Starting phenix.real_space_refine on Sat Mar 7 11:59:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y4w_33608/03_2026/7y4w_33608.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y4w_33608/03_2026/7y4w_33608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y4w_33608/03_2026/7y4w_33608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y4w_33608/03_2026/7y4w_33608.map" model { file = "/net/cci-nas-00/data/ceres_data/7y4w_33608/03_2026/7y4w_33608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y4w_33608/03_2026/7y4w_33608.cif" } resolution = 3.67 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= 0.003 sd= 0.057 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 8 5.49 5 S 230 5.16 5 C 27190 2.51 5 N 7433 2.21 5 O 7915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s 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: 42776 Number of models: 1 Model: "" Number of chains: 14 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: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5835 Classifications: {'peptide': 744} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 38, 'TRANS': 702} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.23, per 1000 atoms: 0.22 Number of scatterers: 42776 At special positions: 0 Unit cell: (178.2, 167.2, 193.6, 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 8 15.00 O 7915 8.00 N 7433 7.00 C 27190 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=0, symmetry=0 Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.9 seconds 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10024 Finding SS restraints... Secondary structure from input PDB file: 251 helices and 31 sheets defined 52.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 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 removed outlier: 3.607A pdb=" N GLY W 32 " --> pdb=" O VAL W 28 " (cutoff:3.500A) 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: 3.986A pdb=" N THR W 84 " --> pdb=" O TYR W 80 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG W 85 " --> pdb=" O GLN W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 94 through 116 removed outlier: 3.946A 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 170 through 188 Processing helix chain 'W' and resid 188 through 195 removed outlier: 3.844A pdb=" N MET W 192 " --> pdb=" O PHE W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 203 through 210 removed outlier: 3.849A pdb=" N TYR W 207 " --> pdb=" O PRO W 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 11 removed outlier: 3.611A pdb=" N ILE X 11 " --> pdb=" O TRP X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 12 through 32 Proline residue: X 26 - end of helix removed outlier: 3.641A pdb=" N GLY X 32 " --> pdb=" O VAL X 28 " (cutoff:3.500A) 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 removed outlier: 3.939A pdb=" N PHE X 60 " --> pdb=" O ILE X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 89 removed outlier: 3.667A pdb=" N THR X 84 " --> pdb=" O TYR X 80 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG X 85 " --> pdb=" O GLN X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 94 through 116 removed outlier: 3.534A pdb=" N TYR X 98 " --> pdb=" O ARG X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 136 removed outlier: 3.635A 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: 4.236A pdb=" N GLU X 173 " --> pdb=" O SER X 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 194 removed outlier: 3.943A pdb=" N MET X 192 " --> pdb=" O PHE X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 210 removed outlier: 4.036A pdb=" N TYR X 207 " --> pdb=" O PRO X 203 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 11 removed outlier: 3.970A 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 removed outlier: 3.531A pdb=" N TYR Y 38 " --> pdb=" O SER Y 35 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 49 Processing helix chain 'Y' and resid 52 through 58 removed outlier: 4.687A pdb=" N ILE Y 56 " --> pdb=" O ILE Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 88 removed outlier: 3.813A pdb=" N TYR Y 72 " --> pdb=" O THR Y 68 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR Y 84 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG Y 85 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU Y 86 " --> pdb=" O TYR Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 116 removed outlier: 3.638A 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 163 Processing helix chain 'Y' and resid 169 through 188 removed outlier: 3.622A pdb=" N GLU Y 173 " --> pdb=" O SER Y 169 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU Y 178 " --> pdb=" O LEU Y 174 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL Y 179 " --> pdb=" O ILE Y 175 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY Y 180 " --> pdb=" O GLY Y 176 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N HIS Y 181 " --> pdb=" O ASN Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 194 Processing helix chain 'Z' and resid 2 through 11 Processing helix chain 'Z' and resid 12 through 31 removed outlier: 3.883A pdb=" N ALA Z 20 " --> pdb=" O ARG Z 16 " (cutoff:3.500A) removed outlier: 4.263A 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 39 Processing helix chain 'Z' and resid 42 through 49 Processing helix chain 'Z' and resid 52 through 59 removed outlier: 4.597A pdb=" N ILE Z 56 " --> pdb=" O ILE Z 52 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR Z 59 " --> pdb=" O PRO Z 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 89 removed outlier: 3.963A pdb=" N TYR Z 72 " --> pdb=" O THR Z 68 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG Z 85 " --> pdb=" O GLN Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 94 through 116 removed outlier: 3.528A pdb=" N LEU Z 99 " --> pdb=" O PRO Z 95 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU Z 102 " --> pdb=" O TYR Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 135 removed outlier: 3.702A 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: 4.872A pdb=" N GLY Z 176 " --> pdb=" O ASN Z 172 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL Z 179 " --> pdb=" O ILE Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 194 removed outlier: 3.699A pdb=" N LEU Z 194 " --> pdb=" O TYR Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 203 through 210 removed outlier: 3.751A 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 Processing helix chain 'A' and resid 120 through 123 removed outlier: 3.750A 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: 4.059A 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: 4.489A pdb=" N HIS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.628A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.571A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.262A pdb=" N GLU A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (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: 3.841A 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 402 removed outlier: 3.730A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.687A pdb=" N LYS A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.681A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.572A 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: 4.072A 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 507 removed outlier: 4.128A 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 556 through 569 removed outlier: 4.151A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.753A 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 650 through 662 removed outlier: 3.609A pdb=" N LYS A 658 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 713 removed outlier: 3.720A pdb=" N CYS A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 696 " --> pdb=" O GLN A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.736A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 766 removed outlier: 3.961A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 766 " --> pdb=" O LEU A 762 " (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 93 removed outlier: 3.503A pdb=" N ARG B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 Processing helix chain 'B' and resid 129 through 134 removed outlier: 3.958A 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: 3.906A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.546A pdb=" N LEU B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.842A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 286 " --> pdb=" O SER B 282 " (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 373 through 385 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 407 through 425 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.685A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.349A 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: 3.722A 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 552 removed outlier: 3.775A pdb=" N PHE