Starting phenix.real_space_refine on Sun Jul 5 04:21:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sq9_40699/07_2026/8sq9_40699.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sq9_40699/07_2026/8sq9_40699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sq9_40699/07_2026/8sq9_40699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sq9_40699/07_2026/8sq9_40699.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sq9_40699/07_2026/8sq9_40699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sq9_40699/07_2026/8sq9_40699.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8sq9_40699/07_2026/8sq9_40699.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sq9_40699/07_2026/8sq9_40699.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.958 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 73 5.49 5 Mg 4 5.21 5 S 87 5.16 5 C 8027 2.51 5 N 2209 2.21 5 O 2923 1.98 5 H 12087 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 25412 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 14726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 926, 14659 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Conformer: "B" Number of residues, atoms: 926, 14659 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} bond proxies already assigned to first conformer: 14778 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2773 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1152 Classifications: {'peptide': 73} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 72} Chain: "D" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 2849 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1461 Classifications: {'peptide': 98} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 1023 Classifications: {'RNA': 32} Modifications used: {'3*END': 1, 'rna3p_pur': 15, 'rna3p_pyr': 17} Link IDs: {'rna3p': 31} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 1122 Classifications: {'RNA': 35} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 17, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 33} Chain: "A" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 250 Unusual residues: {' MG': 4, ' ZN': 2, 'WSB': 2} Classifications: {'undetermined': 8, 'water': 186} Link IDs: {None: 193} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "T" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4824 SG CYS A 301 31.115 87.929 108.501 1.00 78.43 S ATOM 4901 SG CYS A 306 32.066 91.480 109.803 1.00 82.22 S ATOM 4966 SG CYS A 310 32.955 88.054 111.554 1.00 68.52 S ATOM 7723 SG CYS A 487 29.931 89.626 87.986 1.00 61.74 S ATOM 10238 SG CYS A 645 30.043 92.848 88.727 1.00 69.49 S ATOM 10248 SG CYS A 646 28.660 90.357 91.035 1.00 79.21 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS A 41 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.50 residue: pdb=" N AARG A 726 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 726 " occ=0.50 Time building chain proxies: 6.08, per 1000 atoms: 0.24 Number of scatterers: 25412 At special positions: 0 Unit cell: (91.934, 135.763, 163.557, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 87 16.00 P 73 15.00 Mg 4 11.99 O 2923 8.00 N 2209 7.00 C 8027 6.00 H 12087 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2826 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 11 sheets defined 53.0% alpha, 15.7% beta 26 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 4.32 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.672A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.525A pdb=" N HIS A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.540A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.781A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 235 through 248 Proline residue: A 243 - end of helix removed outlier: 3.843A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.599A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.671A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.656A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.619A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 457 removed outlier: 3.548A pdb=" N ASP A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 478 through 481 removed outlier: 3.720A pdb=" N ASP A 481 " --> pdb=" O LYS A 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 481' Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.550A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.857A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.597A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 