Starting phenix.real_space_refine on Wed May 21 18:36:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c39_45162/05_2025/9c39_45162.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c39_45162/05_2025/9c39_45162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c39_45162/05_2025/9c39_45162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c39_45162/05_2025/9c39_45162.map" model { file = "/net/cci-nas-00/data/ceres_data/9c39_45162/05_2025/9c39_45162.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c39_45162/05_2025/9c39_45162.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= -0.001 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 14031 2.51 5 N 3735 2.21 5 O 4270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22110 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3202 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3175 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 123 Chain: "C" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1018 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1011 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 124} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 127} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1525 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 184} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1087 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 134} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 3212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3212 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 14, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 99 Chain: "I" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1153 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 3, 'TRANS': 152} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 45 Chain: "J" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1016 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "K" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 797 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 782 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 789 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "O" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 770 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 748 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 16.46, per 1000 atoms: 0.74 Number of scatterers: 22110 At special positions: 0 Unit cell: (119.952, 130.56, 312.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 4270 8.00 N 3735 7.00 C 14031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS H 261 " - pdb=" SG CYS H 323 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.08 Conformation dependent library (CDL) restraints added in 3.3 seconds 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5570 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 48 sheets defined 27.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 40 through 54 removed outlier: 3.760A pdb=" N ILE A 45 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LYS A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 69 removed outlier: 3.908A pdb=" N ILE A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 114 through 119 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 225 through 245 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 265 through 282 Processing helix chain 'A' and resid 319 through 335 removed outlier: 3.547A pdb=" N ILE A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 358 through 378 Processing helix chain 'A' and resid 379 through 387 Processing helix chain 'A' and resid 406 through 419 removed outlier: 3.577A pdb=" N ALA A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.734A pdb=" N ARG A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 3.723A pdb=" N ILE B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 71 removed outlier: 4.061A pdb=" N ILE B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 101 removed outlier: 3.550A pdb=" N ASN B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 200 through 202 No H-bonds generated for 'chain 'B' and resid 200 through 202' Processing helix chain 'B' and resid 220 through 224 removed outlier: 3.640A pdb=" N ASN B 224 " --> pdb=" O PRO B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 245 Processing helix chain 'B' and resid 265 through 282 Processing helix chain 'B' and resid 319 through 336 removed outlier: 3.517A pdb=" N TYR B 327 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 358 through 375 Processing helix chain 'B' and resid 378 through 387 Processing helix chain 'B' and resid 406 through 419 removed outlier: 4.385A pdb=" N ALA B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 removed outlier: 3.681A pdb=" N ARG B 434 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 23 through 27 removed outlier: 3.874A pdb=" N ILE C 27 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'C' and resid 44 through 63 Processing helix chain 'C' and resid 77 through 90 removed outlier: 4.206A pdb=" N SER C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 112 Processing helix chain 'D' and resid 10 through 19 Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 44 through 63 removed outlier: 3.726A pdb=" N ILE D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 78 through 90 removed outlier: 3.578A pdb=" N ALA D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'F' and resid 4 through 20 Processing helix chain 'F' and resid 97 through 109 Processing helix chain 'F' and resid 111 through 