cc_start: 0.8350 (t80) cc_final: 0.8148 (t80) REVERT: C 398 LEU cc_start: 0.8531 (mp) cc_final: 0.8324 (mp) REVERT: C 512 MET cc_start: 0.7408 (ttm) cc_final: 0.6864 (ttm) REVERT: C 536 GLN cc_start: 0.8804 (pp30) cc_final: 0.8557 (pp30) REVERT: C 576 MET cc_start: 0.8957 (ttt) cc_final: 0.8690 (ptm) REVERT: C 616 ASN cc_start: 0.8889 (t0) cc_final: 0.8525 (t0) REVERT: C 769 LYS cc_start: 0.9209 (tppp) cc_final: 0.8864 (tppt) REVERT: D 52 ASP cc_start: 0.8522 (p0) cc_final: 0.8154 (p0) REVERT: D 101 ASP cc_start: 0.8338 (p0) cc_final: 0.8080 (p0) REVERT: E 61 PHE cc_start: 0.7138 (t80) cc_final: 0.6738 (t80) REVERT: E 102 GLN cc_start: 0.8015 (mp10) cc_final: 0.7508 (tm-30) REVERT: E 126 MET cc_start: 0.3897 (mtt) cc_final: 0.3681 (mtt) REVERT: F 55 TYR cc_start: 0.8479 (m-80) cc_final: 0.8063 (m-10) REVERT: I 69 MET cc_start: 0.7730 (mmp) cc_final: 0.6917 (mmm) REVERT: J 69 LEU cc_start: 0.7396 (tp) cc_final: 0.6966 (tp) REVERT: K 113 MET cc_start: 0.4000 (tpt) cc_final: 0.3440 (ttt) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.2019 time to fit residues: 147.8356 Evaluate side-chains 332 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 59 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 81 optimal weight: 0.2980 chunk 342 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 420 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 404 optimal weight: 30.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 796 GLN F 53 ASN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 102 GLN I 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.104023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.086650 restraints weight = 194819.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.084858 restraints weight = 180784.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085011 restraints weight = 175569.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.085396 restraints weight = 128882.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.085413 restraints weight = 121836.187| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34950 Z= 0.144 Angle : 0.669 10.069 47468 Z= 0.343 Chirality : 0.047 0.399 5349 Planarity : 0.005 0.071 5999 Dihedral : 7.267 91.474 5258 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.31 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 4267 helix: 0.48 (0.14), residues: 1294 sheet: -1.25 (0.18), residues: 831 loop : -1.49 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 118 TYR 0.025 0.002 TYR E 53 PHE 0.028 0.002 PHE G 155 TRP 0.024 0.001 TRP I 68 HIS 0.006 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (34892) covalent geometry : angle 0.65776 / 0.34 (47334) SS BOND : bond 0.00256 / 0.15 ( 25) SS BOND : angle 1.21879 / 0.81 ( 50) hydrogen bonds : bond 0.03726 / 2.52 ( 1340) hydrogen bonds : angle 5.76111 / 4.13 ( 3813) Misc. bond : bond 0.00260 / 0.16 ( 5) link_ALPHA1-4 : bond 0.01142 / 0.58 ( 2) link_ALPHA1-4 : angle 2.81440 / 1.32 ( 6) link_BETA1-4 : bond 0.00193 / 0.10 ( 3) link_BETA1-4 : angle 2.41082 / 1.25 ( 9) link_NAG-ASN : bond 0.00531 / 0.37 ( 23) link_NAG-ASN : angle 2.98046 / 2.01 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.9019 (mm) cc_final: 0.8456 (pp) REVERT: A 237 MET cc_start: 0.7909 (mmp) cc_final: 0.7674 (mmm) REVERT: A 240 MET cc_start: 0.8849 (mmm) cc_final: 0.8226 (mmm) REVERT: A 634 MET cc_start: 0.8638 (mmt) cc_final: 0.8207 (mmt) REVERT: B 90 MET cc_start: 0.5793 (ppp) cc_final: 0.5058 (ppp) REVERT: B 112 MET cc_start: 0.7973 (mtt) cc_final: 0.7519 (mmt) REVERT: B 114 ASP cc_start: 0.9067 (m-30) cc_final: 0.8804 (m-30) REVERT: B 180 TYR cc_start: 0.7701 (p90) cc_final: 0.7457 (p90) REVERT: B 536 MET cc_start: 0.6643 (ppp) cc_final: 0.6243 (ppp) REVERT: B 564 MET cc_start: 0.7226 (tpt) cc_final: 0.6897 (mmm) REVERT: B 653 MET cc_start: 0.7887 (ppp) cc_final: 0.7035 (ppp) REVERT: B 705 MET