578 " --> pdb=" O LYS A 574 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.532A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 847 through 851 Processing helix chain 'A' and resid 856 through 867 removed outlier: 3.570A pdb=" N LEU A 862 " --> pdb=" O ARG A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.739A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.619A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 11 through 28 removed outlier: 4.273A pdb=" N PHE B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 98 removed outlier: 3.669A pdb=" N SER B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 110 Processing helix chain 'B' and resid 118 through 125 removed outlier: 4.071A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.713A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.906A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.847A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.558A pdb=" N VAL C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.724A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 82 removed outlier: 3.578A pdb=" N LYS D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.534A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'G' and resid 95 through 105 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 8.224A pdb=" N ASN A 52 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG A 74 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 38 removed outlier: 5.461A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 52 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASN A 52 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG A 74 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.020A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.114A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 3.608A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 758 removed outlier: 3.932A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB1, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.045A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 65 through 68 removed outlier: 4.283A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA G 16 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP G 26 " --> pdb=" O ALA G 16 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA G 43 " --> pdb=" O TYR G 31 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASN G 33 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL G 41 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER G 46 " --> pdb=" O TYR G 87 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1781 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 6.20 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12054 1.03 - 1.23: 344 1.23 - 1.43: 5640 1.43 - 1.63: 7399 1.63 - 1.82: 139 Bond restraints: 25576 Sorted by residual: bond pdb=" C LYS A 73 " pdb=" O LYS A 73 " ideal model delta sigma weight residual 1.234 1.149 0.085 1.22e-02 6.72e+03 4.86e+01 bond pdb=" O3B WSB A1005 " pdb=" PG WSB A1005 " ideal model delta sigma weight residual 1.745 1.611 0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" O3B WSB A1008 " pdb=" PG WSB A1008 " ideal model delta sigma weight residual 1.745 1.616 0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" C VAL A 72 " pdb=" N LYS A 73 " ideal model delta sigma weight residual 1.331 1.272 0.060 1.37e-02 5.33e+03 1.90e+01 bond pdb=" CA BLYS A 73 " pdb=" CB BLYS A 73 " ideal model delta sigma weight residual 1.535 1.447 0.088 2.09e-02 2.29e+03 1.78e+01 ... (remaining 25571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 45178 1.53 - 3.07: 748 3.07 - 4.60: 72 4.60 - 6.13: 8 6.13 - 7.66: 2 Bond angle restraints: 46008 Sorted by residual: angle pdb=" O LYS A 73 " pdb=" C LYS A 73 " pdb=" N ARG A 74 " ideal model delta sigma weight residual 123.27 118.26 5.01 1.16e+00 7.43e-01 1.86e+01 angle pdb=" CA ALYS A 73 " pdb=" C LYS A 73 " pdb=" N ARG A 74 " ideal model delta sigma weight residual 116.01 121.57 -5.56 1.51e+00 4.39e-01 1.36e+01 angle pdb=" C LYS A 574 " pdb=" N LEU A 575 " pdb=" CA LEU A 575 " ideal model delta sigma weight residual 120.28 116.01 4.27 1.34e+00 5.57e-01 1.01e+01 angle pdb=" C ASP A 618 " pdb=" N TYR A 619 " pdb=" CA TYR A 619 " ideal model delta sigma weight residual 120.49 116.50 3.99 