120 Processing helix chain 'G' and resid 69 through 85 removed outlier: 4.217A pdb=" N GLN G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 49 Processing helix chain 'H' and resid 55 through 65 removed outlier: 3.571A pdb=" N GLN H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 133 Processing helix chain 'H' and resid 185 through 196 removed outlier: 3.550A pdb=" N TYR H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 222 removed outlier: 3.740A pdb=" N ALA H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 236 removed outlier: 3.855A pdb=" N ALA H 235 " --> pdb=" O ASP H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 244 removed outlier: 3.561A pdb=" N SER H 243 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 244 " --> pdb=" O LEU H 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 240 through 244' Processing helix chain 'H' and resid 246 through 255 Processing helix chain 'H' and resid 272 through 281 removed outlier: 4.129A pdb=" N GLY H 280 " --> pdb=" O TYR H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 321 Processing helix chain 'H' and resid 345 through 368 removed outlier: 4.112A pdb=" N LEU H 366 " --> pdb=" O SER H 362 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU H 367 " --> pdb=" O LEU H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 399 removed outlier: 3.745A pdb=" N ALA H 396 " --> pdb=" O SER H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 415 Processing helix chain 'H' and resid 416 through 423 removed outlier: 3.625A pdb=" N LYS H 420 " --> pdb=" O ALA H 416 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 100 Processing helix chain 'I' and resid 131 through 135 removed outlier: 3.572A pdb=" N LYS I 134 " --> pdb=" O ASN I 131 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I 135 " --> pdb=" O ASP I 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 131 through 135' Processing helix chain 'J' and resid 129 through 134 removed outlier: 3.723A pdb=" N TYR J 133 " --> pdb=" O SER J 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 14 Processing helix chain 'L' and resid 5 through 14 removed outlier: 3.730A pdb=" N ALA L 14 " --> pdb=" O ASN L 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 13 removed outlier: 3.551A pdb=" N LEU M 13 " --> pdb=" O LYS M 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 14 Processing helix chain 'O' and resid 5 through 14 Processing helix chain 'P' and resid 5 through 15 removed outlier: 3.804A pdb=" N LYS P 11 " --> pdb=" O ASP P 7 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR P 15 " --> pdb=" O LYS P 11 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76 removed outlier: 3.831A pdb=" N VAL A 398 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 396 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA4, first strand: chain 'A' and resid 162 through 163 removed outlier: 4.015A pdb=" N GLY A 173 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 251 through 254 Processing sheet with id=AA6, first strand: chain 'B' and resid 306 through 309 removed outlier: 3.653A pdb=" N GLU B 306 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 290 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU B 255 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TRP A 292 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR D 99 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.662A pdb=" N ARG B 74 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 398 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU B 396 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AB1, first strand: chain 'B' and resid 162 through 163 removed outlier: 4.001A pdb=" N GLY B 173 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 73 removed outlier: 3.527A pdb=" N VAL C 71 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP C 65 " --> pdb=" O ARG D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 88 through 89 removed outlier: 7.307A pdb=" N HIS E 114 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP E 104 " --> pdb=" O HIS E 114 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU E 116 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR E 102 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE E 118 " --> pdb=" O PHE E 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 21 Processing sheet with id=AB5, first strand: chain 'E' and resid 54 through 58 Processing sheet with id=AB6, first strand: chain 'F' and resid 34 through 36 removed outlier: 4.061A pdb=" N VAL F 79 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL F 93 " --> pdb=" O ALA F 147 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL F 150 " --> pdb=" O THR F 129 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR F 129 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR F 152 " --> pdb=" O LEU F 127 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 71 through 74 removed outlier: 4.061A pdb=" N VAL F 79 " --> pdb=" O ASP F 161 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL F 93 " --> pdb=" O ALA F 147 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 187 through 194 removed outlier: 10.314A pdb=" N ARG F 169 " --> pdb=" O LYS H 426 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N ILE H 428 " --> pdb=" O ARG F 169 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE F 171 " --> pdb=" O ILE H 428 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N PHE H 430 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP F 173 " --> pdb=" O PHE H 430 