cc_start: 0.7425 (mmm) cc_final: 0.7067 (mmm) REVERT: B 808 MET cc_start: 0.8089 (tmm) cc_final: 0.7801 (tmm) REVERT: B 823 MET cc_start: 0.6010 (mmp) cc_final: 0.5735 (mmm) REVERT: C 74 MET cc_start: 0.8559 (mmt) cc_final: 0.8275 (mmt) REVERT: C 321 PHE cc_start: 0.8641 (t80) cc_final: 0.8399 (t80) REVERT: C 512 MET cc_start: 0.7641 (ttm) cc_final: 0.7391 (ttm) REVERT: C 536 GLN cc_start: 0.8977 (pp30) cc_final: 0.8645 (pp30) REVERT: C 576 MET cc_start: 0.9123 (ttt) cc_final: 0.8793 (ptm) REVERT: C 616 ASN cc_start: 0.8979 (t0) cc_final: 0.8775 (t0) REVERT: C 751 GLU cc_start: 0.7755 (tp30) cc_final: 0.7537 (tp30) REVERT: C 769 LYS cc_start: 0.9299 (tppp) cc_final: 0.9070 (tppt) REVERT: D 52 ASP cc_start: 0.8589 (p0) cc_final: 0.8284 (p0) REVERT: D 101 ASP cc_start: 0.8436 (p0) cc_final: 0.8195 (p0) REVERT: D 358 MET cc_start: 0.8036 (mtp) cc_final: 0.7730 (mpp) REVERT: E 61 PHE cc_start: 0.7390 (t80) cc_final: 0.7049 (t80) REVERT: E 102 GLN cc_start: 0.7930 (mp10) cc_final: 0.7633 (tm-30) REVERT: E 124 TYR cc_start: 0.7049 (t80) cc_final: 0.6150 (t80) REVERT: F 55 TYR cc_start: 0.8761 (m-80) cc_final: 0.8154 (m-10) REVERT: I 69 MET cc_start: 0.7814 (mmp) cc_final: 0.6948 (mmm) REVERT: J 49 ASP cc_start: 0.7306 (t70) cc_final: 0.7085 (m-30) REVERT: J 69 LEU cc_start: 0.7663 (tp) cc_final: 0.7337 (tp) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.2048 time to fit residues: 151.9993 Evaluate side-chains 337 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 194 optimal weight: 9.9990 chunk 211 optimal weight: 0.0770 chunk 241 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 223 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 304 optimal weight: 10.0000 chunk 161 optimal weight: 7.9990 chunk 353 optimal weight: 9.9990 chunk 270 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 overall best weight: 3.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 102 GLN I 104 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.103206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.086084 restraints weight = 195657.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085153 restraints weight = 206686.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.085860 restraints weight = 170806.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.086047 restraints weight = 124375.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.086279 restraints weight = 126507.379| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34950 Z= 0.174 Angle : 0.695 10.207 47468 Z= 0.357 Chirality : 0.048 0.393 5349 Planarity : 0.005 0.070 5999 Dihedral : 7.242 92.482 5258 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.73 % Favored : 92.15 % Rotamer: Outliers : 0.03 % Allowed : 0.76 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.13), residues: 4267 helix: 0.47 (0.14), residues: 1299 sheet: -1.27 (0.18), residues: 847 loop : -1.54 (0.13), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 337 TYR 0.031 0.002 TYR E 53 PHE 0.036 0.002 PHE B 756 TRP 0.031 0.002 TRP A 611 HIS 0.006 0.001 HIS D 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (34892) covalent geometry : angle 0.68329 / 0.35 (47334) SS BOND : bond 0.00300 / 0.19 ( 25) SS BOND : angle 1.35085 / 0.88 ( 50) hydrogen bonds : bond 0.03809 / 2.59 ( 1340) hydrogen bonds : angle 5.83458 / 4.17 ( 3813) Misc. bond : bond 0.00251 / 0.15 ( 5) link_ALPHA1-4 : bond 0.01086 / 0.55 ( 2) link_ALPHA1-4 : angle 2.80958 / 1.35 ( 6) link_BETA1-4 : bond 0.00110 / 0.06 ( 3) link_BETA1-4 : angle 2.59138 / 1.34 ( 9) link_NAG-ASN : bond 0.00541 / 0.37 ( 23) link_NAG-ASN : angle 2.99514 / 2.02 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8979 (mm) cc_final: 0.8343 (pp) REVERT: A 237 MET cc_start: 0.7872 (mmp) cc_final: 0.7666 (mmm) REVERT: A 240 MET cc_start: 0.8810 (mmm) cc_final: 0.8196 (mmm) REVERT: A 634 MET cc_start: 0.8565 (mmt) cc_final: 