1.42e+00 4.96e-01 7.88e+00 angle pdb=" N ASP A 235 " pdb=" CA ASP A 235 " pdb=" C ASP A 235 " ideal model delta sigma weight residual 112.72 109.23 3.49 1.28e+00 6.10e-01 7.43e+00 ... (remaining 46003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.38: 11846 34.38 - 68.77: 310 68.77 - 103.15: 32 103.15 - 137.54: 6 137.54 - 171.92: 8 Dihedral angle restraints: 12202 sinusoidal: 7009 harmonic: 5193 Sorted by residual: dihedral pdb=" O4' G T 123 " pdb=" C1' G T 123 " pdb=" N9 G T 123 " pdb=" C4 G T 123 " ideal model delta sinusoidal sigma weight residual -106.00 -176.03 70.03 1 1.70e+01 3.46e-03 2.19e+01 dihedral pdb=" O2B WSB A1008 " pdb=" C3A WSB A1008 " pdb=" PB WSB A1008 " pdb=" PA WSB A1008 " ideal model delta sinusoidal sigma weight residual 274.23 136.50 137.73 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" CA ASP A 465 " pdb=" C ASP A 465 " pdb=" N ILE A 466 " pdb=" CA ILE A 466 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 12199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1838 0.049 - 0.098: 255 0.098 - 0.147: 66 0.147 - 0.196: 3 0.196 - 0.244: 1 Chirality restraints: 2163 Sorted by residual: chirality pdb=" CA ALYS A 73 " pdb=" N LYS A 73 " pdb=" C LYS A 73 " pdb=" CB ALYS A 73 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PHE A 571 " pdb=" N PHE A 571 " pdb=" C PHE A 571 " pdb=" CB PHE A 571 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" C3' WSB A1005 " pdb=" C2' WSB A1005 " pdb=" C4' WSB A1005 " pdb=" O3' WSB A1005 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 2160 not shown) Planarity restraints: 3591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 73 " -0.080 2.00e-02 2.50e+03 4.63e-02 2.14e+01 pdb=" O LYS A 73 " 0.030 2.00e-02 2.50e+03 pdb=" CA BLYS A 73 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 74 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 73 " -0.056 2.00e-02 2.50e+03 3.26e-02 1.07e+01 pdb=" O LYS A 73 " 0.021 2.00e-02 2.50e+03 pdb=" CA ALYS A 73 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 74 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 72 " 0.013 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" N LYS A 73 " -0.042 2.00e-02 2.50e+03 pdb=" CA BLYS A 73 " 0.010 2.00e-02 2.50e+03 pdb=" H BLYS A 73 " 0.018 2.00e-02 2.50e+03 ... (remaining 3588 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 964 2.18 - 2.78: 48575 2.78 - 3.39: 69049 3.39 - 3.99: 93308 3.99 - 4.60: 144044 Nonbonded interactions: 355940 Sorted by model distance: nonbonded pdb="HH22 ARG A 733 " pdb=" O GLU G 3 " model vdw 1.575 2.450 nonbonded pdb=" H ASP D 161 " pdb=" O LYS D 165 " model vdw 1.588 2.450 nonbonded pdb=" O LYS D 39 " pdb="HD21 ASN D 43 " model vdw 1.599 2.450 nonbonded pdb=" O TYR A 915 " pdb=" HH TYR A 921 " model vdw 1.605 2.450 nonbonded pdb=" OD1 ASP D 161 " pdb=" H ALA D 162 " model vdw 1.611 2.450 ... (remaining 355935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 6 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 9 through 22 or (resid 23 t \ hrough 24 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 25 through 191)) selection = (chain 'D' and (resid 6 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 27 through 31 or (resid 3 \ 2 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 33 through 34 or (resid 35 through 37 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 38 through 39 or (resid 40 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 41 through 42 or (resid 43 and (name N or name CA or name C or name O or \ name CB or name HA )) or resid 44 through 191)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 37.110 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 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 : 0.007 0.582 13497 Z= 0.293 Angle : 0.532 12.163 18636 Z= 0.289 Chirality : 0.039 0.244 2163 Planarity : 0.003 0.046 2125 Dihedral : 14.700 137.735 5329 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 2.38 % Allowed : 6.50 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1462 helix: 1.28 (0.21), residues: 694 sheet: -0.74 (0.37), residues: 182 loop : -1.17 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 467 TYR 0.013 0.001 TYR A 80 PHE 0.023 0.001 PHE A 571 TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.22 (13489) covalent geometry : angle 0.52124 / 0.29 (18630) hydrogen bonds : bond 0.16128 / 10.67 ( 688) hydrogen bonds : angle 5.92572 / 4.05 ( 1903) metal coordination : bond 0.23357 / 16.02 ( 8) metal coordination : angle 5.83225 / 3.