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLY H 432 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU F 175 " --> pdb=" O GLY H 432 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU H 434 " --> pdb=" O GLU F 175 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL F 177 " --> pdb=" O LEU H 434 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR H 404 " --> pdb=" O ILE H 433 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 187 through 194 removed outlier: 10.314A pdb=" N ARG F 169 " --> pdb=" O LYS H 426 " (cutoff:3.500A) removed outlier: 9.183A pdb=" N ILE H 428 " --> pdb=" O ARG F 169 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE F 171 " --> pdb=" O ILE H 428 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N PHE H 430 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP F 173 " --> pdb=" O PHE H 430 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLY H 432 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU F 175 " --> pdb=" O GLY H 432 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU H 434 " --> pdb=" O GLU F 175 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL F 177 " --> pdb=" O LEU H 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 13 through 15 Processing sheet with id=AC2, first strand: chain 'G' and resid 30 through 34 removed outlier: 3.645A pdb=" N CYS G 134 " --> pdb=" O GLY G 59 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE G 131 " --> pdb=" O GLN G 114 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'G' and resid 106 through 109 removed outlier: 3.673A pdb=" N ILE G 109 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS G 136 " --> pdb=" O ILE G 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 75 through 78 removed outlier: 5.077A pdb=" N ALA H 204 " --> pdb=" O PHE H 227 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE H 226 " --> pdb=" O VAL H 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 83 through 84 removed outlier: 4.039A pdb=" N TYR H 83 " --> pdb=" O ILE H 157 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 109 through 112 removed outlier: 3.996A pdb=" N GLN H 109 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL H 101 " --> pdb=" O GLN H 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 326 through 328 Processing sheet with id=AC9, first strand: chain 'I' and resid 23 through 29 removed outlier: 7.429A pdb=" N ASP I 24 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N SER N 105 " --> pdb=" O ASP I 24 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU I 26 " --> pdb=" O SER N 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ASP N 107 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL I 28 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 23 through 29 removed outlier: 7.429A pdb=" N ASP I 24 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 8.912A pdb=" N SER N 105 " --> pdb=" O ASP I 24 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU I 26 " --> pdb=" O SER N 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ASP N 107 " --> pdb=" O LEU I 26 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL I 28 " --> pdb=" O ASP N 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 33 through 40 removed outlier: 3.504A pdb=" N SER I 35 " --> pdb=" O SER M 105 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR I 39 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE M 101 " --> pdb=" O TYR I 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 33 through 40 removed outlier: 3.504A pdb=" N SER I 35 " --> pdb=" O SER M 105 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR I 39 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE M 101 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY M 97 " --> pdb=" O VAL M 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 51 through 58 removed outlier: 7.214A pdb=" N ILE I 127 " --> pdb=" O PRO I 114 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA I 103 " --> pdb=" O MET I 115 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU I 159 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL I 148 " --> pdb=" O THR I 157 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR I 157 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N VAL I 73 " --> pdb=" O ARG I 164 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 26 through 28 removed outlier: 7.431A pdb=" N LEU J 26 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ASP L 107 " --> pdb=" O LEU J 26 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL J 28 " --> pdb=" O ASP L 107 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 33 through 35 removed outlier: 3.503A pdb=" N SER J 35 " --> pdb=" O SER K 105 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER K 105 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE K 106 " --> pdb=" O ILE K 53 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AD8, first strand: chain 'J' and resid 72 through 76 removed outlier: 6.100A pdb=" N VAL J 73 " --> pdb=" O ARG J 164 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN J 166 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE J 75 " --> pdb=" O ASN J 166 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N THR J 157 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL J 148 " --> pdb=" O THR J 157 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU J 159 " --> pdb=" O VAL J 146 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 88 through 89 removed outlier: 3.709A pdb=" N LYS J 93 " --> pdb=" O ASN J 89 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 