Starting phenix.real_space_refine on Sat Mar 7 12:09:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y53_33611/03_2026/7y53_33611.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y53_33611/03_2026/7y53_33611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y53_33611/03_2026/7y53_33611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y53_33611/03_2026/7y53_33611.map" model { file = "/net/cci-nas-00/data/ceres_data/7y53_33611/03_2026/7y53_33611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y53_33611/03_2026/7y53_33611.cif" } resolution = 3.61 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= 0.004 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 230 5.16 5 C 27256 2.51 5 N 7466 2.21 5 O 7990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42966 Number of models: 1 Model: "" Number of chains: 16 Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "X" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "Y" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "Z" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "A" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "B" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "C" Number of atoms: 5809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5809 Classifications: {'peptide': 741} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 38, 'TRANS': 699} Chain: "D" Number of atoms: 5829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5829 Classifications: {'peptide': 743} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain: "E" Number of atoms: 5911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5911 Classifications: {'peptide': 753} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 710} Chain: "F" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5921 Classifications: {'peptide': 755} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 712} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.17, per 1000 atoms: 0.24 Number of scatterers: 42966 At special positions: 0 Unit cell: (178.2, 166.1, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 230 16.00 P 24 15.00 O 7990 8.00 N 7466 7.00 C 27256 6.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 1.9 seconds 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10018 Finding SS restraints... Secondary structure from input PDB file: 245 helices and 30 sheets defined 52.0% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'W' and resid 2 through 10 Processing helix chain 'W' and resid 12 through 32 Proline residue: W 26 - end of helix Processing helix chain 'W' and resid 35 through 39 Processing helix chain 'W' and resid 42 through 49 Processing helix chain 'W' and resid 56 through 60 Processing helix chain 'W' and resid 68 through 89 removed outlier: 4.145A pdb=" N THR W 84 " --> pdb=" O TYR W 80 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG W 85 " --> pdb=" O GLN W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 116 removed outlier: 4.164A pdb=" N TYR W 98 " --> pdb=" O ARG W 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 122 through 137 Processing helix chain 'W' and resid 154 through 166 Processing helix chain 'W' and resid 169 through 188 removed outlier: 4.462A pdb=" N GLU W 173 " --> pdb=" O SER W 169 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 194 removed outlier: 3.810A pdb=" N MET W 192 " --> pdb=" O PHE W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 203 through 210 removed outlier: 3.638A pdb=" N TYR W 207 " --> pdb=" O PRO W 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 11 removed outlier: 3.597A pdb=" N ILE X 11 " --> pdb=" O TRP X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 31 Proline residue: X 26 - end of helix Processing helix chain 'X' and resid 35 through 39 Processing helix chain 'X' and resid 42 through 49 Processing helix chain 'X' and resid 56 through 61 Processing helix chain 'X' and resid 68 through 89 removed outlier: 4.028A pdb=" N THR X 84 " --> pdb=" O TYR X 80 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG X 85 " --> pdb=" O GLN X 81 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY X 89 " --> pdb=" O ARG X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 116 Processing helix chain 'X' and resid 122 through 137 removed outlier: 3.667A pdb=" N ILE X 126 " --> pdb=" O MET X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 166 Processing helix chain 'X' and resid 169 through 188 removed outlier: 4.281A pdb=" N GLU X 173 " --> pdb=" O SER X 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 194 removed outlier: 3.867A pdb=" N MET X 192 " --> pdb=" O PHE X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 210 removed outlier: 3.786A pdb=" N TYR X 207 " --> pdb=" O PRO X 203 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 11 removed outlier: 3.863A pdb=" N ILE Y 11 " --> pdb=" O TRP Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 31 Proline residue: Y 26 - end of helix Processing helix chain 'Y' and resid 35 through 39 Processing helix chain 'Y' and resid 42 through 49 Processing helix chain 'Y' and resid 52 through 58 removed outlier: 4.400A pdb=" N ILE Y 56 " --> pdb=" O ILE Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 88 removed outlier: 3.850A pdb=" N TYR Y 72 " --> pdb=" O THR Y 68 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR Y 84 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU Y 86 " --> pdb=" O TYR Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 116 removed outlier: 3.538A pdb=" N TYR Y 98 " --> pdb=" O ARG Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 137 Processing helix chain 'Y' and resid 154 through 166 removed outlier: 3.611A pdb=" N ILE Y 165 " --> pdb=" O GLY Y 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 169 through 188 removed outlier: 3.548A pdb=" N GLU Y 173 " --> pdb=" O SER Y 169 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU Y 178 " --> pdb=" O LEU Y 174 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL Y 179 " --> pdb=" O ILE Y 175 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY Y 180 " --> pdb=" O GLY Y 176 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N HIS Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 194 removed outlier: 3.977A pdb=" N MET Y 192 " --> pdb=" O PHE Y 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 11 Processing helix chain 'Z' and resid 12 through 32 removed outlier: 3.590A pdb=" N ALA Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA Z 21 " --> pdb=" O TYR Z 17 " (cutoff:3.500A) Proline residue: Z 26 - end of helix Processing helix chain 'Z' and resid 35 through 40 removed outlier: 3.975A pdb=" N PHE Z 40 " --> pdb=" O ALA Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 49 Processing helix chain 'Z' and resid 52 through 59 removed outlier: 4.548A pdb=" N ILE Z 56 " --> pdb=" O ILE Z 52 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR Z 59 " --> pdb=" O PRO Z 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 89 removed outlier: 4.105A pdb=" N TYR Z 72 " --> pdb=" O THR Z 68 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG Z 85 " --> pdb=" O GLN Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 116 Processing helix chain 'Z' and resid 121 through 137 removed outlier: 3.737A pdb=" N LEU Z 125 " --> pdb=" O LEU Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 154 through 166 Processing helix chain 'Z' and resid 170 through 188 removed outlier: 3.897A pdb=" N GLY Z 176 " --> pdb=" O ASN Z 172 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL Z 179 " --> pdb=" O ILE Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 194 removed outlier: 3.924A pdb=" N ASP Z 193 " --> pdb=" O ARG Z 189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 203 through 210 removed outlier: 3.731A pdb=" N TYR Z 207 " --> pdb=" O PRO Z 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.582A pdb=" N ARG A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 removed outlier: 3.651A pdb=" N VAL A 123 " --> pdb=" O ASP A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 202 through 206 removed outlier: 4.004A pdb=" N ILE A 206 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 Proline residue: A 223 - end of helix removed outlier: 4.269A pdb=" N HIS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.829A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.907A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.501A pdb=" N ARG A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.605A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.707A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.542A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.766A pdb=" N GLN A 458 " --> pdb=" O TRP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.787A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.737A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 