B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) 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: 3.973A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 650 through 662 removed outlier: 3.890A pdb=" N VAL B 654 " --> pdb=" O GLU B 650 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 662 " --> pdb=" O LYS B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 714 removed outlier: 3.720A pdb=" N ALA B 694 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N CYS B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 742 removed outlier: 3.783A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 766 removed outlier: 3.815A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG B 766 " --> pdb=" O LEU B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 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 92 removed outlier: 3.565A pdb=" N ARG C 89 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.591A pdb=" N GLU C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C 196 " --> pdb=" O GLU C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.042A pdb=" N GLU C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 196 through 201' Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.517A pdb=" N ASP C 205 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 5.469A 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 Processing helix chain 'C' and resid 250 through 263 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: 3.802A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.960A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 335 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.995A pdb=" N ILE C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.832A 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 Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.671A pdb=" N ALA C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 448 through 458 Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.658A 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: 3.699A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.651A pdb=" N CYS C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 552 removed outlier: 3.993A 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 579 through 587 removed outlier: 4.519A pdb=" N ALA C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY C 587 " --> pdb=" O ALA C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 610 removed outlier: 3.952A pdb=" N VAL C 600 " --> pdb=" O ALA C 596 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 661 removed outlier: 4.139A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE C 656 " --> pdb=" O SER C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 679 Processing helix chain 'C' and resid 683 through 716 Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.790A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 removed outlier: 3.733A 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: 3.863A 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: 3.934A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 3.610A 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: 3.585A pdb=" N ILE D 206 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 5.088A 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: 3.594A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 270 through 276 removed outlier: 3.596A pdb=" N ILE D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.832A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.597A 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 354 through 359 removed outlier: 3.995A 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: 3.985A 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 436 through 443 Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.608A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 494 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'D' and resid 499 through 506 removed outlier: 3.846A 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 555 through 569 removed outlier: 3.585A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) 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: 3.574A 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: 3.566A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 716 removed outlier: 3.608A pdb=" N ALA D 694 " --> pdb=" O ILE D 690 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS D 695 " --> pdb=" O CYS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 Processing helix chain 'D' and resid 749 through 763 removed outlier: 3.891A 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 removed outlier: 3.776A pdb=" N VAL E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.835A 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 Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 276 removed outlier: 3.762A pdb=" N ILE E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 305 through 309 Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 354 through 359 removed outlier: 4.000A 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: 3.808A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 445 Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.937A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 493 Processing helix chain 'E' and resid 493 through 499 removed outlier: 4.057A pdb=" N VAL E 497 " --> pdb=" O VAL E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 507 removed outlier: 3.766A 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 removed outlier: 3.989A pdb=" N PHE E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 569 removed outlier: 3.974A pdb=" N VAL E 559 " --> pdb=" O SER E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 587 removed outlier: 3.609A pdb=" N GLY E 587 " --> pdb=" O ALA E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 610 removed outlier: 4.455A pdb=" N ALA E 596 " --> pdb=" O ASP E 592 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL E 600 " --> pdb=" O ALA E 596 " (cutoff:3.500A) removed outlier: 3.517A 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 653 through 662 removed outlier: 4.068A pdb=" N LEU E 657 " --> pdb=" O ARG E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 679 Processing helix chain 'E' and resid 683 through 714 removed outlier: 3.778A pdb=" N LEU E 687 " --> pdb=" O SER E 683 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS E 695 " --> pdb=" O CYS E 691 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN E 714 " --> pdb=" O GLU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 742 removed outlier: 3.843A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 765 removed outlier: 3.505A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 Processing helix chain 'F' and resid 85 through 92 Processing helix chain 'F' and resid 120 through 123 removed outlier: 3.747A 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 140 Processing helix chain 'F' and resid 202 through 206 removed outlier: 3.590A pdb=" N ASP F 205 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 226 removed outlier: 4.455A 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 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 279 through 293 removed outlier: 3.984A pdb=" N GLU F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) removed outlier: 3.539A 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 312 through 316 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 374 through 385 removed outlier: 3.601A pdb=" N LEU F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 407 through 426 removed outlier: 3.737A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 431 Processing helix chain 'F' and resid 438 through 444 Processing helix chain 'F' and resid 448 through 458 Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 499 removed outlier: 4.450A 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: 4.081A 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 552 Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.589A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (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 662 Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.632A pdb=" N LEU F 675 " --> pdb=" O ASP F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 716 removed outlier: 3.766A pdb=" N ALA F 694 " --> pdb=" O ILE F 690 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS F 695 " --> pdb=" O CYS F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 741 Processing helix chain 'F' and resid 748 through 764 removed outlier: 3.851A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 246 through 247 removed outlier: 6.125A pdb=" N ILE A 114 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 246 through 247 removed outlier: 3.560A pdb=" N ILE B 114 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG B 113 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR B 168 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 