0.8190 (mmt) REVERT: A 770 GLN cc_start: 0.8607 (pm20) cc_final: 0.8351 (pm20) REVERT: B 90 MET cc_start: 0.5489 (ppp) cc_final: 0.4782 (ppp) REVERT: B 112 MET cc_start: 0.7927 (mtt) cc_final: 0.7507 (mmt) REVERT: B 114 ASP cc_start: 0.9035 (m-30) cc_final: 0.8793 (m-30) REVERT: B 180 TYR cc_start: 0.7790 (p90) cc_final: 0.7519 (p90) REVERT: B 564 MET cc_start: 0.7284 (tpt) cc_final: 0.6985 (mmm) REVERT: B 565 LEU cc_start: 0.8954 (mm) cc_final: 0.8735 (mm) REVERT: B 606 TRP cc_start: 0.7493 (t-100) cc_final: 0.7275 (t-100) REVERT: B 653 MET cc_start: 0.7890 (ppp) cc_final: 0.7060 (ppp) REVERT: B 705 MET cc_start: 0.7479 (mmm) cc_final: 0.7041 (mmm) REVERT: B 808 MET cc_start: 0.8269 (tmm) cc_final: 0.7978 (tmm) REVERT: C 74 MET cc_start: 0.8503 (mmt) cc_final: 0.8206 (mmt) REVERT: C 137 PHE cc_start: 0.7867 (t80) cc_final: 0.7515 (t80) REVERT: C 536 GLN cc_start: 0.9059 (pp30) cc_final: 0.8747 (pp30) REVERT: C 576 MET cc_start: 0.9072 (ttt) cc_final: 0.8787 (ptm) REVERT: C 769 LYS cc_start: 0.9273 (tppp) cc_final: 0.8922 (tppt) REVERT: D 52 ASP cc_start: 0.8546 (p0) cc_final: 0.8214 (p0) REVERT: D 101 ASP cc_start: 0.8339 (p0) cc_final: 0.8122 (p0) REVERT: E 61 PHE cc_start: 0.7110 (t80) cc_final: 0.6694 (t80) REVERT: E 102 GLN cc_start: 0.7922 (mp10) cc_final: 0.7431 (tm-30) REVERT: E 124 TYR cc_start: 0.6746 (t80) cc_final: 0.5692 (t80) REVERT: F 21 ILE cc_start: 0.4615 (tp) cc_final: 0.4198 (tt) REVERT: F 55 TYR cc_start: 0.8567 (m-80) cc_final: 0.8048 (m-10) REVERT: I 69 MET cc_start: 0.7685 (mmp) cc_final: 0.6872 (mmm) REVERT: J 69 LEU cc_start: 0.7306 (tp) cc_final: 0.6916 (tp) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.2037 time to fit residues: 147.1101 Evaluate side-chains 325 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 130 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 239 optimal weight: 9.9990 chunk 407 optimal weight: 40.0000 chunk 378 optimal weight: 8.9990 chunk 404 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 397 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 79 optimal weight: 30.0000 chunk 411 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 ASN D 217 GLN ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS K 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.103128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.086496 restraints weight = 195539.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.085424 restraints weight = 222021.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.086000 restraints weight = 185024.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.086379 restraints weight = 129390.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.086624 restraints weight = 125646.042| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34950 Z= 0.174 Angle : 0.700 10.162 47468 Z= 0.359 Chirality : 0.048 0.395 5349 Planarity : 0.005 0.070 5999 Dihedral : 7.227 93.364 5258 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.69 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 4267 helix: 0.49 (0.14), residues: 1294 sheet: -1.26 (0.18), residues: 841 loop : -1.50 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 431 TYR 0.027 0.002 TYR E 53 PHE 0.032 0.002 PHE K 49 TRP 0.025 0.002 TRP I 129 HIS 0.006 0.001 HIS D 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (34892) covalent geometry : angle 0.68864 / 0.36 (47334) SS BOND : bond 0.00342 / 0.23 ( 25) SS BOND : angle 1.25786 / 0.83 ( 50) hydrogen bonds : bond 0.03824 / 2.60 ( 1340) hydrogen bonds : angle 5.84819 / 4.18 ( 3813) Misc. bond : bond 0.00232 / 0.14 ( 5) link_ALPHA1-4 : bond 0.01303 / 0.67 ( 2) link_ALPHA1-4 : angle 2.88667 / 1.37 ( 6) link_BETA1-4 : bond 0.00243 / 0.12 ( 3) link_BETA1-4 : angle 2.57294 / 1.34 ( 9) link_NAG-ASN : bond 0.00543 / 0.37 ( 23) link_NAG-ASN : angle 2.98571 / 2.01 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 