543 through 550 Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.875A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 593 through 610 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.781A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 651 No H-bonds generated for 'chain 'A' and resid 649 through 651' Processing helix chain 'A' and resid 652 through 662 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.534A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 713 removed outlier: 3.619A pdb=" N LEU A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 4.043A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 765 removed outlier: 4.262A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 85 through 92 removed outlier: 3.501A pdb=" N ARG B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 removed outlier: 3.600A pdb=" N VAL B 123 " --> pdb=" O ASP B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.608A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 202 through 206 removed outlier: 4.127A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.809A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 281 through 295 removed outlier: 4.119A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 319 through 334 Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.885A pdb=" N ARG B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.636A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.507A pdb=" N LYS B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.815A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 593 through 610 removed outlier: 3.712A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.571A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 removed outlier: 3.570A pdb=" N LEU B 675 " --> pdb=" O ASP B 671 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 714 removed outlier: 3.631A pdb=" N ALA B 694 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.957A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 765 removed outlier: 3.715A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.674A pdb=" N ARG C 89 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 removed outlier: 3.690A pdb=" N GLU C 124 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.837A pdb=" N VAL C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 5.257A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.713A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.583A pdb=" N ILE C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.972A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 319 through 335 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.584A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.941A pdb=" N ARG C 359 " --> pdb=" O ALA C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.692A pdb=" N THR C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 425 Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.594A pdb=" N GLN C 458 " --> pdb=" O TRP C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.005A pdb=" N TYR C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 3.546A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.604A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 removed outlier: 3.865A pdb=" N TRP C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 580 through 586 removed outlier: 3.559A pdb=" N ARG C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 610 removed outlier: 4.100A pdb=" N ARG C 599 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 661 removed outlier: 3.597A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 716 Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.921A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 removed outlier: 3.631A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 85 through 93 Processing helix chain 'D' and resid 120 through 123 removed outlier: 4.023A pdb=" N VAL D 123 " --> pdb=" O ASP D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.811A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 129 through 134' Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 202 through 206 removed outlier: 3.747A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.031A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 234 removed outlier: 3.850A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 removed outlier: 3.555A pdb=" N ILE D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 276 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.734A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 309 Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.765A pdb=" N ILE D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.776A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 402 removed outlier: 4.022A pdb=" N VAL D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 427 Processing helix chain 'D' and resid 438 through 443 removed outlier: 4.175A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.580A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.932A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 499 through 507 removed outlier: 4.024A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 543 through 550 Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 580 through 587 Processing helix chain 'D' and resid 593 through 610 Processing helix chain 'D' and resid 625 through 629 removed outlier: 3.670A pdb=" N ILE D 628 " --> pdb=" O ARG D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 661 Processing helix chain 'D' and resid 672 through 679 removed outlier: 3.506A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 716 Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 749 through 763 removed outlier: 3.830A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 202 through 206 removed outlier: 3.746A pdb=" N ASP E 205 " --> pdb=" O GLY E 202 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 206 " --> pdb=" O TYR E 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 202 through 206' Processing helix chain 'E' and resid 209 through 226 removed outlier: 5.134A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.515A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 276 removed outlier: 3.700A pdb=" N ILE E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.558A pdb=" N ASN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 4.023A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 354 through 359 removed outlier: 3.897A pdb=" N ARG E 359 " --> pdb=" O ALA E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 395 through 403 Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.833A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 444 removed outlier: 3.974A pdb=" N SER E 444 " --> pdb=" O VAL E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.712A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.201A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 543 through 552 Processing helix chain 'E' and resid 556 through 559 Processing helix chain 'E' and resid 560 through 569 Processing helix chain 'E' and resid 580 through 587 Processing helix chain 'E' and resid 593 through 610 removed outlier: 3.591A pdb=" N VAL E 600 " --> pdb=" O ALA E 596 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE E 601 " --> pdb=" O ALA E 597 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 Processing helix chain 'E' and resid 652 through 662 Processing helix chain 'E' and resid 673 through 679 removed outlier: 4.411A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 714 removed outlier: 4.245A pdb=" N LEU E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 738 removed outlier: 3.788A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 766 removed outlier: 4.240A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU E 762 " --> pdb=" O PHE E 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 85 through 92 removed outlier: 3.579A pdb=" N ARG F 89 " --> pdb=" O ASN F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 123 removed outlier: 3.715A pdb=" N VAL F 123 " --> pdb=" O ASP F 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 134 through 139 Processing helix chain 'F' and resid 209 through 226 removed outlier: 3.726A pdb=" N MET F 219 " --> pdb=" O GLN F 215 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 228 through 234 Processing helix chain 'F' and resid 250 through 263 removed outlier: 3.502A pdb=" N ILE F 254 " --> pdb=" O GLY F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 277 removed outlier: 4.020A pdb=" N ILE F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 4.238A pdb=" N SER F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 374 through 385 removed outlier: 3.617A pdb=" N LEU F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 