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.7212 (m-80) cc_final: 0.6554 (m-80) REVERT: A 277 GLU cc_start: 0.7247 (mp0) cc_final: 0.6878 (mp0) REVERT: A 304 ASP cc_start: 0.8092 (m-30) cc_final: 0.7773 (m-30) REVERT: A 542 MET cc_start: 0.8665 (tpt) cc_final: 0.8265 (tpt) REVERT: A 571 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.5678 (m-80) REVERT: A 807 LYS cc_start: 0.8222 (mttm) cc_final: 0.7815 (mtmt) REVERT: A 846 ASP cc_start: 0.7529 (m-30) cc_final: 0.7225 (m-30) REVERT: B 80 ARG cc_start: 0.7218 (ttt180) cc_final: 0.6974 (ttt180) REVERT: B 92 PHE cc_start: 0.7322 (m-80) cc_final: 0.7072 (m-10) REVERT: B 174 MET cc_start: 0.5526 (tpt) cc_final: 0.4889 (tpt) REVERT: D 78 ASP cc_start: 0.7141 (t0) cc_final: 0.6674 (t70) outliers start: 30 outliers final: 17 residues processed: 200 average time/residue: 0.9922 time to fit residues: 223.1496 Evaluate side-chains 168 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 HIS A 468 GLN B 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.173132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.116688 restraints weight = 52145.862| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.99 r_work: 0.2916 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.0758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13497 Z= 0.179 Angle : 0.520 5.430 18636 Z= 0.285 Chirality : 0.039 0.183 2163 Planarity : 0.004 0.042 2125 Dihedral : 14.333 129.303 2687 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.53 % Rotamer: Outliers : 2.06 % Allowed : 10.39 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.22), residues: 1462 helix: 1.35 (0.21), residues: 719 sheet: -0.93 (0.35), residues: 198 loop : -1.18 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 105 TYR 0.014 0.001 TYR A 80 PHE 0.023 0.001 PHE A 571 TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS A 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (13489) covalent geometry : angle 0.51664 / 0.28 (18630) hydrogen bonds : bond 0.05417 / 3.65 ( 688) hydrogen bonds : angle 4.50759 / 3.13 ( 1903) metal coordination : bond 0.01911 / 1.10 ( 8) metal coordination : angle 3.20783 / 2.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7719 (t0) cc_final: 0.7448 (t70) REVERT: A 277 GLU cc_start: 0.7629 (mp0) cc_final: 0.7319 (mp0) REVERT: A 304 ASP cc_start: 0.8254 (m-30) cc_final: 0.7882 (m-30) REVERT: B 174 MET cc_start: 0.6040 (tpt) cc_final: 0.5372 (tpt) REVERT: C 58 VAL cc_start: 0.7837 (OUTLIER) cc_final: 0.7581 (t) REVERT: D 78 ASP cc_start: 0.7026 (t0) cc_final: 0.6598 (t70) REVERT: G 69 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5532 (mp) outliers start: 26 outliers final: 20 residues processed: 175 average time/residue: 0.8852 time to fit residues: 174.0504 Evaluate side-chains 168 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 118 ASN B 179 ASN ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.174093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119924 restraints weight = 46234.501| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.92 r_work: 0.2934 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13497 Z= 0.169 Angle : 0.495 5.365 18636 Z= 0.271 Chirality : 0.038 0.179 2163 Planarity : 0.003 0.041 2125 Dihedral : 14.175 133.200 2682 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Rotamer: Outliers : 2.22 % Allowed : 11.82 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1462 helix: 1.44 (0.21), residues: 721 sheet: -0.95 (0.35), residues: 198 loop : -1.18 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 733 TYR 0.013 0.001 TYR A 80 PHE 0.022 0.001 PHE A 571 TRP 0.008 0.001 TRP A 916 HIS 0.006 0.001 HIS A 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (13489) covalent geometry : angle 0.49270 / 0.27 (18630) hydrogen bonds : bond 0.05099 / 3.45 ( 688) hydrogen bonds : angle 4.32962 / 3.01 ( 1903) metal coordination : bond 0.01463 / 0.82 ( 8) metal coordination : angle 2.50294 / 1.