141 through 142 removed outlier: 3.736A pdb=" N VAL Y 142 " --> pdb=" O PHE Y 150 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE Y 150 " --> pdb=" O VAL Y 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Y' and resid 246 through 247 removed outlier: 3.514A pdb=" N ILE C 182 " --> pdb=" O PHE Y 246 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Z' and resid 246 through 247 removed outlier: 6.779A pdb=" N ARG D 113 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR D 168 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 26 through 29 removed outlier: 6.251A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL A 39 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA8, first strand: chain 'A' and resid 267 through 270 removed outlier: 6.353A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY A 240 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N VAL A 367 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU A 242 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 542 removed outlier: 7.187A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 26 through 29 removed outlier: 6.211A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL B 39 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 26 " --> pdb=" O ILE B 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 146 removed outlier: 3.682A pdb=" N CYS B 174 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 267 through 270 removed outlier: 6.609A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE B 241 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THR B 347 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 243 " --> pdb=" O THR B 347 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY B 240 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL B 367 " --> pdb=" O GLY B 240 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU B 242 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 538 through 542 removed outlier: 7.182A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 24 through 29 removed outlier: 7.555A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N LYS C 81 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N SER C 42 " --> pdb=" O LYS C 81 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL C 39 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP C 74 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU C 41 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP C 55 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 147 Processing sheet with id=AB7, first strand: chain 'C' and resid 267 through 270 removed outlier: 6.565A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 538 through 542 removed outlier: 3.573A pdb=" N VAL C 573 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 514 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR C 623 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE C 516 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 25 through 29 removed outlier: 8.491A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 83 " --> pdb=" O SER D 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.723A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 267 through 269 removed outlier: 6.052A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY D 240 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL D 367 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU D 242 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.985A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 25 through 29 removed outlier: 8.289A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 83 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 151 through 155 removed outlier: 7.090A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE E 114 " --> pdb=" O HIS E 183 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 145 through 147 Processing sheet with id=AC7, first strand: chain 'E' and resid 267 through 269 removed outlier: 6.082A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 538 through 542 removed outlier: 7.222A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 25 through 29 removed outlier: 7.625A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N MET F 84 " --> pdb=" O ILE F 27 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP F 29 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL F 39 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 151 through 155 removed outlier: 5.516A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 167 " --> pdb=" O HIS F 115 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 145 through 147 Processing sheet with id=AD3, first strand: chain 'F' and resid 267 through 269 removed outlier: 3.677A pdb=" N PHE F 267 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE F 302 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE F 241 " --> pdb=" O ALA F 345 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N THR F 347 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU F 243 " --> pdb=" O THR F 347 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU F 242 " --> pdb=" O VAL F 367 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 538 through 542 removed outlier: 7.177A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLY F 513 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE F 643 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU F 515 " --> pdb=" O ILE F 643 " (cutoff:3.500A) 1895 hydrogen bonds defined for protein. 5475 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: 9.64 Time building geometry restraints manager: 4.55 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: 14335 1.34 - 1.46: 8651 1.46 - 1.58: 20268 1.58 - 1.70: 12 1.70 - 1.82: 380 Bond restraints: 43646 Sorted by residual: bond pdb=" CB PRO F 298 " pdb=" CG PRO F 298 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.73e+00 bond pdb=" CA GLY F 521 " pdb=" C GLY F 521 " ideal model delta sigma weight residual 1.530 1.514 0.016 1.04e-02 9.25e+03 2.48e+00 bond pdb=" N GLY F 521 " pdb=" CA GLY F 521 " ideal model delta sigma weight residual 1.464 1.448 0.017 1.12e-02 7.97e+03 2.18e+00 bond pdb=" C LYS F 543 " pdb=" N GLY F 544 " ideal model delta sigma weight residual 1.340 1.330 0.010 6.60e-03 2.30e+04 2.12e+00 bond pdb=" C ALA F 297 " pdb=" N PRO F 298 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.02e+00 ... (remaining 43641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 58346 2.51 - 5.01: 636 5.01 - 7.52: 77 7.52 - 10.02: 5 10.02 - 12.53: 2 Bond angle restraints: 59066 Sorted by residual: angle pdb=" C GLN A 337 " pdb=" CA GLN A 337 " pdb=" CB GLN A 337 " ideal model delta sigma weight residual 117.23 110.38 6.85 1.36e+00 5.41e-01 2.54e+01 angle pdb=" CB ARG F 338 " pdb=" CG ARG F 338 " pdb=" CD ARG F 338 " ideal model delta sigma weight residual 111.30 122.23 -10.93 2.30e+00 1.89e-01 2.26e+01 angle pdb=" C GLU F 194 " pdb=" N GLU F 195 " pdb=" CA GLU F 195 " ideal model delta sigma weight residual 121.54 130.16 -8.62 1.91e+00 2.74e-01 2.04e+01 angle pdb=" C GLY F 769 " pdb=" N SER F 770 " pdb=" CA SER F 770 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C GLU B 712 " pdb=" N ARG B 713 " pdb=" CA ARG B 713 " ideal model delta sigma weight residual 122.31 114.97 7.34 2.00e+00 2.50e-01 1.35e+01 ... (remaining 59061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.99: 25531 27.99 - 55.99: 1011 55.99 - 83.98: 87 83.98 - 111.98: 13 111.98 - 139.97: 3 Dihedral angle restraints: 26645 sinusoidal: 11120 harmonic: 15525 Sorted by residual: 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 -60.00 79.98 -139.97 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C2' ADP A 901 " pdb=" C1' ADP A 901 " pdb=" N9 ADP A 901 " pdb=" C4 ADP A 901 " ideal model delta sinusoidal sigma weight residual 91.55 -151.57 -116.88 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 55.18 -115.18 1 2.00e+01 2.50e-03 3.42e+01 ... (remaining 26642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 5154 0.051 - 0.102: 1090 0.102 - 0.153: 282 0.153 - 0.204: 11 0.204 - 0.255: 1 Chirality restraints: 6538 Sorted by residual: chirality pdb=" CG LEU F 335 " pdb=" CB LEU F 335 " pdb=" CD1 LEU F 335 " pdb=" CD2 LEU F 335 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PRO F 298 " pdb=" N PRO F 298 " pdb=" C PRO F 298 " pdb=" CB PRO F 298 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL X 170 " pdb=" CA VAL X 170 " pdb=" CG1 VAL X 170 " pdb=" CG2 VAL X 170 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 6535 not shown) Planarity restraints: 7734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 297 " 0.066 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO F 298 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO F 298 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO F 298 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 454 " -0.020 2.00e-02 2.50e+03 2.49e-02 1.55e+01 pdb=" CG TRP D 454 