425 removed outlier: 3.725A pdb=" N LYS F 425 " --> pdb=" O GLN F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 removed outlier: 3.793A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.521A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 499 removed outlier: 3.664A pdb=" N ARG F 487 " --> pdb=" O GLU F 483 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.915A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 543 through 553 removed outlier: 3.979A pdb=" N GLY F 553 " --> pdb=" O THR F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 569 removed outlier: 4.342A pdb=" N VAL F 559 " --> pdb=" O SER F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 587 Processing helix chain 'F' and resid 593 through 610 Processing helix chain 'F' and resid 650 through 661 removed outlier: 3.789A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.705A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 716 removed outlier: 3.582A pdb=" N ASN F 716 " --> pdb=" O GLU F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 742 removed outlier: 3.623A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 765 removed outlier: 3.894A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER F 765 " --> pdb=" O THR F 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 246 through 247 removed outlier: 6.152A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 141 through 142 Processing sheet with id=AA3, first strand: chain 'X' and resid 246 through 247 removed outlier: 3.561A pdb=" N PHE X 246 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE B 114 " --> pdb=" O HIS B 183 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 29 removed outlier: 5.996A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 100 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.547A pdb=" N CYS A 174 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 270 removed outlier: 3.542A pdb=" N PHE A 302 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.649A pdb=" N ILE A 540 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 25 through 29 removed outlier: 8.091A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 146 removed outlier: 3.676A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 267 through 269 removed outlier: 3.517A pdb=" N PHE B 302 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 538 through 542 removed outlier: 7.041A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 24 through 29 removed outlier: 7.592A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP C 74 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU C 41 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 69 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 145 through 147 removed outlier: 4.544A pdb=" N ALA C 177 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ARG C 113 " --> pdb=" O ALA C 177 " (cutoff:3.500A) removed outlier: 10.233A pdb=" N ASP C 179 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N HIS C 115 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N VAL C 181 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N LEU C 117 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N HIS C 183 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 267 through 270 removed outlier: 6.625A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 540 through 542 removed outlier: 5.855A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 25 through 30 removed outlier: 3.635A pdb=" N ARG D 83 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 151 through 155 removed outlier: 3.782A pdb=" N PHE D 152 " --> pdb=" O PHE D 163 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 145 through 146 removed outlier: 3.854A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 267 through 269 removed outlier: 6.650A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 538 through 542 removed outlier: 7.347A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 25 through 29 removed outlier: 8.503A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 117 through 118 Processing sheet with id=AC5, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AC6, first strand: chain 'E' and resid 267 through 269 removed outlier: 6.050A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE E 241 " --> pdb=" O ALA E 345 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR E 347 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 243 " --> pdb=" O THR E 347 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 538 through 542 removed outlier: 7.121A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N THR E 623 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE E 516 " --> pdb=" O THR E 623 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 25 through 29 removed outlier: 7.873A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN F 103 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 151 through 155 removed outlier: 5.607A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG F 113 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD2, first strand: chain 'F' and resid 267 through 269 removed outlier: 3.866A pdb=" N PHE F 302 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 538 through 542 removed outlier: 7.295A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLY F 513 " --> pdb=" O LEU F 639 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR F 517 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1881 hydrogen bonds defined for protein. 5433 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.27 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14347 1.34 - 1.46: 9294 1.46 - 1.59: 19795 1.59 - 1.71: 36 1.71 - 1.83: 380 Bond restraints: 43852 Sorted by residual: bond pdb=" C VAL C 728 " pdb=" N PRO C 729 " ideal model delta sigma weight residual 1.336 1.373 -0.037 1.08e-02 8.57e+03 1.19e+01 bond pdb=" C SER F 664 " pdb=" N PRO F 665 " ideal model delta sigma weight residual 1.326 1.359 -0.032 1.44e-02 4.82e+03 5.04e+00 bond pdb=" CA ASP F 725 " pdb=" CB ASP F 725 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.33e-02 5.65e+03 3.38e+00 bond pdb=" C TYR E 495 " pdb=" N PRO E 496 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.14e+00 bond pdb=" CA GLU B 34 " pdb=" CB GLU B 34 " ideal model delta sigma weight residual 1.518 1.547 -0.029 2.08e-02 2.31e+03 1.98e+00 ... (remaining 43847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 58065 2.13 - 4.27: 1085 4.27 - 6.40: 222 6.40 - 8.54: 17 8.54 - 10.67: 3 Bond angle restraints: 59392 Sorted by residual: angle pdb=" N VAL E 559 " pdb=" CA VAL E 559 " pdb=" C VAL E 559 " ideal model delta sigma weight residual 112.90 107.84 5.06 9.60e-01 1.09e+00 2.77e+01 angle pdb=" N VAL B 220 " pdb=" CA VAL B 220 " pdb=" C VAL B 220 " ideal model delta sigma weight residual 113.71 109.27 4.44 9.50e-01 1.11e+00 2.18e+01 angle pdb=" CB ARG F 713 " pdb=" CG ARG F 713 " pdb=" CD ARG F 713 " ideal model delta sigma weight residual 111.30 121.97 -10.67 2.30e+00 1.89e-01 2.15e+01 angle pdb=" C LEU B 492 " pdb=" N VAL B 493 " pdb=" CA VAL B 493 " ideal model delta sigma weight residual 122.77 117.97 4.80 1.05e+00 9.07e-01 2.09e+01 angle pdb=" C GLU B 34 " pdb=" CA GLU B 34 " pdb=" CB GLU B 34 " ideal model delta sigma weight residual 115.79 110.43 5.36 1.19e+00 7.06e-01 2.03e+01 ... (remaining 59387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 26153 35.04 - 70.08: 473 70.08 - 105.12: 68 105.12 - 140.15: 19 140.15 - 175.19: 2 Dihedral angle restraints: 26715 sinusoidal: 11199 harmonic: 15516 Sorted by residual: dihedral pdb=" CA ASP F 726 " pdb=" C ASP F 726 " pdb=" N PRO F 727 " pdb=" CA PRO F 727 " ideal model delta harmonic sigma weight residual -180.00 -141.89 -38.11 0 5.00e+00 4.00e-02 5.81e+01 dihedral pdb=" O1B ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PB ADP F 902 " pdb=" PA ADP F 902 " ideal model delta sinusoidal sigma weight residual 300.00 124.80 175.19 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP E 901 " pdb=" O5' ADP E 901 " pdb=" PA ADP E 901 " pdb=" O2A ADP E 901 " ideal model delta sinusoidal sigma weight residual 300.00 148.45 151.55 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 26712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5236 0.055 - 0.111: 1151 0.111 - 0.166: 169 0.166 - 0.221: 10 0.221 - 0.276: 1 Chirality restraints: 6567 Sorted by residual: chirality pdb=" CB ILE F 300 " pdb=" CA ILE F 300 " pdb=" CG1 ILE F 300 " pdb=" CG2 ILE F 300 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA MET D 427 " pdb=" N MET D 427 " pdb=" C MET D 427 " pdb=" CB MET D 427 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG D 711 " pdb=" N ARG D 711 " pdb=" C ARG D 711 " pdb=" CB ARG D 711 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 6564 not shown) Planarity restraints: 7737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 