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASP cc_start: 0.7730 (t0) cc_final: 0.7432 (t70) REVERT: A 62 ASP cc_start: 0.7530 (t0) cc_final: 0.7166 (p0) REVERT: A 277 GLU cc_start: 0.7674 (mp0) cc_final: 0.7361 (mp0) REVERT: A 304 ASP cc_start: 0.8219 (m-30) cc_final: 0.7876 (m-30) REVERT: A 846 ASP cc_start: 0.7980 (m-30) cc_final: 0.7737 (m-30) REVERT: C 58 VAL cc_start: 0.7739 (OUTLIER) cc_final: 0.7457 (t) REVERT: D 78 ASP cc_start: 0.7187 (t0) cc_final: 0.6734 (t70) REVERT: G 69 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5481 (mp) outliers start: 28 outliers final: 19 residues processed: 171 average time/residue: 0.9651 time to fit residues: 186.6881 Evaluate side-chains 165 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 2 optimal weight: 0.0980 chunk 79 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 789 GLN ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118500 restraints weight = 50935.939| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.04 r_work: 0.2942 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13497 Z= 0.141 Angle : 0.477 5.683 18636 Z= 0.260 Chirality : 0.037 0.177 2163 Planarity : 0.003 0.039 2125 Dihedral : 14.050 133.296 2675 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 1.90 % Allowed : 12.61 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.23), residues: 1462 helix: 1.52 (0.21), residues: 722 sheet: -0.93 (0.35), residues: 198 loop : -1.16 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 18 TYR 0.013 0.001 TYR A 80 PHE 0.025 0.001 PHE A 571 TRP 0.008 0.001 TRP A 916 HIS 0.007 0.001 HIS A 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13489) covalent geometry : angle 0.47526 / 0.26 (18630) hydrogen bonds : bond 0.04609 / 3.11 ( 688) hydrogen bonds : angle 4.19079 / 2.91 ( 1903) metal coordination : bond 0.01184 / 0.66 ( 8) metal coordination : angle 2.24148 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8109 (OUTLIER) cc_final: 0.6700 (t80) REVERT: A 54 CYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7708 (m) REVERT: A 60 ASP cc_start: 0.7840 (t0) cc_final: 0.7557 (t70) REVERT: A 62 ASP cc_start: 0.7669 (t0) cc_final: 0.7294 (p0) REVERT: A 277 GLU cc_start: 0.7674 (mp0) cc_final: 0.7390 (mp0) REVERT: A 285 ARG cc_start: 0.8954 (ttm-80) cc_final: 0.8679 (ttm110) REVERT: A 304 ASP cc_start: 0.8259 (m-30) cc_final: 0.7919 (m-30) REVERT: A 846 ASP cc_start: 0.7983 (m-30) cc_final: 0.7750 (m-30) REVERT: C 3 MET cc_start: 0.8980 (tpt) cc_final: 0.8461 (tpt) REVERT: C 58 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7471 (t) REVERT: D 78 ASP cc_start: 0.7187 (t0) cc_final: 0.6726 (t70) REVERT: G 69 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5281 (mp) REVERT: G 97 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7777 (tm) outliers start: 24 outliers final: 15 residues processed: 165 average time/residue: 0.9466 time to fit residues: 176.1113 Evaluate side-chains 163 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 118 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.171503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116932 restraints weight = 47347.007| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.96 r_work: 0.2912 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13497 Z= 0.209 Angle : 0.513 6.270 18636 Z= 0.282 Chirality : 0.039 0.195 2163 Planarity : 0.004 0.043 2125 Dihedral : 14.047 135.766 2674 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 2.54 % Allowed : 12.77 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1462 helix: 1.47 (0.21), residues: 722 sheet: -1.10 (0.35), residues: 193 loop : -1.17 (0.25), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.018 0.002 TYR B 135 PHE 0.024 0.002 PHE A 571 TRP 0.008 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (13489) covalent geometry : angle 0.51161 / 0.28 (18630) hydrogen bonds : bond 0.05215 / 3.53 ( 688) hydrogen bonds : angle 4.26006 / 2.96 ( 1903) metal coordination : bond 0.01327 / 0.73 ( 8) metal coordination : angle 2.15948 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.6598 (OUTLIER) cc_final: 0.6243 (m) REVERT: A 32 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.6638 (t80) REVERT: A 60 ASP cc_start: 0.7733 (t0) cc_final: 0.7452 (t70) REVERT: A 62 ASP cc_start: 0.7648 (t0) cc_final: 0.7245 (p0) REVERT: A 285 ARG cc_start: 0.9007 (ttm-80) cc_final: 0.8729 (ttm110) REVERT: A 304 ASP cc_start: 0.8306 (m-30) cc_final: 0.7975 (m-30) REVERT: A 846 ASP cc_start: 0.8007 (m-30) cc_final: 0.7778 (m-30) REVERT: B 165 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7323 (mttm) REVERT: D 78 ASP cc_start: 0.7178 (t0) cc_final: 0.6720 (t70) REVERT: G 69 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5271 (mp) REVERT: G 97 