41 through 42 removed outlier: 3.631A pdb=" N VAL K 22 " --> pdb=" O SER K 73 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N THR K 68 " --> pdb=" O SER K 89 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N SER K 89 " --> pdb=" O THR K 68 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N SER K 70 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA K 83 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASP K 76 " --> pdb=" O CYS K 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N CYS K 81 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 59 through 63 Processing sheet with id=AE3, first strand: chain 'L' and resid 41 through 42 removed outlier: 3.655A pdb=" N VAL L 41 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE L 72 " --> pdb=" O THR L 84 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR L 84 " --> pdb=" O PHE L 72 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU L 74 " --> pdb=" O VAL L 82 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 59 through 63 Processing sheet with id=AE5, first strand: chain 'L' and resid 67 through 69 Processing sheet with id=AE6, first strand: chain 'M' and resid 41 through 42 removed outlier: 9.821A pdb=" N THR M 68 " --> pdb=" O SER M 89 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N SER M 89 " --> pdb=" O THR M 68 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER M 70 " --> pdb=" O LEU M 87 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA M 83 " --> pdb=" O LEU M 74 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 41 through 42 removed outlier: 7.243A pdb=" N HIS N 71 " --> pdb=" O SER N 89 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N SER N 89 " --> pdb=" O HIS N 71 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N SER N 73 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N LEU N 87 " --> pdb=" O SER N 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 41 through 42 removed outlier: 3.567A pdb=" N VAL O 41 " --> pdb=" O ILE O 21 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N HIS O 71 " --> pdb=" O SER O 89 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N SER O 89 " --> pdb=" O HIS O 71 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N SER O 73 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N LEU O 87 " --> pdb=" O SER O 73 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N TRP O 75 " --> pdb=" O GLY O 85 " (cutoff:3.500A) removed outlier: 12.304A pdb=" N GLY O 85 " --> pdb=" O TRP O 75 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 52 through 54 Processing sheet with id=AF1, first strand: chain 'O' and resid 59 through 63 Processing sheet with id=AF2, first strand: chain 'P' and resid 41 through 42 removed outlier: 3.738A pdb=" N PHE P 72 " --> pdb=" O GLY P 85 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA P 83 " --> pdb=" O LEU P 74 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 67 through 68 836 hydrogen bonds defined for protein. 2304 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.71 Time building geometry restraints manager: 7.02 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: 7292 1.34 - 1.46: 4979 1.46 - 1.58: 10137 1.58 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 22531 Sorted by residual: bond pdb=" N VAL H 332 " pdb=" CA VAL H 332 " ideal model delta sigma weight residual 1.456 1.491 -0.035 8.70e-03 1.32e+04 1.58e+01 bond pdb=" N VAL A 448 " pdb=" CA VAL A 448 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 8.78e+00 bond pdb=" N HIS B 103 " pdb=" CA HIS B 103 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.14e+00 bond pdb=" N ILE O 6 " pdb=" CA ILE O 6 " ideal model delta sigma weight residual 1.463 1.493 -0.030 1.14e-02 7.69e+03 6.78e+00 bond pdb=" N ASP B 104 " pdb=" CA ASP B 104 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.32e-02 5.74e+03 6.41e+00 ... (remaining 22526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 30202 2.75 - 5.50: 440 5.50 - 8.26: 43 8.26 - 11.01: 6 11.01 - 13.76: 2 Bond angle restraints: 30693 Sorted by residual: angle pdb=" C SER O 46 " pdb=" N GLU O 47 " pdb=" CA GLU O 47 " ideal model delta sigma weight residual 120.67 130.93 -10.26 1.34e+00 5.57e-01 5.87e+01 angle pdb=" N PRO A 454 " pdb=" CA PRO A 454 " pdb=" CB PRO A 454 " ideal model delta sigma weight residual 103.00 96.95 6.05 1.10e+00 8.26e-01 3.03e+01 angle pdb=" N VAL E 99 " pdb=" CA VAL E 99 " pdb=" C VAL E 99 " ideal model delta sigma weight residual 106.21 111.90 -5.69 1.07e+00 8.73e-01 2.82e+01 angle pdb=" N ILE H 138 " pdb=" CA ILE H 138 " pdb=" C ILE H 138 " ideal model delta sigma weight residual 113.71 109.01 4.70 9.50e-01 1.11e+00 2.45e+01 angle pdb=" N GLU A 450 " pdb=" CA GLU A 450 " pdb=" C GLU A 450 " ideal model delta sigma weight residual 113.12 107.36 5.76 1.25e+00 6.40e-01 2.12e+01 ... (remaining 30688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 11592 17.96 - 35.92: 1516 35.92 - 53.88: 339 53.88 - 71.85: 59 71.85 - 89.81: 22 Dihedral angle restraints: 13528 sinusoidal: 4928 harmonic: 8600 Sorted by residual: dihedral pdb=" CA GLN F 52 " pdb=" C GLN F 52 " pdb=" N PRO F 53 " pdb=" CA PRO F 53 " ideal model delta harmonic sigma weight residual -180.00 -140.58 -39.42 0 5.00e+00 4.00e-02 6.22e+01 dihedral pdb=" CA GLU J 91 " pdb=" C GLU J 91 " pdb=" N ASN J 92 " pdb=" CA ASN J 92 " ideal model delta harmonic sigma weight residual 180.00 143.01 36.99 0 5.00e+00 4.00e-02 5.47e+01 dihedral pdb=" CD ARG G 123 " pdb=" NE ARG G 123 " pdb=" CZ ARG G 123 " pdb=" NH1 ARG G 123 " ideal