726 " -0.081 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO F 727 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO F 727 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO F 727 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 551 " 0.023 2.00e-02 2.50e+03 2.92e-02 2.13e+01 pdb=" CG TRP C 551 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP C 551 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 551 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 551 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP C 551 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 551 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 551 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 551 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP C 551 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA F 297 " 0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO F 298 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO F 298 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 298 " 0.051 5.00e-02 4.00e+02 ... (remaining 7734 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 766 2.68 - 3.23: 42251 3.23 - 3.79: 64631 3.79 - 4.34: 81772 4.34 - 4.90: 133125 Nonbonded interactions: 322545 Sorted by model distance: nonbonded pdb=" OG1 THR Y 202 " pdb=" OH TYR Y 207 " model vdw 2.119 3.040 nonbonded pdb=" O ASN C 624 " pdb=" OH TYR C 755 " model vdw 2.123 3.040 nonbonded pdb=" O ASN B 624 " pdb=" OH TYR B 755 " model vdw 2.139 3.040 nonbonded pdb=" OG SER D 664 " pdb=" O LYS F 505 " model vdw 2.156 3.040 nonbonded pdb=" NH2 ARG E 653 " pdb=" O THR E 679 " model vdw 2.173 3.120 ... (remaining 322540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 763 or resid 901 through 902)) selection = (chain 'B' and (resid 23 through 763 or resid 901 through 902)) selection = chain 'C' selection = (chain 'D' and (resid 23 through 763 or resid 901 through 902)) selection = (chain 'E' and (resid 23 through 763 or resid 901 through 902)) selection = (chain 'F' and (resid 23 through 763 or resid 901 through 902)) } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.120 Process input model: 40.390 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.006 0.891 43853 Z= 0.457 Angle : 0.709 10.669 59392 Z= 0.367 Chirality : 0.046 0.276 6567 Planarity : 0.005 0.125 7737 Dihedral : 15.238 175.193 16697 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.63 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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: -0.33 (0.12), residues: 5362 helix: 0.89 (0.11), residues: 2374 sheet: 0.21 (0.21), residues: 691 loop : -1.55 (0.13), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 711 TYR 0.029 0.001 TYR C 755 PHE 0.045 0.001 PHE C 552 TRP 0.074 0.002 TRP C 551 HIS 0.010 0.001 HIS E 499 Details of bonding type rmsd covalent geometry : bond 0.00360 (43852) covalent geometry : angle 0.70897 (59392) hydrogen bonds : bond 0.17859 ( 1881) hydrogen bonds : angle 6.03078 ( 5433) Misc. bond : bond 0.89107 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 82 TYR cc_start: 0.8089 (m-80) cc_final: 0.7682 (m-80) REVERT: W 106 TRP cc_start: 0.7038 (t60) cc_final: 0.6794 (t60) REVERT: X 57 THR cc_start: 0.6454 (p) cc_final: 0.6214 (p) REVERT: Y 116 MET cc_start: 0.5638 (mmp) cc_final: 0.5240 (mmm) REVERT: Y 192 MET cc_start: 0.6109 (ptt) cc_final: 0.5828 (ptt) REVERT: Z 127 MET cc_start: 0.8995 (pmm) cc_final: 0.8147 (pmm) REVERT: Z 163 ASN cc_start: 0.8419 (t0) cc_final: 0.8192 (p0) REVERT: Z 173 GLU cc_start: 0.8623 (mp0) cc_final: 0.8109 (mp0) REVERT: Z 198 ASN cc_start: 0.8092 (t0) cc_final: 0.7845 (t0) REVERT: B 561 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7587 (tm-30) REVERT: C 244 TYR cc_start: 0.7932 (p90) cc_final: 0.7661 (p90) REVERT: C 531 ILE cc_start: 0.9238 (tp) cc_final: 0.9033 (tp) REVERT: D 582 ILE cc_start: 0.7684 (mm) cc_final: 0.7455 (mm) REVERT: D 720 MET cc_start: 0.0445 (mtp) cc_final: 0.0177 (mtm) REVERT: E 46 MET cc_start: 0.6860 (mtp) cc_final: 0.5230 (tpt) REVERT: E 244 TYR cc_start: 0.7468 (p90) cc_final: 0.6808 (p90) REVERT: E 561 GLU cc_start: 0.7574 (pm20) cc_final: 0.7273 (pm20) REVERT: F 244 TYR cc_start: 0.7827 (p90) cc_final: 0.7584 (p90) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.2482 time to fit residues: 187.4139 Evaluate side-chains 328 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 394 optimal weight: 7.9990 chunk 430 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 0.8980 chunk 523 optimal weight: 0.7980 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 163 ASN Y 172 ASN Y 181 HIS ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS ** D 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 538 ASN D 603 GLN D 714 GLN E 404 HIS F 404 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.126143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.094428 restraints weight = 111432.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.094325 restraints weight = 71171.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095525 restraints weight = 63548.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.095595 restraints weight = 49071.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095774 restraints weight = 44351.503| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 43853 Z= 0.144 Angle : 0.674 9.250 59392 Z= 0.331 Chirality : 0.045 0.187 6567 Planarity : 0.005 0.097 7737 Dihedral : 9.267 166.383 6027 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.93 % Favored : 91.68 % Rotamer: Outliers : 0.67 % Allowed : 7.62 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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: -0.23 (0.12), residues: 5362 helix: 0.94 (0.11), residues: 2458 sheet: 0.37 (0.21), residues: 668 loop : -1.59 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 16 TYR 0.036 0.001 TYR D 495 PHE 0.018 0.001 PHE B 360 TRP 0.055 0.002 TRP E 551 HIS 0.008 0.001 HIS F 404 Details of bonding type rmsd covalent geometry : bond 0.00321 (43852) covalent geometry : angle 0.67448 (59392) hydrogen bonds : bond 0.04589 ( 1881) hydrogen bonds : angle 4.72975 ( 5433) Misc. bond : bond 0.00715 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 371 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 38 TYR cc_start: 0.3200 (OUTLIER) cc_final: 0.1834 (t80) REVERT: W 82 TYR cc_start: 0.7999 (m-80) cc_final: 0.7618 (m-80) REVERT: W 106 TRP cc_start: 0.7032 (t60) cc_final: 0.6771 (t60) REVERT: X 57 THR cc_start: 0.6591 (p) cc_final: 0.6390 (p) REVERT: X 192 MET cc_start: 0.8953 (ppp) cc_final: 0.8647 (ppp) REVERT: Y 204 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7211 (mm-40) REVERT: Z 1 MET cc_start: 0.4215 (ttt) cc_final: 0.3676 (tmm) REVERT: Z 163 ASN cc_start: 0.8544 (t0) cc_final: 0.8312 (p0) REVERT: Z 173 GLU cc_start: 0.9000 (mp0) cc_final: 0.8249 (mp0) REVERT: Z 192 MET cc_start: 0.7734 (ptt) cc_final: 0.7456 (ptp) REVERT: Z 198 ASN cc_start: 0.8202 (t0) cc_final: 0.7988 (t0) REVERT: A 663 LYS cc_start: 0.6217 (pptt) cc_final: 0.5890 (tmmt) REVERT: B 561 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7668 (tm-30) REVERT: C 531 ILE cc_start: 0.9217 (tp) cc_final: 0.8974 (tp) REVERT: C 702 SER cc_start: 0.8720 (t) cc_final: 0.8240 (p) REVERT: D 508 MET cc_start: 0.4085 (OUTLIER) cc_final: 0.2661 (tmm) REVERT: D 582 ILE cc_start: 0.7682 (mm) cc_final: 0.7428 (mm) REVERT: D 651 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7311 (tttm) REVERT: D 720 MET cc_start: 0.0304 (mtp) cc_final: 0.0016 (mtm) REVERT: E 46 MET cc_start: 0.6844 (mtp) cc_final: 0.5304 (tpt) REVERT: E 315 LYS cc_start: 0.8482 (tppt) cc_final: 0.8153 (tptt) REVERT: E 427 MET cc_start: 0.8501 (tmm) cc_final: 0.8293 (tmm) REVERT: E 608 MET cc_start: 0.8598 (tmm) cc_final: 0.8313 (tmm) REVERT: F 244 TYR cc_start: 0.7686 (p90) cc_final: 0.7441 (p90) REVERT: F 740 MET cc_start: 0.8675 (tmm) cc_final: 0.8444 (tmm) outliers start: 31 outliers final: 14 residues processed: 385 average time/residue: 0.2433 time to fit residues: 160.0471 Evaluate side-chains 353 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 336 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 151 LYS Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 474 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 176 optimal weight: 0.1980 chunk 335 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 213 optimal weight: 5.9990 chunk 333 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 ASN Y 163 ASN Y 172 ASN ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 499 HIS ** E 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.125122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093130 restraints weight = 111032.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.093138 restraints weight = 70929.