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7779 (tm) outliers start: 32 outliers final: 23 residues processed: 168 average time/residue: 0.9829 time to fit residues: 185.8708 Evaluate side-chains 166 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 89 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.175090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120913 restraints weight = 49633.109| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.96 r_work: 0.2949 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13497 Z= 0.140 Angle : 0.473 5.573 18636 Z= 0.258 Chirality : 0.037 0.172 2163 Planarity : 0.003 0.039 2125 Dihedral : 14.007 136.173 2674 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % Rotamer: Outliers : 2.54 % Allowed : 13.01 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1462 helix: 1.59 (0.21), residues: 722 sheet: -0.95 (0.35), residues: 198 loop : -1.16 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 18 TYR 0.012 0.001 TYR A 80 PHE 0.021 0.001 PHE A 571 TRP 0.008 0.001 TRP A 916 HIS 0.004 0.001 HIS A 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (13489) covalent geometry : angle 0.47165 / 0.26 (18630) hydrogen bonds : bond 0.04519 / 3.05 ( 688) hydrogen bonds : angle 4.13995 / 2.88 ( 1903) metal coordination : bond 0.01203 / 0.66 ( 8) metal coordination : angle 2.10971 / 1.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.6414 (OUTLIER) cc_final: 0.6030 (m) REVERT: A 32 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.6653 (t80) REVERT: A 54 CYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7647 (m) REVERT: A 60 ASP cc_start: 0.7837 (t0) cc_final: 0.7592 (t70) REVERT: A 62 ASP cc_start: 0.7715 (t0) cc_final: 0.7345 (p0) REVERT: A 277 GLU cc_start: 0.7731 (mp0) cc_final: 0.7458 (mp0) REVERT: A 285 ARG cc_start: 0.8989 (ttm-80) cc_final: 0.8706 (ttm110) REVERT: A 304 ASP cc_start: 0.8326 (m-30) cc_final: 0.8001 (m-30) REVERT: A 662 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8779 (t) REVERT: A 846 ASP cc_start: 0.7978 (m-30) cc_final: 0.7751 (m-30) REVERT: B 165 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7445 (mttm) REVERT: C 58 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7496 (t) REVERT: D 78 ASP cc_start: 0.7183 (t0) cc_final: 0.6726 (t70) REVERT: G 69 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5336 (mp) REVERT: G 97 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7816 (tm) outliers start: 32 outliers final: 20 residues processed: 169 average time/residue: 0.9110 time to fit residues: 174.3959 Evaluate side-chains 169 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 132 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.172692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117823 restraints weight = 48141.743| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.99 r_work: 0.2923 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13497 Z= 0.169 Angle : 0.488 6.423 18636 Z= 0.267 Chirality : 0.038 0.183 2163 Planarity : 0.004 0.040 2125 Dihedral : 14.019 137.646 2674 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.09 % Favored : 94.85 % Rotamer: Outliers : 2.70 % Allowed : 13.08 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.23), residues: 1462 helix: 1.59 (0.21), residues: 722 sheet: -0.92 (0.36), residues: 191 loop : -1.14 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 18 TYR 0.013 0.001 TYR A 80 PHE 0.023 0.001 PHE A 571 TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (13489) covalent geometry : angle 0.48692 / 0.27 (18630) hydrogen bonds : bond 0.04769 / 3.22 ( 688) hydrogen bonds : angle 4.15404 / 2.89 ( 1903) metal coordination : bond 0.01151 / 0.63 ( 8) metal coordination : angle 1.99863 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.6398 (OUTLIER) cc_final: 0.6026 (m) REVERT: A 32 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.6627 (t80) REVERT: A 54 CYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7724 (m) REVERT: A 60 ASP cc_start: 0.7812 (t0) cc_final: 0.7560 (t70) REVERT: A 62 ASP cc_start: 0.7699 (t0) cc_final: 0.7284 (p0) REVERT: A 277 GLU cc_start: 0.7680 (mp0) cc_final: 0.7380 (mp0) REVERT: A 285 ARG cc_start: 0.9005 (ttm-80) cc_final: 0.8712 (ttm110) REVERT: A 304 ASP cc_start: 0.8326 (m-30) cc_final: 0.7997 (m-30) REVERT: A 648 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8007 (tp) REVERT: A 846 ASP cc_start: 0.8035 (m-30) cc_final: 0.7801 (m-30) REVERT: B 165 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7323 (mttm) REVERT: B 189 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7733 (mt) REVERT: C 3 MET cc_start: 0.9018 (tpt) cc_final: 0.8481 (tpt) REVERT: D 78 ASP cc_start: 0.7133 (t0) cc_final: 0.6678 (t70) REVERT: G 69 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5293 (mp) REVERT: G 97 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7785 (tm) outliers start: 34 outliers final: 24 residues processed: 169 average time/residue: 0.9315 time to fit residues: 178.2515 Evaluate side-chains 171 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.173696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117933 restraints weight = 50722.631| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.05 r_work: 0.2916 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13497 Z= 0.174 Angle : 0.489 6.309 18636 Z= 0.267 Chirality : 0.038 0.180 2163 Planarity : 0.004 0.048 2125 Dihedral : 14.030 137.749 2673 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.12 % Rotamer: Outliers : 2.70 % Allowed : 13.08 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.23), residues: 1462 helix: 1.59 (0.21), residues: 721 sheet: -0.94 (0.36), residues: 191 loop : -1.12 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 18 TYR 0.016 0.001 TYR B 135 PHE 0.022 0.001 PHE A 571 TRP 0.008 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (13489) covalent geometry : angle 0.48788 / 0.27 (18630) hydrogen bonds : bond 0.04770 / 3.22 ( 688) hydrogen bonds : angle 4.16146 / 2.90 ( 1903) metal coordination : bond 0.01242 / 0.68 ( 8) metal coordination : angle 2.08757 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 VAL cc_start: 0.6389 (OUTLIER) cc_final: 0.6015 (m) REVERT: A 32 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.6630 (t80) REVERT: A 54 CYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7719 (m) REVERT: A 60 ASP cc_start: 0.7826 (t0) cc_final: 0.7619 (t70) REVERT: A 62 ASP cc_start: 0.7661 (t0) cc_final: 0.7258 (p0) REVERT: A 277 GLU cc_start: 0.7752 (mp0) cc_final: 0.7463 (mp0) REVERT: A 285 ARG cc_start: 0.9009 (ttm-80) cc_final: 0.8748 (ttm110) REVERT: A 304 ASP cc_start: 0.8315 (m-30) cc_final: 0.8024 (m-30) REVERT: A 846 ASP cc_start: 0.8033 (m-30) cc_final: 0.7799 (m-30) REVERT: B 165 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7284 (mttm) REVERT: B 189 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7717 (mt) REVERT: D 78 ASP cc_start: 0.7108 (t0) cc_final: 0.6656 (t70) REVERT: G 69 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5307 (mp) REVERT: G 97 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7772 (tm) outliers start: 34 outliers final: 23 residues processed: 168 average time/residue: 0.9432 time to fit residues: 178.9797 Evaluate side-chains 168 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain G residue 26 ASP Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 99 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.173880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118942 restraints weight = 50255.279| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.97 r_work: 0.2933 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13497 Z= 0.133 Angle : 0.468 6.094 18636 Z= 0.255 Chirality : 0.037 0.167 2163 Planarity : 0.003 0.039 2125 Dihedral : 14.013 138.181 2673 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Rotamer: Outliers : 2.22 % Allowed : 13.72 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.23), residues: 1462 helix: 1.70 (0.21), residues: 721 sheet: -0.90 (0.36), residues: 191 loop : -1.05 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 18 TYR 0.017 0.001 TYR B 135 PHE 0.021 0.001 PHE A 571 TRP 0.008 0.001 TRP A 916 HIS 0.004 0.001 HIS A 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (13489) covalent geometry : angle 0.46687 / 0.25 (18630) hydrogen bonds : bond 0.04379 / 2.96 ( 688) hydrogen bonds : angle 4.09112 / 2.85 ( 1903) metal coordination : bond 0.01085 / 0.60 ( 8) metal coordination : angle 1.96684 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.6670 (t80) REVERT: A 54 CYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7694 (m) REVERT: A 62 ASP cc_start: 0.7627 (t0) cc_final: 0.7263 (p0) REVERT: A 277 GLU cc_start: 0.7749 (mp0) cc_final: 0.7464 (mp0) REVERT: A 285 ARG cc_start: 0.8989 (ttm-80) cc_final: 