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP D 454 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP D 454 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 454 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP D 454 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 454 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 454 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 454 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D 454 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 297 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO C 298 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " -0.038 5.00e-02 4.00e+02 ... (remaining 7731 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 838 2.69 - 3.24: 42640 3.24 - 3.79: 65081 3.79 - 4.35: 80784 4.35 - 4.90: 132785 Nonbonded interactions: 322128 Sorted by model distance: nonbonded pdb=" OG SER F 748 " pdb=" OD1 ASN F 750 " model vdw 2.137 3.040 nonbonded pdb=" OG1 THR Y 202 " pdb=" OH TYR Y 207 " model vdw 2.168 3.040 nonbonded pdb=" NE1 TRP Y 7 " pdb=" OH TYR Y 80 " model vdw 2.192 3.120 nonbonded pdb=" OD1 ASP Z 193 " pdb=" NZ LYS D 109 " model vdw 2.218 3.120 nonbonded pdb=" OG1 THR B 127 " pdb=" OG1 THR B 436 " model vdw 2.227 3.040 ... (remaining 322123 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 764) selection = (chain 'B' and resid 23 through 764) selection = (chain 'C' and resid 23 through 764) selection = (chain 'D' and resid 23 through 764) selection = (chain 'E' and resid 23 through 764) selection = (chain 'F' and resid 23 through 764) } 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: 2.740 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: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 37.740 Find NCS groups from input model: 1.040 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.002 0.083 43646 Z= 0.116 Angle : 0.618 12.526 59066 Z= 0.316 Chirality : 0.044 0.255 6538 Planarity : 0.005 0.099 7734 Dihedral : 14.252 139.973 16621 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.11 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: 5365 helix: 1.10 (0.11), residues: 2406 sheet: 0.41 (0.20), residues: 669 loop : -1.32 (0.14), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 713 TYR 0.019 0.001 TYR B 244 PHE 0.017 0.001 PHE Z 185 TRP 0.062 0.001 TRP D 454 HIS 0.006 0.001 HIS F 340 Details of bonding type rmsd covalent geometry : bond 0.00241 (43646) covalent geometry : angle 0.61823 (59066) hydrogen bonds : bond 0.16789 ( 1895) hydrogen bonds : angle 5.88605 ( 5475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 1.612 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 162 PHE cc_start: 0.7426 (t80) cc_final: 0.7146 (t80) REVERT: X 83 SER cc_start: 0.8472 (t) cc_final: 0.8269 (t) REVERT: Y 81 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8283 (tm-30) REVERT: Z 34 ILE cc_start: 0.7240 (mm) cc_final: 0.6896 (mm) REVERT: Z 42 TRP cc_start: 0.7998 (t-100) cc_final: 0.7678 (t-100) REVERT: A 51 LEU cc_start: 0.7663 (mt) cc_final: 0.7236 (mp) REVERT: A 244 TYR cc_start: 0.8240 (p90) cc_final: 0.7839 (p90) REVERT: A 674 PHE cc_start: 0.8130 (t80) cc_final: 0.7343 (t80) REVERT: A 757 MET cc_start: 0.8811 (tmm) cc_final: 0.8511 (tmm) REVERT: B 561 GLU cc_start: 0.8461 (pp20) cc_final: 0.8164 (pp20) REVERT: C 84 MET cc_start: 0.7473 (tpt) cc_final: 0.6880 (tpt) REVERT: C 720 MET cc_start: 0.3953 (pmm) cc_final: 0.3562 (pmm) REVERT: D 244 TYR cc_start: 0.7520 (p90) cc_final: 0.7210 (p90) REVERT: D 313 ARG cc_start: 0.8027 (tpt170) cc_final: 0.7470 (tpt-90) REVERT: D 349 ARG cc_start: 0.7532 (ttt90) cc_final: 0.7240 (mtp85) REVERT: D 564 ASP cc_start: 0.8578 (t70) cc_final: 0.8371 (t0) REVERT: D 720 MET cc_start: 0.1267 (ttt) cc_final: 0.0819 (ppp) REVERT: F 427 MET cc_start: 0.7492 (tpp) cc_final: 0.7225 (tpp) REVERT: F 602 ASN cc_start: 0.7944 (m110) cc_final: 0.7659 (m110) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.2232 time to fit residues: 173.6213 Evaluate side-chains 355 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 1.646 ------------------------------------------------------------------------------- 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: 30.0000 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 0.7980 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 0.5980 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 105 ASN X 198 ASN D 714 GLN E 735 HIS F 115 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.102718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.076805 restraints weight = 144337.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.076117 restraints weight = 95320.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.076999 restraints weight = 74478.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078079 restraints weight = 61745.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.078123 restraints weight = 54973.242| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 43646 Z= 0.135 Angle : 0.615 13.853 59066 Z= 0.310 Chirality : 0.044 0.199 6538 Planarity : 0.005 0.100 7734 Dihedral : 5.485 122.867 5943 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.15 % Favored : 91.41 % Rotamer: Outliers : 0.78 % Allowed : 7.13 % Favored : 92.08 % 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: 0.10 (0.12), residues: 5365 helix: 1.22 (0.11), residues: 2454 sheet: 0.53 (0.20), residues: 663 loop : -1.41 (0.14), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 16 TYR 0.016 0.001 TYR Y 80 PHE 0.020 0.001 PHE A 674 TRP 0.034 0.001 TRP D 454 HIS 0.004 0.001 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00305 (43646) covalent geometry : angle 0.61486 (59066) hydrogen bonds : bond 0.04436 ( 1895) hydrogen bonds : angle 4.65144 ( 5475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 372 time to evaluate : 1.731 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: W 162 PHE cc_start: 0.7195 (t80) cc_final: 0.6912 (t80) REVERT: X 59 THR cc_start: 0.8614 (p) cc_final: 0.8312 (t) REVERT: X 116 MET cc_start: 0.8451 (mmm) cc_final: 0.7796 (tmm) REVERT: X 127 MET cc_start: 0.8566 (mmt) cc_final: 0.8335 (mmm) REVERT: Y 1 MET cc_start: 0.5296 (tpt) cc_final: 0.2812 (pmm) REVERT: Y 81 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8408 (tm-30) REVERT: Y 116 MET cc_start: 0.8476 (tmm) cc_final: 0.8091 (tmm) REVERT: Y 140 MET cc_start: 0.8050 (mtp) cc_final: 0.7840 (mtt) REVERT: Y 163 ASN cc_start: 0.8907 (t0) cc_final: 0.8701 (t0) REVERT: Z 42 TRP cc_start: 0.7961 (t-100) cc_final: 0.7492 (t-100) REVERT: Z 44 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7578 (mm-30) REVERT: Z 82 TYR cc_start: 0.8205 (m-80) cc_final: 0.7995 (m-80) REVERT: Z 99 LEU cc_start: 0.9205 (tt) cc_final: 0.8978 (tt) REVERT: Z 117 ASP cc_start: 0.8417 (t70) cc_final: 0.8058 (t0) REVERT: Z 185 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8124 (t80) REVERT: A 244 TYR cc_start: 0.8402 (p90) cc_final: 0.7866 (p90) REVERT: A 577 ASP cc_start: 0.7814 (t0) cc_final: 0.7463 (t0) REVERT: A 678 MET cc_start: 0.7098 (ptm) cc_final: 0.6730 (ptm) REVERT: A 757 MET cc_start: 0.8869 (tmm) cc_final: 0.8548 (tmm) REVERT: B 561 GLU cc_start: 0.8518 (pp20) cc_final: 0.8191 (pp20) REVERT: B 577 ASP cc_start: 0.7900 (t0) cc_final: 0.7697 (t0) REVERT: C 278 LEU cc_start: 0.7563 (tp) cc_final: 0.7359 (tt) REVERT: C 682 PHE cc_start: 0.7843 (m-10) cc_final: 0.7275 (m-80) REVERT: C 720 MET cc_start: 0.3870 (pmm) cc_final: 0.3491 (pmm) REVERT: D 109 LYS cc_start: 0.7589 (tptt) cc_final: 0.7377 (tptt) REVERT: D 244 TYR cc_start: 0.7509 (p90) cc_final: 0.7186 (p90) REVERT: D 349 ARG cc_start: 0.7518 (ttt90) cc_final: 0.7296 (mtp85) REVERT: D 564 ASP cc_start: 0.8601 (t70) cc_final: 0.8379 (t0) REVERT: D 720 MET cc_start: 0.1727 (ttt) cc_final: 0.0498 (ppp) REVERT: E 173 TYR cc_start: 0.7877 (p90) cc_final: 0.7141 (p90) REVERT: F 602 ASN cc_start: 0.8024 (m110) cc_final: 0.7797 (m110) outliers start: 36 outliers final: 22 residues processed: 391 average time/residue: 0.2222 time to fit residues: 150.0114 Evaluate side-chains 368 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 345 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Y residue 174 LEU Chi-restraints excluded: chain Y residue 192 MET Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 185 PHE Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain D residue 469 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 386 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 447 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 359 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 330 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 454 optimal weight: 8.9990 chunk 352 optimal weight: 9.9990 chunk 438 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN B 692 GLN F 735 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.102657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.076602 restraints weight = 143216.