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.094068 restraints weight = 60792.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094579 restraints weight = 46542.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.095515 restraints weight = 43074.658| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 43853 Z= 0.152 Angle : 0.656 12.055 59392 Z= 0.318 Chirality : 0.045 0.180 6567 Planarity : 0.005 0.093 7737 Dihedral : 8.975 151.620 6027 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.96 % Favored : 91.68 % Rotamer: Outliers : 1.02 % Allowed : 10.62 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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: -0.22 (0.12), residues: 5362 helix: 0.99 (0.11), residues: 2462 sheet: 0.29 (0.20), residues: 669 loop : -1.59 (0.13), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 16 TYR 0.024 0.001 TYR C 244 PHE 0.017 0.001 PHE D 552 TRP 0.045 0.002 TRP E 551 HIS 0.006 0.001 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00350 (43852) covalent geometry : angle 0.65586 (59392) hydrogen bonds : bond 0.04273 ( 1881) hydrogen bonds : angle 4.51291 ( 5433) Misc. bond : bond 0.00702 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 355 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 38 TYR cc_start: 0.3202 (OUTLIER) cc_final: 0.2274 (t80) REVERT: W 82 TYR cc_start: 0.8043 (m-80) cc_final: 0.7642 (m-80) REVERT: W 106 TRP cc_start: 0.7067 (t60) cc_final: 0.6795 (t60) REVERT: X 57 THR cc_start: 0.6705 (p) cc_final: 0.6462 (p) REVERT: X 192 MET cc_start: 0.9033 (ppp) cc_final: 0.8711 (ppp) REVERT: Y 172 ASN cc_start: 0.8331 (m110) cc_final: 0.7794 (p0) REVERT: Y 202 THR cc_start: 0.5798 (OUTLIER) cc_final: 0.5554 (m) REVERT: Y 204 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7054 (mm-40) REVERT: Z 1 MET cc_start: 0.4323 (ttt) cc_final: 0.3730 (tmm) REVERT: Z 163 ASN cc_start: 0.8379 (t0) cc_final: 0.8163 (p0) REVERT: Z 173 GLU cc_start: 0.8976 (mp0) cc_final: 0.8260 (mp0) REVERT: Z 192 MET cc_start: 0.7766 (ptt) cc_final: 0.7448 (ptp) REVERT: Z 198 ASN cc_start: 0.8146 (t0) cc_final: 0.7888 (t0) REVERT: A 286 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8568 (tt) REVERT: A 322 ARG cc_start: 0.6849 (mpt180) cc_final: 0.6530 (mpt180) REVERT: B 561 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7610 (tm-30) REVERT: C 702 SER cc_start: 0.8848 (t) cc_final: 0.8334 (p) REVERT: D 508 MET cc_start: 0.4425 (OUTLIER) cc_final: 0.4177 (ttm) REVERT: D 651 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7365 (tttm) REVERT: E 46 MET cc_start: 0.6727 (mtp) cc_final: 0.5110 (tpt) REVERT: E 84 MET cc_start: 0.6826 (ppp) cc_final: 0.6579 (ppp) REVERT: E 427 MET cc_start: 0.8543 (tmm) cc_final: 0.8273 (tmm) REVERT: E 607 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7058 (mp0) REVERT: E 608 MET cc_start: 0.8718 (tmm) cc_final: 0.8294 (tmm) REVERT: F 162 GLU cc_start: 0.7482 (mp0) cc_final: 0.7089 (mp0) REVERT: F 244 TYR cc_start: 0.7649 (p90) cc_final: 0.7416 (p90) REVERT: F 607 GLU cc_start: 0.7943 (mp0) cc_final: 0.7740 (mp0) REVERT: F 740 MET cc_start: 0.8745 (tmm) cc_final: 0.8498 (tmm) outliers start: 47 outliers final: 26 residues processed: 378 average time/residue: 0.2400 time to fit residues: 155.5053 Evaluate side-chains 359 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 328 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 169 SER Chi-restraints excluded: chain Y residue 202 THR Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 211 optimal weight: 2.9990 chunk 380 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 520 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 399 optimal weight: 6.9990 chunk 486 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS E 404 HIS ** E 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.123707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086455 restraints weight = 110795.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.089116 restraints weight = 66907.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089928 restraints weight = 46654.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.090528 restraints weight = 40604.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090624 restraints weight = 37160.120| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 43853 Z= 0.181 Angle : 0.675 13.422 59392 Z= 0.327 Chirality : 0.045 0.178 6567 Planarity : 0.005 0.094 7737 Dihedral : 8.876 144.998 6027 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.22 % Favored : 91.42 % Rotamer: Outliers : 1.46 % Allowed : 13.08 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % 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: -0.30 (0.12), residues: 5362 helix: 0.93 (0.11), residues: 2456 sheet: 0.19 (0.20), residues: 663 loop : -1.62 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 64 TYR 0.022 0.001 TYR C 244 PHE 0.017 0.001 PHE E 131 TRP 0.048 0.002 TRP E 551 HIS 0.007 0.001 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00424 (43852) covalent geometry : angle 0.67515 (59392) hydrogen bonds : bond 0.04336 ( 1881) hydrogen bonds : angle 4.49340 ( 5433) Misc. bond : bond 0.00274 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 349 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 106 TRP cc_start: 0.6923 (t60) cc_final: 0.6612 (t60) REVERT: X 57 THR cc_start: 0.6921 (p) cc_final: 0.6682 (p) REVERT: X 122 MET cc_start: 0.7646 (tmt) cc_final: 0.7225 (tmm) REVERT: X 192 MET cc_start: 0.8973 (ppp) cc_final: 0.8643 (ppp) REVERT: Y 204 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7258 (mm-40) REVERT: Z 1 MET cc_start: 0.4681 (ttt) cc_final: 0.3843 (tmm) REVERT: Z 127 MET cc_start: 0.9217 (pmm) cc_final: 0.8721 (ppp) REVERT: Z 163 ASN cc_start: 0.8573 (t0) cc_final: 0.8314 (p0) REVERT: Z 173 GLU cc_start: 0.9019 (mp0) cc_final: 0.8283 (mp0) REVERT: Z 192 MET cc_start: 0.8099 (ptt) cc_final: 0.7794 (ptp) REVERT: Z 198 ASN cc_start: 0.8255 (t0) cc_final: 0.7959 (t0) REVERT: A 46 MET cc_start: 0.6970 (ttm) cc_final: 0.6761 (ttp) REVERT: A 278 LEU cc_start: 0.8690 (tp) cc_final: 0.8454 (tt) REVERT: A 286 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8690 (tt) REVERT: B 561 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 578 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7532 (mt-10) REVERT: C 173 TYR cc_start: 0.6824 (p90) cc_final: 0.6379 (p90) REVERT: D 508 MET cc_start: 0.4546 (OUTLIER) cc_final: 0.4339 (ttm) REVERT: D 651 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7453 (tttm) REVERT: D 720 MET cc_start: -0.0089 (OUTLIER) cc_final: -0.0495 (mtp) REVERT: D 730 GLU cc_start: 0.5345 (OUTLIER) cc_final: 0.4822 (pm20) REVERT: E 84 MET cc_start: 0.6909 (ppp) cc_final: 0.6707 (ppp) REVERT: E 315 LYS cc_start: 0.8280 (tppt) cc_final: 0.7989 (tptt) REVERT: E 427 MET cc_start: 0.8532 (tmm) cc_final: 0.8246 (tmm) REVERT: E 607 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7131 (mp0) REVERT: E 608 MET cc_start: 0.8796 (tmm) cc_final: 0.8528 (tmm) REVERT: F 162 GLU cc_start: 0.7619 (mp0) cc_final: 0.7376 (mp0) REVERT: F 740 MET cc_start: 0.8649 (tmm) cc_final: 0.8352 (tmm) outliers start: 67 outliers final: 35 residues processed: 394 average time/residue: 0.2414 time to fit residues: 162.4022 Evaluate side-chains 367 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 327 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 78 PHE Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 651 LYS Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 530 optimal weight: 8.9990 chunk 171 optimal weight: 0.4980 chunk 416 optimal weight: 4.9990 chunk 356 optimal weight: 1.9990 chunk 284 optimal weight: 0.0270 chunk 251 optimal weight: 50.0000 chunk 417 optimal weight: 4.9990 chunk 372 optimal weight: 10.0000 chunk 426 optimal weight: 4.9990 chunk 446 optimal weight: 7.9990 chunk 323 optimal weight: 0.9980 overall best weight: 1.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 172 ASN ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 602 ASN E 404 HIS E 735 HIS F 714 GLN ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.124532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.087248 restraints weight = 110267.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.090353 restraints weight = 66085.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.091004 restraints weight = 45262.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.091817 restraints weight = 38136.