0.8734 (ttm110) REVERT: A 304 ASP cc_start: 0.8337 (m-30) cc_final: 0.8043 (m-30) REVERT: A 846 ASP cc_start: 0.7949 (m-30) cc_final: 0.7721 (m-30) REVERT: B 189 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7743 (mt) REVERT: C 3 MET cc_start: 0.9008 (tpt) cc_final: 0.8486 (tpt) REVERT: D 78 ASP cc_start: 0.7112 (t0) cc_final: 0.6658 (t70) REVERT: G 32 TYR cc_start: 0.7368 (p90) cc_final: 0.7076 (p90) REVERT: G 69 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5272 (mp) outliers start: 28 outliers final: 20 residues processed: 167 average time/residue: 0.9471 time to fit residues: 178.8349 Evaluate side-chains 163 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.1980 chunk 131 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.174441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118463 restraints weight = 51136.965| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.11 r_work: 0.2923 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 13497 Z= 0.153 Angle : 0.476 6.288 18636 Z= 0.259 Chirality : 0.037 0.175 2163 Planarity : 0.003 0.038 2125 Dihedral : 14.018 138.378 2673 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.81 % Favored : 95.12 % Rotamer: Outliers : 1.98 % Allowed : 13.96 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.23), residues: 1462 helix: 1.67 (0.21), residues: 721 sheet: -0.96 (0.36), residues: 193 loop : -1.03 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 18 TYR 0.016 0.001 TYR B 135 PHE 0.022 0.001 PHE A 571 TRP 0.008 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (13489) covalent geometry : angle 0.47493 / 0.26 (18630) hydrogen bonds : bond 0.04539 / 3.07 ( 688) hydrogen bonds : angle 4.10203 / 2.85 ( 1903) metal coordination : bond 0.01065 / 0.59 ( 8) metal coordination : angle 1.96420 / 1.21 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2924 Ramachandran restraints generated. 1462 Oldfield, 0 Emsley, 1462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 26 is missing expected H atoms. Skipping. Residue LEU 35 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue LYS 84 is missing expected H atoms. Skipping. Residue LYS 92 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.6672 (t80) REVERT: A 54 CYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7695 (m) REVERT: A 62 ASP cc_start: 0.7642 (t0) cc_final: 0.7295 (p0) REVERT: A 277 GLU cc_start: 0.7742 (mp0) cc_final: 0.7452 (mp0) REVERT: A 285 ARG cc_start: 0.8997 (ttm-80) cc_final: 0.8740 (ttm110) REVERT: A 304 ASP cc_start: 0.8318 (m-30) cc_final: 0.7980 (m-30) REVERT: A 846 ASP cc_start: 0.7942 (m-30) cc_final: 0.7714 (m-30) REVERT: B 189 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7722 (mt) REVERT: D 78 ASP cc_start: 0.7119 (t0) cc_final: 0.6660 (t70) REVERT: G 32 TYR cc_start: 0.7443 (p90) cc_final: 0.7088 (p90) REVERT: G 69 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5254 (mp) outliers start: 25 outliers final: 20 residues processed: 163 average time/residue: 0.9029 time to fit residues: 166.5281 Evaluate side-chains 165 residues out of total 1279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 145 optimal weight: 20.0000 chunk 108 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.174362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119993 restraints weight = 44940.524| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.94 r_work: 0.2968 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13497 Z= 0.129 Angle : 0.460 6.089 18636 Z= 0.250 Chirality : 0.037 0.163 2163 Planarity : 0.003 0.036 2125 Dihedral : 14.003 138.262 2673 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 2.22 % Allowed : 13.88 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.23), residues: 1462 helix: 1.74 (0.21), residues: 721 sheet: -0.83 (0.37), residues: 181 loop : -1.03 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 18 TYR 0.014 0.001 TYR B 135 PHE 0.020 0.001 PHE A 571 TRP 0.009 0.001 TRP A 916 HIS 0.004 0.001 HIS A 725 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (13489) covalent geometry : angle 0.45843 / 0.25 (18630) hydrogen bonds : bond 0.04274 / 2.88 ( 688) hydrogen bonds : angle 4.05863 / 2.82 ( 1903) metal coordination : bond 0.01023 / 0.57 ( 8) metal coordination : angle 1.96706 / 1.22 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10020.75 seconds wall clock time: 170 minutes 8.73 seconds (10208.73 seconds total)