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.076107 restraints weight = 93996.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.076985 restraints weight = 72949.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.078115 restraints weight = 60868.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.078135 restraints weight = 53383.733| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 43646 Z= 0.118 Angle : 0.588 14.505 59066 Z= 0.292 Chirality : 0.044 0.199 6538 Planarity : 0.004 0.099 7734 Dihedral : 5.409 118.074 5943 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.79 % Favored : 91.76 % Rotamer: Outliers : 1.20 % Allowed : 9.31 % Favored : 89.50 % 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: 0.18 (0.12), residues: 5365 helix: 1.35 (0.11), residues: 2447 sheet: 0.48 (0.20), residues: 683 loop : -1.41 (0.14), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 16 TYR 0.020 0.001 TYR C 110 PHE 0.025 0.001 PHE A 674 TRP 0.024 0.001 TRP D 454 HIS 0.003 0.001 HIS E 404 Details of bonding type rmsd covalent geometry : bond 0.00264 (43646) covalent geometry : angle 0.58757 (59066) hydrogen bonds : bond 0.03804 ( 1895) hydrogen bonds : angle 4.37664 ( 5475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 375 time to evaluate : 1.668 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 162 PHE cc_start: 0.7237 (t80) cc_final: 0.7016 (t80) REVERT: X 59 THR cc_start: 0.8603 (p) cc_final: 0.8293 (t) REVERT: X 116 MET cc_start: 0.8462 (mmm) cc_final: 0.7767 (tmm) REVERT: Y 1 MET cc_start: 0.5708 (tpt) cc_final: 0.2842 (pmm) REVERT: Y 81 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8372 (tm-30) REVERT: Y 116 MET cc_start: 0.8346 (tmm) cc_final: 0.7928 (tmm) REVERT: Y 163 ASN cc_start: 0.8911 (t0) cc_final: 0.8638 (t0) REVERT: Z 42 TRP cc_start: 0.8009 (t-100) cc_final: 0.7527 (t-100) REVERT: Z 82 TYR cc_start: 0.8214 (m-80) cc_final: 0.8002 (m-80) REVERT: Z 99 LEU cc_start: 0.9249 (tt) cc_final: 0.9005 (tt) REVERT: Z 185 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8307 (t80) REVERT: Z 192 MET cc_start: 0.8426 (ttm) cc_final: 0.8092 (ttm) REVERT: A 244 TYR cc_start: 0.8373 (p90) cc_final: 0.7820 (p90) REVERT: A 458 GLN cc_start: 0.8800 (pp30) cc_final: 0.8168 (pp30) REVERT: A 577 ASP cc_start: 0.7809 (t0) cc_final: 0.7459 (t0) REVERT: A 757 MET cc_start: 0.8879 (tmm) cc_final: 0.8559 (tmm) REVERT: B 577 ASP cc_start: 0.7983 (t0) cc_final: 0.7741 (t0) REVERT: C 608 MET cc_start: 0.8900 (ttt) cc_final: 0.8692 (ttm) REVERT: C 678 MET cc_start: 0.7397 (mpp) cc_final: 0.7175 (mpp) REVERT: C 682 PHE cc_start: 0.7741 (m-10) cc_final: 0.7160 (m-80) REVERT: C 720 MET cc_start: 0.3853 (pmm) cc_final: 0.3480 (pmm) REVERT: D 198 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8691 (pp) REVERT: D 244 TYR cc_start: 0.7531 (p90) cc_final: 0.7169 (p90) REVERT: D 304 ASP cc_start: 0.8908 (t0) cc_final: 0.8368 (p0) REVERT: D 353 ILE cc_start: 0.9239 (mm) cc_final: 0.8966 (tp) REVERT: D 427 MET cc_start: 0.8512 (mmm) cc_final: 0.7739 (tpp) REVERT: D 564 ASP cc_start: 0.8616 (t70) cc_final: 0.8369 (t0) REVERT: D 720 MET cc_start: 0.1620 (ttt) cc_final: 0.0592 (ppp) REVERT: E 173 TYR cc_start: 0.7931 (p90) cc_final: 0.7211 (p90) REVERT: F 602 ASN cc_start: 0.8008 (m110) cc_final: 0.7778 (m110) REVERT: F 740 MET cc_start: 0.8559 (tmm) cc_final: 0.8014 (tmm) outliers start: 55 outliers final: 36 residues processed: 406 average time/residue: 0.2174 time to fit residues: 153.4652 Evaluate side-chains 382 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 344 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 174 LEU Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 185 PHE Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain C residue 52 PHE Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 383 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 279 optimal weight: 0.0570 chunk 57 optimal weight: 9.9990 chunk 463 optimal weight: 9.9990 chunk 483 optimal weight: 4.9990 chunk 361 optimal weight: 4.9990 chunk 460 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 371 optimal weight: 0.0060 chunk 285 optimal weight: 0.0670 overall best weight: 0.2652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.103786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.077433 restraints weight = 142940.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.077297 restraints weight = 89363.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.078187 restraints weight = 69845.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.079167 restraints weight = 58956.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.079168 restraints weight = 52614.654| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 43646 Z= 0.104 Angle : 0.589 15.915 59066 Z= 0.288 Chirality : 0.043 0.203 6538 Planarity : 0.004 0.095 7734 Dihedral : 5.300 116.339 5943 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.42 % Favored : 92.15 % Rotamer: Outliers : 1.17 % Allowed : 11.68 % Favored : 87.15 % 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: 0.28 (0.12), residues: 5365 helix: 1.44 (0.11), residues: 2450 sheet: 0.45 (0.20), residues: 697 loop : -1.38 (0.14), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 338 TYR 0.015 0.001 TYR Y 80 PHE 0.016 0.001 PHE A 674 TRP 0.034 0.001 TRP C 454 HIS 0.004 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00223 (43646) covalent geometry : angle 0.58880 (59066) hydrogen bonds : bond 0.03182 ( 1895) hydrogen bonds : angle 4.15035 ( 5475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 386 time to evaluate : 1.648 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: X 59 THR cc_start: 0.8525 (p) cc_final: 0.8213 (t) REVERT: X 83 SER cc_start: 0.8508 (t) cc_final: 0.8267 (t) REVERT: X 116 MET cc_start: 0.8399 (mmm) cc_final: 0.7958 (tmm) REVERT: X 160 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7502 (tp) REVERT: Y 1 MET cc_start: 0.5507 (tpt) cc_final: 0.2786 (pmm) REVERT: Y 81 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8422 (tm-30) REVERT: Y 116 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7922 (tmm) REVERT: Y 118 MET cc_start: 0.7898 (ptp) cc_final: 0.7482 (ptt) REVERT: Y 163 ASN cc_start: 0.8861 (t0) cc_final: 0.8537 (t0) REVERT: Z 42 TRP cc_start: 0.7989 (t-100) cc_final: 0.7478 (t-100) REVERT: Z 82 TYR cc_start: 0.8207 (m-80) cc_final: 0.7966 (m-80) REVERT: Z 99 LEU cc_start: 0.9230 (tt) cc_final: 0.8977 (tt) REVERT: Z 192 MET cc_start: 0.8369 (ttm) cc_final: 0.8028 (ttm) REVERT: A 244 TYR cc_start: 0.8331 (p90) cc_final: 0.7766 (p90) REVERT: A 458 GLN cc_start: 0.8704 (pp30) cc_final: 0.8037 (pp30) REVERT: A 577 ASP cc_start: 0.7712 (t0) cc_final: 0.7383 (t0) REVERT: A 757 MET cc_start: 0.8882 (tmm) cc_final: 0.8569 (tmm) REVERT: B 577 ASP cc_start: 0.7984 (t0) cc_final: 0.7732 (t0) REVERT: C 278 LEU cc_start: 0.7301 (tp) cc_final: 0.7042 (tt) REVERT: C 678 MET cc_start: 0.7412 (mpp) cc_final: 0.7117 (mpp) REVERT: C 682 PHE cc_start: 0.7579 (m-10) cc_final: 0.7049 (m-80) REVERT: C 720 MET cc_start: 0.3984 (pmm) cc_final: 0.3544 (pmm) REVERT: D 198 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8656 (pp) REVERT: D 244 TYR cc_start: 0.7458 (p90) cc_final: 0.7125 (p90) REVERT: D 304 ASP cc_start: 0.8933 (t0) cc_final: 0.8401 (p0) REVERT: D 353 ILE cc_start: 0.9187 (mm) cc_final: 0.8929 (tp) REVERT: D 427 MET cc_start: 0.8495 (mmm) cc_final: 0.7710 (tpp) REVERT: D 564 ASP cc_start: 0.8573 (t70) cc_final: 0.8344 (t0) REVERT: D 720 MET cc_start: 0.1252 (ttt) cc_final: 0.0280 (ppp) REVERT: D 757 MET cc_start: 0.8394 (ppp) cc_final: 0.8107 (ppp) REVERT: E 173 TYR cc_start: 0.7808 (p90) cc_final: 0.7206 (p90) REVERT: E 432 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8069 (mp) REVERT: F 602 ASN cc_start: 0.7876 (m110) cc_final: 0.7604 (m110) REVERT: F 740 MET cc_start: 0.8553 (tmm) cc_final: 0.8018 (tmm) outliers start: 54 outliers final: 34 residues processed: 419 average time/residue: 0.2152 time to fit residues: 156.2720 Evaluate side-chains 383 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 345 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain X residue 160 LEU Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Y residue 116 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 561 GLU Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 330 optimal weight: 0.7980 chunk 321 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 426 optimal weight: 5.9990 chunk 357 optimal weight: 8.9990 chunk 387 optimal weight: 40.0000 chunk 283 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 51 GLN A 538 ASN A 735 HIS ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 538 ASN F 538 ASN F 750 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.105177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.076010 restraints weight = 133387.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078969 restraints weight = 79055.