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.091814 restraints weight = 35572.288| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 43853 Z= 0.137 Angle : 0.654 11.915 59392 Z= 0.314 Chirality : 0.044 0.192 6567 Planarity : 0.005 0.091 7737 Dihedral : 8.654 146.605 6027 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.89 % Favored : 91.81 % Rotamer: Outliers : 1.46 % Allowed : 14.43 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.33 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.12), residues: 5362 helix: 1.05 (0.11), residues: 2450 sheet: 0.25 (0.20), residues: 664 loop : -1.60 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 599 TYR 0.023 0.001 TYR F 244 PHE 0.014 0.001 PHE D 682 TRP 0.045 0.002 TRP E 551 HIS 0.008 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00313 (43852) covalent geometry : angle 0.65365 (59392) hydrogen bonds : bond 0.03851 ( 1881) hydrogen bonds : angle 4.34472 ( 5433) Misc. bond : bond 0.00080 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 353 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.4809 (ttt) cc_final: 0.3241 (tmm) REVERT: W 38 TYR cc_start: 0.3465 (OUTLIER) cc_final: 0.2450 (t80) REVERT: W 106 TRP cc_start: 0.6871 (t60) cc_final: 0.6587 (t60) REVERT: X 122 MET cc_start: 0.7732 (tmt) cc_final: 0.7258 (tmm) REVERT: X 192 MET cc_start: 0.9001 (ppp) cc_final: 0.8637 (ppp) REVERT: Y 172 ASN cc_start: 0.8500 (m110) cc_final: 0.7910 (p0) REVERT: Y 204 GLN cc_start: 0.8253 (tp-100) cc_final: 0.7231 (mm-40) REVERT: Z 1 MET cc_start: 0.4716 (ttt) cc_final: 0.3823 (tmm) REVERT: Z 127 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8658 (ppp) REVERT: Z 163 ASN cc_start: 0.8616 (t0) cc_final: 0.8312 (p0) REVERT: Z 173 GLU cc_start: 0.9036 (mp0) cc_final: 0.8065 (mp0) REVERT: Z 192 MET cc_start: 0.7962 (ptt) cc_final: 0.7612 (ptp) REVERT: Z 198 ASN cc_start: 0.8267 (t0) cc_final: 0.7972 (t0) REVERT: A 46 MET cc_start: 0.6626 (ttm) cc_final: 0.6391 (ttp) REVERT: A 278 LEU cc_start: 0.8660 (tp) cc_final: 0.8416 (tt) REVERT: B 561 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7665 (tm-30) REVERT: C 173 TYR cc_start: 0.6829 (p90) cc_final: 0.6352 (p90) REVERT: C 702 SER cc_start: 0.8858 (t) cc_final: 0.8347 (p) REVERT: C 744 ARG cc_start: 0.5359 (mmt180) cc_final: 0.4341 (mmt-90) REVERT: D 417 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8003 (mm-30) REVERT: D 720 MET cc_start: -0.0081 (OUTLIER) cc_final: -0.0487 (mtp) REVERT: D 730 GLU cc_start: 0.5238 (OUTLIER) cc_final: 0.4755 (pm20) REVERT: E 427 MET cc_start: 0.8470 (tmm) cc_final: 0.8188 (tmm) REVERT: E 607 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7012 (mp0) REVERT: E 608 MET cc_start: 0.8797 (tmm) cc_final: 0.8507 (tmm) REVERT: F 162 GLU cc_start: 0.7627 (mp0) cc_final: 0.7347 (mp0) REVERT: F 740 MET cc_start: 0.8640 (tmm) cc_final: 0.8326 (tmm) outliers start: 67 outliers final: 37 residues processed: 396 average time/residue: 0.2114 time to fit residues: 144.3780 Evaluate side-chains 368 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 327 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 720 MET Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 377 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 105 optimal weight: 0.4980 chunk 525 optimal weight: 10.0000 chunk 218 optimal weight: 6.9990 chunk 503 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 GLN A 337 GLN A 340 HIS B 115 HIS D 317 HIS F 199 ASN ** F 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.123190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085801 restraints weight = 111271.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.089194 restraints weight = 66715.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.089776 restraints weight = 43811.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090327 restraints weight = 38325.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090473 restraints weight = 35157.796| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 43853 Z= 0.179 Angle : 0.681 12.286 59392 Z= 0.328 Chirality : 0.045 0.185 6567 Planarity : 0.005 0.091 7737 Dihedral : 8.576 149.467 6027 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.43 % Favored : 91.29 % Rotamer: Outliers : 1.74 % Allowed : 15.43 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.12), residues: 5362 helix: 0.97 (0.11), residues: 2455 sheet: 0.18 (0.20), residues: 664 loop : -1.64 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 313 TYR 0.039 0.001 TYR D 495 PHE 0.034 0.001 PHE B 575 TRP 0.049 0.002 TRP E 551 HIS 0.006 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00419 (43852) covalent geometry : angle 0.68130 (59392) hydrogen bonds : bond 0.04145 ( 1881) hydrogen bonds : angle 4.38881 ( 5433) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 339 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.4969 (ttt) cc_final: 0.3739 (tmm) REVERT: W 106 TRP cc_start: 0.6939 (t60) cc_final: 0.6626 (t60) REVERT: X 122 MET cc_start: 0.7960 (tmt) cc_final: 0.7598 (tmt) REVERT: X 192 MET cc_start: 0.9017 (ppp) cc_final: 0.8618 (ppp) REVERT: Y 172 ASN cc_start: 0.8353 (m110) cc_final: 0.7787 (p0) REVERT: Y 204 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7213 (mm-40) REVERT: Z 1 MET cc_start: 0.4833 (ttt) cc_final: 0.3956 (tmm) REVERT: Z 127 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8648 (ppp) REVERT: Z 163 ASN cc_start: 0.8638 (t0) cc_final: 0.8348 (p0) REVERT: Z 173 GLU cc_start: 0.9023 (mp0) cc_final: 0.8066 (mp0) REVERT: Z 192 MET cc_start: 0.7783 (ptt) cc_final: 0.7436 (ptp) REVERT: Z 198 ASN cc_start: 0.8278 (t0) cc_final: 0.7985 (t0) REVERT: A 278 LEU cc_start: 0.8664 (tp) cc_final: 0.8417 (tt) REVERT: B 489 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9102 (mm) REVERT: B 561 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7833 (tm-30) REVERT: C 173 TYR cc_start: 0.6790 (p90) cc_final: 0.6262 (p90) REVERT: C 427 MET cc_start: 0.8088 (tpp) cc_final: 0.7835 (tpp) REVERT: C 702 SER cc_start: 0.8883 (t) cc_final: 0.8370 (p) REVERT: D 417 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8022 (mm-30) REVERT: D 730 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.4977 (pm20) REVERT: E 46 MET cc_start: 0.6385 (ptp) cc_final: 0.4744 (tpt) REVERT: E 315 LYS cc_start: 0.8212 (tppt) cc_final: 0.7934 (tptt) REVERT: E 427 MET cc_start: 0.8477 (tmm) cc_final: 0.8196 (tmm) REVERT: E 607 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7026 (mp0) REVERT: E 608 MET cc_start: 0.8822 (tmm) cc_final: 0.8504 (tmm) REVERT: F 162 GLU cc_start: 0.7670 (mp0) cc_final: 0.7365 (mp0) REVERT: F 608 MET cc_start: 0.8009 (mtm) cc_final: 0.7691 (mtm) REVERT: F 740 MET cc_start: 0.8626 (tmm) cc_final: 0.8281 (tmm) outliers start: 80 outliers final: 51 residues processed: 395 average time/residue: 0.2300 time to fit residues: 156.1429 Evaluate side-chains 384 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 330 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 714 GLN Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 425 LYS Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 480 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 455 optimal weight: 0.6980 chunk 246 optimal weight: 30.0000 chunk 428 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 423 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 81 GLN Z 240 HIS A 340 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.125488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.089311 restraints weight = 110051.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091459 restraints weight = 66960.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.091696 restraints weight = 46314.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.092250 restraints weight = 47747.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092614 restraints weight = 40075.539| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 43853 Z= 0.115 Angle : 0.646 14.248 59392 Z= 0.309 Chirality : 0.044 0.224 6567 Planarity : 0.005 0.086 7737 Dihedral : 8.265 147.924 6027 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.37 % Favored : 92.33 % Rotamer: Outliers : 1.41 % Allowed : 16.21 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 5362 helix: 1.13 (0.11), residues: 2432 sheet: 0.30 (0.20), residues: 665 loop : -1.61 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 713 TYR 0.026 0.001 TYR D 495 PHE 0.029 0.001 PHE B 575 TRP 0.045 0.001 TRP E 551 HIS 0.011 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00254 (43852) covalent geometry : angle 0.64616 (59392) hydrogen bonds : bond 0.03332 ( 1881) hydrogen bonds : angle 4.17526 ( 5433) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 354 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.5027 (ttt) cc_final: 0.3789 (tmm) REVERT: W 106 TRP cc_start: 0.6829 (t60) cc_final: 0.6531 (t60) REVERT: X 122 MET cc_start: 0.7971 (tmt) cc_final: 0.7452 (tmm) REVERT: X 192 MET cc_start: 0.9033 (ppp) cc_final: 0.8654 (ppp) REVERT: Y 1 MET cc_start: 0.5596 (pmm) cc_final: 0.5383 (pmm) REVERT: Y 172 ASN cc_start: 0.8305 (m110) cc_final: 0.7817 (p0) REVERT: Y 174 