LEU cc_start: 0.8913 (mm) cc_final: 0.8343 (pp) REVERT: A 240 MET cc_start: 0.8750 (mmm) cc_final: 0.8136 (mmm) REVERT: A 634 MET cc_start: 0.8475 (mmt) cc_final: 0.8081 (mmt) REVERT: A 770 GLN cc_start: 0.8585 (pm20) cc_final: 0.8310 (pm20) REVERT: B 90 MET cc_start: 0.5467 (ppp) cc_final: 0.4799 (ppp) REVERT: B 112 MET cc_start: 0.7825 (mtt) cc_final: 0.7422 (mmt) REVERT: B 114 ASP cc_start: 0.8994 (m-30) cc_final: 0.8767 (m-30) REVERT: B 180 TYR cc_start: 0.7760 (p90) cc_final: 0.7461 (p90) REVERT: B 564 MET cc_start: 0.7300 (tpt) cc_final: 0.7027 (mmm) REVERT: B 606 TRP cc_start: 0.7482 (t-100) cc_final: 0.7255 (t-100) REVERT: B 653 MET cc_start: 0.7753 (ppp) cc_final: 0.6981 (ppp) REVERT: B 705 MET cc_start: 0.7508 (mmm) cc_final: 0.6979 (mmm) REVERT: C 137 PHE cc_start: 0.7857 (t80) cc_final: 0.7493 (t80) REVERT: C 321 PHE cc_start: 0.8333 (t80) cc_final: 0.8037 (t80) REVERT: C 512 MET cc_start: 0.7587 (ttm) cc_final: 0.7280 (ttm) REVERT: C 576 MET cc_start: 0.9060 (ttt) cc_final: 0.8800 (ptm) REVERT: C 769 LYS cc_start: 0.9317 (tppp) cc_final: 0.8989 (tppt) REVERT: D 52 ASP cc_start: 0.8530 (p0) cc_final: 0.8185 (p0) REVERT: E 61 PHE cc_start: 0.7079 (t80) cc_final: 0.6631 (t80) REVERT: E 102 GLN cc_start: 0.7876 (mp10) cc_final: 0.7387 (tm-30) REVERT: E 121 TYR cc_start: 0.6870 (t80) cc_final: 0.6582 (t80) REVERT: E 124 TYR cc_start: 0.6629 (t80) cc_final: 0.5561 (t80) REVERT: F 21 ILE cc_start: 0.4587 (tp) cc_final: 0.4119 (tt) REVERT: F 55 TYR cc_start: 0.8476 (m-80) cc_final: 0.8044 (m-10) REVERT: I 69 MET cc_start: 0.7701 (mmp) cc_final: 0.6889 (mmm) REVERT: J 49 ASP cc_start: 0.6253 (m-30) cc_final: 0.5974 (m-30) REVERT: J 69 LEU cc_start: 0.7214 (tp) cc_final: 0.6859 (tp) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.2001 time to fit residues: 141.1569 Evaluate side-chains 327 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 72 optimal weight: 1.9990 chunk 367 optimal weight: 0.9990 chunk 403 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 119 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 ASN C 796 GLN D 217 GLN F 99 HIS ** G 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.103471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.086093 restraints weight = 194675.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.084953 restraints weight = 190954.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.085402 restraints weight = 167015.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.085624 restraints weight = 123214.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.085853 restraints weight = 127262.047| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34950 Z= 0.154 Angle : 0.685 10.088 47468 Z= 0.351 Chirality : 0.047 0.399 5349 Planarity : 0.005 0.069 5999 Dihedral : 7.081 93.232 5258 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.43 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.13), residues: 4267 helix: 0.51 (0.14), residues: 1294 sheet: -1.25 (0.18), residues: 847 loop : -1.45 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 431 TYR 0.026 0.002 TYR E 53 PHE 0.032 0.002 PHE E 123 TRP 0.023 0.002 TRP F 58 HIS 0.006 0.001 HIS D 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (34892) covalent geometry : angle 0.67346 / 0.35 (47334) SS BOND : bond 0.00274 / 0.18 ( 25) SS BOND : angle 1.21892 / 0.79 ( 50) hydrogen bonds : bond 0.03744 / 2.54 ( 1340) hydrogen bonds : angle 5.77827 / 4.14 ( 3813) Misc. bond : bond 0.00215 / 0.11 ( 5) link_ALPHA1-4 : bond 0.01300 / 0.67 ( 2) link_ALPHA1-4 : angle 2.83634 / 1.35 ( 6) link_BETA1-4 : bond 0.00231 / 0.11 ( 3) link_BETA1-4 : angle 2.57091 / 1.34 ( 9) link_NAG-ASN : bond 0.00542 / 0.38 ( 23) link_NAG-ASN : angle 2.97144 / 1.99 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5886.72 seconds wall clock time: 103 minutes 8.89 seconds (6188.89 seconds total)