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079976 restraints weight = 55233.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080689 restraints weight = 43166.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.080899 restraints weight = 38684.658| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 43646 Z= 0.184 Angle : 0.635 16.210 59066 Z= 0.316 Chirality : 0.045 0.199 6538 Planarity : 0.005 0.101 7734 Dihedral : 5.373 121.262 5943 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.28 % Favored : 91.31 % Rotamer: Outliers : 1.59 % Allowed : 13.35 % Favored : 85.06 % 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: 0.20 (0.12), residues: 5365 helix: 1.39 (0.11), residues: 2455 sheet: 0.35 (0.20), residues: 692 loop : -1.40 (0.14), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 753 TYR 0.016 0.001 TYR A 134 PHE 0.035 0.002 PHE Y 8 TRP 0.045 0.002 TRP C 454 HIS 0.003 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00425 (43646) covalent geometry : angle 0.63518 (59066) hydrogen bonds : bond 0.03969 ( 1895) hydrogen bonds : angle 4.31930 ( 5475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 339 time to evaluate : 1.527 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: X 59 THR cc_start: 0.8551 (p) cc_final: 0.8252 (t) REVERT: X 116 MET cc_start: 0.8320 (mmm) cc_final: 0.7798 (tmm) REVERT: X 173 GLU cc_start: 0.7636 (pp20) cc_final: 0.6952 (pp20) REVERT: Y 1 MET cc_start: 0.5608 (tpt) cc_final: 0.2497 (pmm) REVERT: Y 116 MET cc_start: 0.8381 (tmm) cc_final: 0.8027 (tmm) REVERT: Y 118 MET cc_start: 0.8425 (ptp) cc_final: 0.7866 (ptp) REVERT: Y 163 ASN cc_start: 0.8839 (t0) cc_final: 0.8565 (t0) REVERT: Y 192 MET cc_start: 0.8044 (ptt) cc_final: 0.7440 (ptt) REVERT: Z 42 TRP cc_start: 0.7635 (t-100) cc_final: 0.7211 (t-100) REVERT: Z 82 TYR cc_start: 0.8158 (m-80) cc_final: 0.7930 (m-80) REVERT: A 244 TYR cc_start: 0.8356 (p90) cc_final: 0.7998 (p90) REVERT: A 296 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8124 (t0) REVERT: A 458 GLN cc_start: 0.8713 (pp30) cc_final: 0.7987 (pp30) REVERT: A 577 ASP cc_start: 0.7630 (t0) cc_final: 0.7343 (t0) REVERT: A 757 MET cc_start: 0.8622 (tmm) cc_final: 0.8291 (tmm) REVERT: B 120 ASP cc_start: 0.7823 (t0) cc_final: 0.7580 (t0) REVERT: B 577 ASP cc_start: 0.7955 (t0) cc_final: 0.7692 (t0) REVERT: C 278 LEU cc_start: 0.7569 (tp) cc_final: 0.7310 (tt) REVERT: C 338 ARG cc_start: 0.7054 (mmp80) cc_final: 0.6847 (mmp80) REVERT: C 682 PHE cc_start: 0.7781 (m-10) cc_final: 0.7221 (m-80) REVERT: C 720 MET cc_start: 0.3959 (pmm) cc_final: 0.3490 (pmm) REVERT: D 46 MET cc_start: 0.8558 (mpp) cc_final: 0.8046 (mpp) REVERT: D 198 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8550 (pp) REVERT: D 244 TYR cc_start: 0.7544 (p90) cc_final: 0.7103 (p90) REVERT: D 321 GLU cc_start: 0.7742 (mp0) cc_final: 0.7486 (mp0) REVERT: D 353 ILE cc_start: 0.9253 (mm) cc_final: 0.9006 (tp) REVERT: D 427 MET cc_start: 0.8608 (mmm) cc_final: 0.7707 (tpp) REVERT: D 720 MET cc_start: 0.1547 (ttt) cc_final: 0.0202 (ppp) REVERT: E 173 TYR cc_start: 0.7771 (p90) cc_final: 0.7553 (p90) REVERT: E 432 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8228 (mp) outliers start: 73 outliers final: 47 residues processed: 388 average time/residue: 0.2240 time to fit residues: 150.8372 Evaluate side-chains 384 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 334 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 88 THR Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 182 LEU Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 471 optimal weight: 50.0000 chunk 404 optimal weight: 3.9990 chunk 325 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 423 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 439 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.104601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.079624 restraints weight = 134102.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.079152 restraints weight = 84779.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.080204 restraints weight = 70889.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.079814 restraints weight = 63205.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.080221 restraints weight = 55638.805| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 43646 Z= 0.189 Angle : 0.641 16.627 59066 Z= 0.320 Chirality : 0.045 0.191 6538 Planarity : 0.005 0.103 7734 Dihedral : 5.490 122.531 5943 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.45 % Allowed : 8.44 % Favored : 91.11 % Rotamer: Outliers : 1.81 % Allowed : 13.96 % Favored : 84.23 % 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: 0.09 (0.12), residues: 5365 helix: 1.31 (0.11), residues: 2451 sheet: 0.22 (0.20), residues: 703 loop : -1.45 (0.14), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 711 TYR 0.025 0.001 TYR Y 82 PHE 0.030 0.001 PHE Y 8 TRP 0.029 0.002 TRP C 454 HIS 0.004 0.001 HIS C 340 Details of bonding type rmsd covalent geometry : bond 0.00436 (43646) covalent geometry : angle 0.64132 (59066) hydrogen bonds : bond 0.03986 ( 1895) hydrogen bonds : angle 4.37456 ( 5475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 334 time to evaluate : 1.437 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: X 59 THR cc_start: 0.8623 (p) cc_final: 0.8342 (t) REVERT: X 116 MET cc_start: 0.8228 (mmm) cc_final: 0.7667 (tmm) REVERT: Y 1 MET cc_start: 0.5897 (tpt) cc_final: 0.2782 (pmm) REVERT: Y 116 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8056 (tmm) REVERT: Y 118 MET cc_start: 0.8622 (ptp) cc_final: 0.7874 (ptt) REVERT: Y 163 ASN cc_start: 0.8932 (t0) cc_final: 0.8681 (t0) REVERT: Y 192 MET cc_start: 0.8134 (ptt) cc_final: 0.7739 (ptt) REVERT: Z 42 TRP cc_start: 0.8019 (t-100) cc_final: 0.7324 (t-100) REVERT: A 244 TYR cc_start: 0.8272 (p90) cc_final: 0.8019 (p90) REVERT: A 577 ASP cc_start: 0.7721 (t0) cc_final: 0.7447 (t0) REVERT: A 647 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7309 (pp) REVERT: A 757 MET cc_start: 0.8780 (tmm) cc_final: 0.8439 (tmm) REVERT: B 120 ASP cc_start: 0.7922 (t0) cc_final: 0.7626 (t0) REVERT: B 577 ASP cc_start: 0.7953 (t0) cc_final: 0.7669 (t0) REVERT: C 720 MET cc_start: 0.4022 (pmm) cc_final: 0.3584 (pmm) REVERT: D 46 MET cc_start: 0.8589 (mpp) cc_final: 0.8001 (mpp) REVERT: D 198 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8689 (pp) REVERT: D 253 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8701 (tt) REVERT: D 304 ASP cc_start: 0.8770 (t0) cc_final: 0.8476 (p0) REVERT: D 321 GLU cc_start: 0.7869 (mp0) cc_final: 0.7585 (mp0) REVERT: D 427 MET cc_start: 0.8477 (mmm) cc_final: 0.7678 (tpp) REVERT: D 720 MET cc_start: 0.1319 (ttt) cc_final: 0.0217 (ppp) REVERT: E 432 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8107 (mp) REVERT: F 244 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.7574 (p90) outliers start: 83 outliers final: 58 residues processed: 388 average time/residue: 0.2260 time to fit residues: 151.7744 Evaluate side-chains 391 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 327 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 88 THR Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 79 LEU Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Y residue 116 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 207 TYR Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 211 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 351 optimal weight: 8.9990 chunk 392 optimal weight: 50.0000 chunk 322 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 358 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 480 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 177 ASN Z 198 ASN ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.102890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.073833 restraints weight = 133525.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.076815 restraints weight = 79788.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.077679 restraints weight = 55716.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.078170 restraints weight = 43961.