LEU cc_start: 0.9189 (mt) cc_final: 0.8987 (mt) REVERT: Y 204 GLN cc_start: 0.8239 (tp-100) cc_final: 0.7227 (mm-40) REVERT: Z 1 MET cc_start: 0.4826 (ttt) cc_final: 0.3973 (tmm) REVERT: Z 127 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8616 (ppp) REVERT: Z 157 TRP cc_start: 0.8642 (m100) cc_final: 0.8171 (m100) REVERT: Z 163 ASN cc_start: 0.8609 (t0) cc_final: 0.8328 (p0) REVERT: Z 173 GLU cc_start: 0.9031 (mp0) cc_final: 0.8068 (mp0) REVERT: Z 192 MET cc_start: 0.7859 (ptt) cc_final: 0.7545 (ptp) REVERT: Z 198 ASN cc_start: 0.8280 (t0) cc_final: 0.7987 (t0) REVERT: A 278 LEU cc_start: 0.8653 (tp) cc_final: 0.8432 (tt) REVERT: A 663 LYS cc_start: 0.6844 (pptt) cc_final: 0.6455 (pptt) REVERT: B 433 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6561 (pp20) REVERT: B 561 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7674 (tm-30) REVERT: C 427 MET cc_start: 0.8111 (tpp) cc_final: 0.7897 (tpp) REVERT: C 702 SER cc_start: 0.8884 (t) cc_final: 0.8367 (p) REVERT: D 417 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7914 (mm-30) REVERT: D 602 ASN cc_start: 0.8373 (m-40) cc_final: 0.8146 (m-40) REVERT: D 730 GLU cc_start: 0.5129 (OUTLIER) cc_final: 0.4662 (pm20) REVERT: E 46 MET cc_start: 0.6129 (ptp) cc_final: 0.4775 (tpt) REVERT: E 315 LYS cc_start: 0.8276 (tppt) cc_final: 0.7944 (tptt) REVERT: E 427 MET cc_start: 0.8449 (tmm) cc_final: 0.8161 (tmm) REVERT: E 607 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6904 (mp0) REVERT: E 608 MET cc_start: 0.8791 (tmm) cc_final: 0.8452 (tmm) REVERT: F 162 GLU cc_start: 0.7608 (mp0) cc_final: 0.7310 (mp0) REVERT: F 740 MET cc_start: 0.8606 (tmm) cc_final: 0.8268 (tmm) outliers start: 65 outliers final: 41 residues processed: 397 average time/residue: 0.2375 time to fit residues: 161.2111 Evaluate side-chains 376 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 332 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 561 GLU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 714 GLN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 386 optimal weight: 3.9990 chunk 471 optimal weight: 0.0070 chunk 456 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 0.0980 chunk 316 optimal weight: 5.9990 chunk 210 optimal weight: 0.0870 chunk 450 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS F 404 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.126025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089353 restraints weight = 110563.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091734 restraints weight = 66188.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092762 restraints weight = 47465.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.093453 restraints weight = 38818.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.093569 restraints weight = 35686.696| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 43853 Z= 0.110 Angle : 0.644 11.246 59392 Z= 0.307 Chirality : 0.044 0.254 6567 Planarity : 0.004 0.083 7737 Dihedral : 8.038 145.910 6027 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.11 % Favored : 92.58 % Rotamer: Outliers : 1.33 % Allowed : 16.54 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.05 (0.12), residues: 5362 helix: 1.21 (0.11), residues: 2441 sheet: 0.35 (0.20), residues: 691 loop : -1.60 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 713 TYR 0.024 0.001 TYR Y 48 PHE 0.024 0.001 PHE B 575 TRP 0.044 0.002 TRP E 551 HIS 0.009 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00239 (43852) covalent geometry : angle 0.64413 (59392) hydrogen bonds : bond 0.03070 ( 1881) hydrogen bonds : angle 4.07539 ( 5433) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 365 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.4946 (ttt) cc_final: 0.3746 (tmm) REVERT: W 38 TYR cc_start: 0.3189 (OUTLIER) cc_final: 0.2344 (t80) REVERT: W 106 TRP cc_start: 0.6741 (t60) cc_final: 0.6496 (t60) REVERT: X 102 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7439 (mt) REVERT: X 122 MET cc_start: 0.7955 (tmt) cc_final: 0.7433 (tmm) REVERT: X 127 MET cc_start: 0.7683 (mmp) cc_final: 0.7475 (mmp) REVERT: X 192 MET cc_start: 0.9023 (ppp) cc_final: 0.8605 (ppp) REVERT: Y 172 ASN cc_start: 0.8279 (m110) cc_final: 0.7804 (p0) REVERT: Y 204 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7097 (mm-40) REVERT: Z 118 MET cc_start: 0.8257 (mpp) cc_final: 0.8037 (mpp) REVERT: Z 127 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8649 (ppp) REVERT: Z 157 TRP cc_start: 0.8605 (m100) cc_final: 0.8105 (m100) REVERT: Z 173 GLU cc_start: 0.9022 (mp0) cc_final: 0.8190 (mp0) REVERT: Z 192 MET cc_start: 0.7829 (ptt) cc_final: 0.7509 (ptp) REVERT: Z 198 ASN cc_start: 0.8246 (t0) cc_final: 0.7949 (t0) REVERT: A 278 LEU cc_start: 0.8586 (tp) cc_final: 0.8370 (tt) REVERT: A 663 LYS cc_start: 0.6716 (pptt) cc_final: 0.6440 (tmmt) REVERT: B 433 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6456 (pp20) REVERT: B 561 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7644 (tm-30) REVERT: C 427 MET cc_start: 0.8044 (tpp) cc_final: 0.7798 (tpp) REVERT: C 531 ILE cc_start: 0.9175 (tp) cc_final: 0.8868 (tp) REVERT: C 702 SER cc_start: 0.8843 (t) cc_final: 0.8330 (p) REVERT: D 417 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7874 (mm-30) REVERT: D 730 GLU cc_start: 0.5271 (OUTLIER) cc_final: 0.4865 (pm20) REVERT: E 427 MET cc_start: 0.8423 (tmm) cc_final: 0.8140 (tmm) REVERT: E 607 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6870 (mp0) REVERT: E 608 MET cc_start: 0.8750 (tmm) cc_final: 0.8422 (tmm) REVERT: F 162 GLU cc_start: 0.7550 (mp0) cc_final: 0.7279 (mp0) REVERT: F 740 MET cc_start: 0.8637 (tmm) cc_final: 0.8296 (tmm) outliers start: 61 outliers final: 43 residues processed: 407 average time/residue: 0.2454 time to fit residues: 170.7966 Evaluate side-chains 390 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 342 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 714 GLN Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 69 optimal weight: 7.9990 chunk 343 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 494 optimal weight: 1.9990 chunk 524 optimal weight: 6.9990 chunk 444 optimal weight: 0.3980 chunk 93 optimal weight: 0.0970 chunk 307 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 380 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS F 115 HIS F 404 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.126355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090811 restraints weight = 110981.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.092338 restraints weight = 67081.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.092970 restraints weight = 50467.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093545 restraints weight = 46997.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.093561 restraints weight = 40282.685| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 43853 Z= 0.111 Angle : 0.660 17.259 59392 Z= 0.313 Chirality : 0.044 0.351 6567 Planarity : 0.005 0.081 7737 Dihedral : 7.938 143.767 6027 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.16 % Favored : 92.50 % Rotamer: Outliers : 1.44 % Allowed : 17.21 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: 0.01 (0.12), residues: 5362 helix: 1.26 (0.11), residues: 2439 sheet: 0.38 (0.20), residues: 699 loop : -1.58 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 599 TYR 0.021 0.001 TYR D 495 PHE 0.029 0.001 PHE X 78 TRP 0.049 0.002 TRP Z 106 HIS 0.011 0.001 HIS F 404 Details of bonding type rmsd covalent geometry : bond 0.00248 (43852) covalent geometry : angle 0.65986 (59392) hydrogen bonds : bond 0.03081 ( 1881) hydrogen bonds : angle 4.05213 ( 5433) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 352 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.4966 (ttt) cc_final: 0.3730 (tmm) REVERT: W 38 TYR cc_start: 0.3212 (OUTLIER) cc_final: 0.2413 (t80) REVERT: W 106 TRP cc_start: 0.6810 (t60) cc_final: 0.6535 (t60) REVERT: X 102 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7450 (mt) REVERT: X 122 MET cc_start: 0.8047 (tmt) cc_final: 0.7390 (tmm) REVERT: X 192 MET cc_start: 0.9017 (ppp) cc_final: 0.8609 (ppp) REVERT: Y 44 GLU cc_start: 0.3867 (mp0) cc_final: 0.3473 (tm-30) REVERT: Y 204 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7074 (mm-40) REVERT: Z 127 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8639 (ppp) REVERT: Z 140 MET cc_start: 0.6888 (tpt) cc_final: 0.6633 (tpt) REVERT: Z 157 TRP cc_start: 0.8634 (m100) cc_final: 0.8148 (m100) REVERT: Z 173 GLU cc_start: 0.9012 (mp0) cc_final: 0.8183 (mp0) REVERT: Z 192 MET cc_start: 0.7718 (ptt) cc_final: 0.7488 (ptt) REVERT: Z 198 ASN cc_start: 0.8233 (t0) cc_final: 0.7931 (t0) REVERT: A 278 LEU cc_start: 0.8595 (tp) cc_final: 0.8374 (tt) REVERT: A 663 LYS cc_start: 0.6757 (pptt) cc_final: 