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.078191 restraints weight = 40250.085| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 43646 Z= 0.260 Angle : 0.721 17.210 59066 Z= 0.362 Chirality : 0.047 0.181 6538 Planarity : 0.005 0.109 7734 Dihedral : 5.724 126.064 5943 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.17 % Favored : 90.38 % Rotamer: Outliers : 1.98 % Allowed : 14.79 % Favored : 83.23 % 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: -0.22 (0.12), residues: 5365 helix: 1.03 (0.11), residues: 2453 sheet: 0.07 (0.19), residues: 705 loop : -1.59 (0.14), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 711 TYR 0.032 0.002 TYR D 244 PHE 0.034 0.002 PHE A 674 TRP 0.032 0.002 TRP D 454 HIS 0.005 0.001 HIS X 240 Details of bonding type rmsd covalent geometry : bond 0.00597 (43646) covalent geometry : angle 0.72107 (59066) hydrogen bonds : bond 0.04733 ( 1895) hydrogen bonds : angle 4.65343 ( 5475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 313 time to evaluate : 1.535 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: X 59 THR cc_start: 0.8741 (p) cc_final: 0.8491 (t) REVERT: X 116 MET cc_start: 0.8223 (mmm) cc_final: 0.7715 (tmm) REVERT: X 130 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9196 (tt) REVERT: X 173 GLU cc_start: 0.7843 (pp20) cc_final: 0.7217 (pp20) REVERT: Y 116 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8085 (tmm) REVERT: Y 118 MET cc_start: 0.8694 (ptp) cc_final: 0.8033 (ptm) REVERT: Y 163 ASN cc_start: 0.8888 (t0) cc_final: 0.8672 (t0) REVERT: Y 192 MET cc_start: 0.8162 (ptt) cc_final: 0.7859 (ptt) REVERT: Y 207 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: Z 82 TYR cc_start: 0.8271 (m-80) cc_final: 0.7756 (m-10) REVERT: A 577 ASP cc_start: 0.7777 (t0) cc_final: 0.7513 (t0) REVERT: A 647 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7375 (pp) REVERT: A 757 MET cc_start: 0.8609 (tmm) cc_final: 0.8231 (tmm) REVERT: B 120 ASP cc_start: 0.7910 (t0) cc_final: 0.7577 (t0) REVERT: B 577 ASP cc_start: 0.8132 (t0) cc_final: 0.7884 (t0) REVERT: C 720 MET cc_start: 0.4205 (pmm) cc_final: 0.3740 (pmm) REVERT: D 46 MET cc_start: 0.8596 (mpp) cc_final: 0.8168 (mpp) REVERT: D 198 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8568 (pp) REVERT: D 253 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8832 (tt) REVERT: D 304 ASP cc_start: 0.8676 (t0) cc_final: 0.8430 (p0) REVERT: D 427 MET cc_start: 0.8662 (mmm) cc_final: 0.7752 (tpp) REVERT: D 720 MET cc_start: 0.1032 (ttt) cc_final: 0.0301 (ppp) REVERT: E 244 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7817 (p90) REVERT: E 432 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8200 (mp) REVERT: F 84 MET cc_start: 0.2906 (tmm) cc_final: 0.2249 (tmm) REVERT: F 244 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7416 (p90) outliers start: 91 outliers final: 67 residues processed: 379 average time/residue: 0.2139 time to fit residues: 142.9949 Evaluate side-chains 384 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 308 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 23 VAL Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 103 LEU Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 88 THR Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 107 ILE Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 130 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Y residue 116 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 207 TYR Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 394 VAL 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 647 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 344 MET Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 629 ILE Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 344 MET Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain F residue 244 TYR Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 639 LEU Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 47 optimal weight: 0.2980 chunk 241 optimal weight: 4.9990 chunk 450 optimal weight: 2.9990 chunk 236 optimal weight: 10.0000 chunk 415 optimal weight: 4.9990 chunk 321 optimal weight: 0.7980 chunk 472 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 489 optimal weight: 1.9990 chunk 423 optimal weight: 1.9990 chunk 338 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 296 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.105629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.076703 restraints weight = 132985.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.079378 restraints weight = 77801.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.080397 restraints weight = 55202.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.081202 restraints weight = 43228.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.081592 restraints weight = 38427.126| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 43646 Z= 0.113 Angle : 0.631 18.509 59066 Z= 0.312 Chirality : 0.044 0.198 6538 Planarity : 0.004 0.100 7734 Dihedral : 5.488 120.755 5943 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.64 % Favored : 91.97 % Rotamer: Outliers : 1.35 % Allowed : 16.12 % Favored : 82.54 % 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: 0.07 (0.12), residues: 5365 helix: 1.34 (0.11), residues: 2446 sheet: 0.13 (0.19), residues: 730 loop : -1.50 (0.14), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 349 TYR 0.030 0.001 TYR A 244 PHE 0.038 0.001 PHE A 674 TRP 0.046 0.001 TRP D 454 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00251 (43646) covalent geometry : angle 0.63114 (59066) hydrogen bonds : bond 0.03403 ( 1895) hydrogen bonds : angle 4.21564 ( 5475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 344 time to evaluate : 1.654 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: X 59 THR cc_start: 0.8483 (p) cc_final: 0.8166 (t) REVERT: X 116 MET cc_start: 0.8066 (mmm) cc_final: 0.7581 (tmm) REVERT: X 127 MET cc_start: 0.8234 (mmm) cc_final: 0.7719 (mmm) REVERT: Y 1 MET cc_start: 0.5689 (tpt) cc_final: 0.2403 (pmm) REVERT: Y 116 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8168 (tmm) REVERT: Y 118 MET cc_start: 0.8497 (ptp) cc_final: 0.7917 (ptt) REVERT: Y 140 MET cc_start: 0.7223 (mpp) cc_final: 0.6933 (mpp) REVERT: Y 192 MET cc_start: 0.8336 (ptt) cc_final: 0.8030 (ptt) REVERT: Z 192 MET cc_start: 0.8346 (ttm) cc_final: 0.8000 (ttm) REVERT: A 244 TYR cc_start: 0.7999 (p90) cc_final: 0.7677 (p90) REVERT: A 577 ASP cc_start: 0.7537 (t0) cc_final: 0.7301 (t0) REVERT: A 757 MET cc_start: 0.8557 (tmm) cc_final: 0.8313 (tmm) REVERT: B 120 ASP cc_start: 0.7652 (t0) cc_final: 0.7352 (t0) REVERT: B 577 ASP cc_start: 0.7967 (t0) cc_final: 0.7735 (t0) REVERT: C 84 MET cc_start: 0.6818 (tpt) cc_final: 0.6413 (tpt) REVERT: C 720 MET cc_start: 0.4223 (pmm) cc_final: 0.3760 (pmm) REVERT: D 46 MET cc_start: 0.8457 (mpp) cc_final: 0.8204 (mpp) REVERT: D 189 ILE cc_start: 0.9043 (tp) cc_final: 0.8689 (tt) REVERT: D 198 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8325 (pp) REVERT: D 253 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8536 (tt) REVERT: D 427 MET cc_start: 0.8655 (mmm) cc_final: 0.7718 (tpp) REVERT: D 508 MET cc_start: 0.8214 (tpt) cc_final: 0.7905 (tpt) REVERT: D 720 MET cc_start: 0.0568 (ttt) cc_final: 0.0004 (ppp) REVERT: E 432 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8188 (mp) REVERT: F 84 MET cc_start: 0.2831 (tmm) cc_final: 0.2366 (tmm) REVERT: F 720 MET cc_start: -0.2313 (ptm) cc_final: -0.2566 (ptp) outliers start: 62 outliers final: 46 residues processed: 393 average time/residue: 0.2284 time to fit residues: 155.9788 Evaluate side-chains 374 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 324 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 101 MET Chi-restraints excluded: chain Y residue 116 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 207 TYR Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain A residue 296 ASN 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 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 116 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 504 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 531 optimal weight: 20.0000 chunk 401 optimal weight: 8.9990 chunk 389 optimal weight: 6.9990 chunk 355 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 206 optimal weight: 0.2980 chunk 506 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 240 HIS A 296 ASN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.105135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079563 restraints weight = 136531.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.079530 restraints weight = 84397.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.080161 restraints weight = 67767.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.081336 restraints weight = 56740.