0.6475 (tmmt) REVERT: B 433 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6552 (pp20) REVERT: B 561 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7661 (tm-30) REVERT: C 531 ILE cc_start: 0.9179 (tp) cc_final: 0.8856 (tp) REVERT: C 702 SER cc_start: 0.8849 (t) cc_final: 0.8334 (p) REVERT: C 744 ARG cc_start: 0.5396 (mmt-90) cc_final: 0.5175 (mmt-90) REVERT: D 417 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7858 (mm-30) REVERT: E 427 MET cc_start: 0.8461 (tmm) cc_final: 0.8167 (tmm) REVERT: E 607 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6901 (mp0) REVERT: E 608 MET cc_start: 0.8770 (tmm) cc_final: 0.8425 (tmm) REVERT: F 162 GLU cc_start: 0.7558 (mp0) cc_final: 0.7261 (mp0) REVERT: F 315 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8264 (mmtm) REVERT: F 608 MET cc_start: 0.7864 (mtm) cc_final: 0.7650 (mtm) REVERT: F 740 MET cc_start: 0.8630 (tmm) cc_final: 0.8281 (tmm) outliers start: 66 outliers final: 51 residues processed: 398 average time/residue: 0.2443 time to fit residues: 166.2893 Evaluate side-chains 398 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 343 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 TYR Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 114 LEU Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 559 VAL Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 714 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 400 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 474 optimal weight: 30.0000 chunk 255 optimal weight: 0.8980 chunk 366 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 355 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 367 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 262 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 172 ASN A 129 ASN A 340 HIS B 602 ASN F 327 GLN F 404 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.121853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.091836 restraints weight = 111106.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.090948 restraints weight = 81018.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.091956 restraints weight = 81799.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.092302 restraints weight = 56612.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093157 restraints weight = 51224.878| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 43853 Z= 0.237 Angle : 0.779 16.533 59392 Z= 0.375 Chirality : 0.047 0.245 6567 Planarity : 0.005 0.085 7737 Dihedral : 8.320 146.717 6027 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.69 % Favored : 91.01 % Rotamer: Outliers : 1.48 % Allowed : 17.41 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.32 (0.12), residues: 5362 helix: 0.91 (0.11), residues: 2464 sheet: 0.27 (0.21), residues: 653 loop : -1.67 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 599 TYR 0.024 0.002 TYR D 495 PHE 0.045 0.002 PHE Y 78 TRP 0.065 0.002 TRP E 551 HIS 0.028 0.002 HIS F 404 Details of bonding type rmsd covalent geometry : bond 0.00555 (43852) covalent geometry : angle 0.77892 (59392) hydrogen bonds : bond 0.04664 ( 1881) hydrogen bonds : angle 4.47556 ( 5433) Misc. bond : bond 0.00055 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10724 Ramachandran restraints generated. 5362 Oldfield, 0 Emsley, 5362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 339 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.4951 (ttt) cc_final: 0.3856 (tmm) REVERT: W 106 TRP cc_start: 0.7302 (t60) cc_final: 0.6939 (t60) REVERT: X 78 PHE cc_start: 0.7827 (m-80) cc_final: 0.7545 (m-80) REVERT: X 102 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7677 (mt) REVERT: X 122 MET cc_start: 0.8471 (tmt) cc_final: 0.8107 (tmt) REVERT: X 192 MET cc_start: 0.8986 (ppp) cc_final: 0.8474 (ppp) REVERT: Y 44 GLU cc_start: 0.4661 (mp0) cc_final: 0.4114 (tm-30) REVERT: Y 172 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7769 (p0) REVERT: Y 204 GLN cc_start: 0.7455 (tp-100) cc_final: 0.6501 (mm-40) REVERT: Z 1 MET cc_start: 0.5368 (tmm) cc_final: 0.4958 (tmm) REVERT: Z 127 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8456 (ppp) REVERT: Z 163 ASN cc_start: 0.8525 (m-40) cc_final: 0.7707 (p0) REVERT: Z 173 GLU cc_start: 0.8832 (mp0) cc_final: 0.8013 (mp0) REVERT: Z 192 MET cc_start: 0.7134 (ptt) cc_final: 0.6872 (ptp) REVERT: Z 198 ASN cc_start: 0.7974 (t0) cc_final: 0.7728 (t0) REVERT: A 278 LEU cc_start: 0.8589 (tp) cc_final: 0.7842 (tt) REVERT: B 433 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6431 (pp20) REVERT: B 489 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9193 (mm) REVERT: B 561 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 602 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7375 (p0) REVERT: D 332 MET cc_start: 0.8913 (tpp) cc_final: 0.8664 (tpp) REVERT: D 417 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7880 (mm-30) REVERT: E 315 LYS cc_start: 0.8343 (tppt) cc_final: 0.7989 (tptt) REVERT: E 427 MET cc_start: 0.8464 (tmm) cc_final: 0.8224 (tmm) REVERT: E 607 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7038 (mp0) REVERT: F 315 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8358 (mmmm) REVERT: F 720 MET cc_start: 0.0920 (mtt) cc_final: 0.0659 (mpp) REVERT: F 740 MET cc_start: 0.8647 (tmm) cc_final: 0.8334 (tmm) outliers start: 68 outliers final: 51 residues processed: 387 average time/residue: 0.2496 time to fit residues: 164.7549 Evaluate side-chains 379 residues out of total 4595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 322 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 73 LEU Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain X residue 64 VAL Chi-restraints excluded: chain X residue 102 LEU Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain Y residue 98 TYR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Y residue 172 ASN Chi-restraints excluded: chain Y residue 179 VAL Chi-restraints excluded: chain Z residue 127 MET Chi-restraints excluded: chain Z residue 188 PHE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 552 PHE Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 602 ASN Chi-restraints excluded: chain B residue 686 ASP Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 762 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 333 ASP Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 551 TRP Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain D residue 697 LEU Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 448 THR Chi-restraints excluded: chain E residue 475 THR Chi-restraints excluded: chain E residue 540 ILE Chi-restraints excluded: chain E residue 548 LEU Chi-restraints excluded: chain E residue 562 ILE Chi-restraints excluded: chain E residue 670 VAL Chi-restraints excluded: chain E residue 714 GLN Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 404 HIS Chi-restraints excluded: chain F residue 429 LEU Chi-restraints excluded: chain F residue 527 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 408 optimal weight: 2.9990 chunk 341 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 225 optimal weight: 0.8980 chunk 356 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 258 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 498 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS B 602 ASN D 602 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.122213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.092021 restraints weight = 111119.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.091033 restraints weight = 79597.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092341 restraints weight = 78424.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092247 restraints weight = 55404.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092421 restraints weight = 51061.063| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.200 43853 Z= 0.224 Angle : 0.862 59.200 59392 Z= 0.446 Chirality : 0.047 0.622 6567 Planarity : 0.006 0.177 7737 Dihedral : 8.367 146.704 6027 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.78 % Favored : 90.90 % Rotamer: Outliers : 1.44 % Allowed : 17.67 % Favored : 80.89 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 5362 helix: 0.86 (0.11), residues: 2464 sheet: 0.25 (0.21), residues: 653 loop : -1.68 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG Y 54 TYR 0.023 0.001 TYR D 495 PHE 0.035 0.002 PHE Y 78 TRP 0.130 0.003 TRP Y 42 HIS 0.167 0.003 HIS F 404 Details of bonding type rmsd covalent geometry : bond 0.00497 (43852) covalent geometry : angle 0.86229 (59392) hydrogen bonds : bond 0.04540 ( 1881) hydrogen bonds : angle 4.47336 ( 5433) Misc. bond : bond 0.00072 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7151.98 seconds wall clock time: 124 minutes 24.35 seconds (7464.35 seconds total)