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.081243 restraints weight = 50368.849| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 43646 Z= 0.116 Angle : 0.635 18.790 59066 Z= 0.312 Chirality : 0.044 0.251 6538 Planarity : 0.004 0.098 7734 Dihedral : 5.409 120.558 5943 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.79 % Favored : 91.84 % Rotamer: Outliers : 1.28 % Allowed : 16.38 % Favored : 82.34 % 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: 0.14 (0.12), residues: 5365 helix: 1.38 (0.11), residues: 2452 sheet: 0.14 (0.19), residues: 739 loop : -1.46 (0.14), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 349 TYR 0.027 0.001 TYR A 244 PHE 0.037 0.001 PHE A 674 TRP 0.052 0.001 TRP D 454 HIS 0.003 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00264 (43646) covalent geometry : angle 0.63522 (59066) hydrogen bonds : bond 0.03324 ( 1895) hydrogen bonds : angle 4.17371 ( 5475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 329 time to evaluate : 1.652 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: X 59 THR cc_start: 0.8594 (p) cc_final: 0.8299 (t) REVERT: X 116 MET cc_start: 0.8123 (mmm) cc_final: 0.7611 (tmm) REVERT: X 127 MET cc_start: 0.8276 (mmm) cc_final: 0.7780 (mmm) REVERT: Y 1 MET cc_start: 0.5948 (tpt) cc_final: 0.2732 (pmm) REVERT: Y 116 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8179 (tmm) REVERT: Y 118 MET cc_start: 0.8577 (ptp) cc_final: 0.8089 (ptm) REVERT: Y 192 MET cc_start: 0.8288 (ptt) cc_final: 0.8019 (ptt) REVERT: A 244 TYR cc_start: 0.8105 (p90) cc_final: 0.7792 (p90) REVERT: A 577 ASP cc_start: 0.7611 (t0) cc_final: 0.7348 (t0) REVERT: A 757 MET cc_start: 0.8782 (tmm) cc_final: 0.8464 (tmm) REVERT: B 120 ASP cc_start: 0.7828 (t0) cc_final: 0.7475 (t0) REVERT: B 577 ASP cc_start: 0.7942 (t0) cc_final: 0.7713 (t0) REVERT: C 720 MET cc_start: 0.4135 (pmm) cc_final: 0.3675 (pmm) REVERT: D 189 ILE cc_start: 0.9059 (tp) cc_final: 0.8713 (tt) REVERT: D 198 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8626 (pp) REVERT: D 253 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8561 (tt) REVERT: D 427 MET cc_start: 0.8547 (mmm) cc_final: 0.7702 (tpp) REVERT: D 508 MET cc_start: 0.8256 (tpt) cc_final: 0.7933 (tpt) REVERT: D 720 MET cc_start: 0.0754 (ttt) cc_final: 0.0060 (ppp) REVERT: E 432 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8060 (mp) REVERT: F 84 MET cc_start: 0.3117 (tmm) cc_final: 0.2506 (tmm) REVERT: F 195 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5857 (mp0) REVERT: F 508 MET cc_start: 0.7242 (tmm) cc_final: 0.7041 (tmm) outliers start: 59 outliers final: 50 residues processed: 371 average time/residue: 0.2174 time to fit residues: 141.8672 Evaluate side-chains 378 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 323 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 103 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain X residue 160 LEU Chi-restraints excluded: chain Y residue 116 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 207 TYR Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 202 THR Chi-restraints excluded: chain A residue 296 ASN 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 670 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 209 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 345 optimal weight: 0.9990 chunk 432 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 334 optimal weight: 0.4980 chunk 232 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 240 HIS ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.104716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079193 restraints weight = 138155.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.079091 restraints weight = 83830.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.079891 restraints weight = 64212.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.081296 restraints weight = 52789.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.081297 restraints weight = 45129.457| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 43646 Z= 0.110 Angle : 0.637 18.915 59066 Z= 0.310 Chirality : 0.044 0.246 6538 Planarity : 0.004 0.095 7734 Dihedral : 5.336 119.465 5943 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.87 % Favored : 91.80 % Rotamer: Outliers : 1.20 % Allowed : 16.55 % Favored : 82.25 % 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: 0.21 (0.12), residues: 5365 helix: 1.43 (0.11), residues: 2452 sheet: 0.18 (0.19), residues: 740 loop : -1.41 (0.14), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 349 TYR 0.025 0.001 TYR A 244 PHE 0.035 0.001 PHE A 674 TRP 0.038 0.001 TRP D 454 HIS 0.002 0.001 HIS A 183 Details of bonding type rmsd covalent geometry : bond 0.00249 (43646) covalent geometry : angle 0.63654 (59066) hydrogen bonds : bond 0.03127 ( 1895) hydrogen bonds : angle 4.10597 ( 5475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 336 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 192 MET cc_start: 0.6834 (ppp) cc_final: 0.6293 (ppp) REVERT: X 59 THR cc_start: 0.8527 (p) cc_final: 0.8198 (t) REVERT: X 116 MET cc_start: 0.8094 (mmm) cc_final: 0.7593 (tmm) REVERT: X 127 MET cc_start: 0.8286 (mmm) cc_final: 0.7791 (mmm) REVERT: X 173 GLU cc_start: 0.7452 (pp20) cc_final: 0.6804 (pp20) REVERT: Y 1 MET cc_start: 0.5865 (tpt) cc_final: 0.2467 (pmm) REVERT: Y 116 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8190 (tmm) REVERT: Y 118 MET cc_start: 0.8521 (ptp) cc_final: 0.8024 (ptm) REVERT: Y 192 MET cc_start: 0.8302 (ptt) cc_final: 0.8050 (ptt) REVERT: A 244 TYR cc_start: 0.8131 (p90) cc_final: 0.7829 (p90) REVERT: A 577 ASP cc_start: 0.7596 (t0) cc_final: 0.7335 (t0) REVERT: A 757 MET cc_start: 0.8750 (tmm) cc_final: 0.8428 (tmm) REVERT: B 120 ASP cc_start: 0.7836 (t0) cc_final: 0.7494 (t0) REVERT: B 577 ASP cc_start: 0.7908 (t0) cc_final: 0.7671 (t0) REVERT: C 84 MET cc_start: 0.6790 (tpt) cc_final: 0.6394 (tpt) REVERT: C 110 TYR cc_start: 0.7809 (OUTLIER) cc_final: 0.7568 (t80) REVERT: C 720 MET cc_start: 0.4082 (pmm) cc_final: 0.3619 (pmm) REVERT: C 757 MET cc_start: 0.8323 (pmm) cc_final: 0.7911 (pmm) REVERT: D 189 ILE cc_start: 0.9064 (tp) cc_final: 0.8731 (tt) REVERT: D 198 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8585 (pp) REVERT: D 427 MET cc_start: 0.8543 (mmm) cc_final: 0.7705 (tpp) REVERT: D 508 MET cc_start: 0.8223 (tpt) cc_final: 0.7908 (tpt) REVERT: E 432 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8075 (mp) REVERT: F 84 MET cc_start: 0.3548 (tmm) cc_final: 0.2998 (tmm) REVERT: F 195 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5829 (mp0) REVERT: F 602 ASN cc_start: 0.7976 (m110) cc_final: 0.7740 (m110) outliers start: 55 outliers final: 44 residues processed: 376 average time/residue: 0.2265 time to fit residues: 148.5419 Evaluate side-chains 377 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 328 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 120 LEU Chi-restraints excluded: chain W residue 182 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 78 PHE Chi-restraints excluded: chain X residue 99 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain Y residue 116 MET Chi-restraints excluded: chain Y residue 155 LEU Chi-restraints excluded: chain Y residue 207 TYR Chi-restraints excluded: chain Z residue 79 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 202 THR 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 670 VAL Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 317 HIS Chi-restraints excluded: chain B residue 404 HIS Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 551 TRP Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 464 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain D residue 244 TYR Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 152 PHE Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 383 ILE Chi-restraints excluded: chain E residue 432 LEU Chi-restraints excluded: chain E residue 469 VAL Chi-restraints excluded: chain F residue 195 GLU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 737 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 198 optimal weight: 1.9990 chunk 314 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 321 optimal weight: 2.9990 chunk 531 optimal weight: 7.9990 chunk 506 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 517 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 405 optimal weight: 3.9990 chunk 287 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 240 HIS ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.105346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080043 restraints weight = 136661.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.080146 restraints weight = 83655.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.080966 restraints weight = 69035.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.080831 restraints weight = 63639.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.081173 restraints weight = 55715.461| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 43646 Z= 0.119 Angle : 0.637 18.936 59066 Z= 0.311 Chirality : 0.044 0.250 6538 Planarity : 0.004 0.094 7734 Dihedral : 5.309 119.804 5943 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.09 % Favored : 91.59 % Rotamer: Outliers : 1.30 % Allowed : 16.59 % Favored : 82.10 % 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: 0.22 (0.12), residues: 5365 helix: 1.44 (0.11), residues: 2456 sheet: 0.23 (0.19), residues: 732 loop : -1.42 (0.14), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 349 TYR 0.022 0.001 TYR A 244 PHE 0.033 0.001 PHE A 674 TRP 0.034 0.001 TRP D 454 HIS 0.003 0.001 HIS C 735 Details of bonding type rmsd covalent geometry : bond 0.00275 (43646) covalent geometry : angle 0.63731 (59066) hydrogen bonds : bond 0.03221 ( 1895) hydrogen bonds : angle 4.13270 ( 5475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6657.51 seconds wall clock time: 116 minutes 13.49 seconds (6973.49 seconds total)