model delta sinusoidal sigma weight residual 0.00 -62.82 62.82 1 1.00e+01 1.00e-02 5.22e+01 ... (remaining 13525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2892 0.055 - 0.110: 609 0.110 - 0.165: 86 0.165 - 0.220: 11 0.220 - 0.275: 3 Chirality restraints: 3601 Sorted by residual: chirality pdb=" CA PRO B 152 " pdb=" N PRO B 152 " pdb=" C PRO B 152 " pdb=" CB PRO B 152 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA PRO A 152 " pdb=" N PRO A 152 " pdb=" C PRO A 152 " pdb=" CB PRO A 152 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR J 106 " pdb=" CA THR J 106 " pdb=" OG1 THR J 106 " pdb=" CG2 THR J 106 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 3598 not shown) Planarity restraints: 3971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 123 " 0.984 9.50e-02 1.11e+02 4.41e-01 1.18e+02 pdb=" NE ARG G 123 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG G 123 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG G 123 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG G 123 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 377 " -0.748 9.50e-02 1.11e+02 3.35e-01 6.84e+01 pdb=" NE ARG A 377 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 377 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 377 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 377 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 33 " 0.566 9.50e-02 1.11e+02 2.54e-01 3.93e+01 pdb=" NE ARG J 33 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG J 33 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG J 33 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 33 " 0.019 2.00e-02 2.50e+03 ... (remaining 3968 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 478 2.66 - 3.22: 21279 3.22 - 3.78: 32889 3.78 - 4.34: 43552 4.34 - 4.90: 71752 Nonbonded interactions: 169950 Sorted by model distance: nonbonded pdb=" O LEU F 118 " pdb=" OG1 THR F 122 " model vdw 2.097 3.040 nonbonded pdb=" OG1 THR H 80 " pdb=" OG1 THR H 181 " model vdw 2.129 3.040 nonbonded pdb=" OG SER G 8 " pdb=" OD2 ASP G 11 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASP E 104 " pdb=" OG SER E 106 " model vdw 2.163 3.040 nonbonded pdb=" O ASN P 25 " pdb=" OG SER P 70 " model vdw 2.164 3.040 ... (remaining 169945 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 17 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 81 or (resid 82 and (name N or nam \ e CA or name C or name O or name CB )) or resid 83 through 127 or (resid 128 thr \ ough 131 and (name N or name CA or name C or name O or name CB )) or (resid 132 \ through 137 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 8 through 139 or (resid 140 through 142 and (name N or name CA or name C or name \ O or name CB )) or resid 143 through 149 or (resid 150 through 151 and (name N \ or name CA or name C or name O or name CB )) or resid 152 through 343 or (resid \ 344 and (name N or name CA or name C or name O or name CB )) or resid 345 throug \ h 407 or (resid 408 and (name N or name CA or name C or name O or name CB )) or \ resid 409 through 439 or (resid 440 and (name N or name CA or name C or name O o \ r name CB )) or resid 441 through 442 or (resid 443 and (name N or name CA or na \ me C or name O or name CB )) or resid 444 through 445 or (resid 446 and (name N \ or name CA or name C or name O or name CB )) or resid 447 through 449 or (resid \ 450 and (name N or name CA or name C or name O or name CB )) or resid 451 throug \ h 454)) selection = (chain 'B' and (resid 17 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 102 or (resid 103 and (name N or n \ ame CA or name C or name O or name CB )) or resid 104 through 160 or (resid 161 \ and (name N or name CA or name C or name O or name CB )) or resid 162 through 30 \ 5 or (resid 306 and (name N or name CA or name C or name O or name CB )) or resi \ d 307 through 345 or (resid 346 through 347 and (name N or name CA or name C or \ name O or name CB )) or resid 348 through 426 or (resid 427 through 428 and (nam \ e N or name CA or name C or name O or name CB )) or resid 429 through 454)) } ncs_group { reference = (chain 'C' and (resid 4 through 22 or (resid 23 and (name N or name CA or name C \ or name O or name CB )) or resid 24 through 25 or (resid 26 and (name N or name \ CA or name C or name O or name CB )) or resid 27 through 132)) selection = (chain 'D' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 129 or (resid 130 and (name N or na \ me CA or name C or name O or name CB )) or resid 131 through 132)) } ncs_group { reference = (chain 'I' and ((resid 25 through 30 and (name N or name CA or name C or name O \ or name CB )) or resid 31 through 40 or (resid 41 through 42 and (name N or name \ CA or name C or name O or name CB )) or resid 43 through 53 or (resid 54 and (n \ ame N or name CA or name C or name O or name CB )) or resid 55 through 61 or (re \ sid 62 and (name N or name CA or name C or name O or name CB )) or resid 66 thro \ ugh 77 or (resid 78 through 80 and (name N or name CA or name C or name O or nam \ e CB )) or resid 81 through 98 or (resid 99 and (name N or name CA or name C or \ name O or name CB )) or resid 100 through 137 or (resid 138 and (name N or name \ CA or name C or name O or name CB )) or resid 139 through 166)) selection = (chain 'J' and (resid 25 through 55 or (resid 56 through 57 and (name N or name \ CA or name C or name O or name CB )) or resid 58 through 70 or (resid 71 and (na \ me N or name CA or name C or name O or name CB )) or resid 72 through 90 or (res \ id 91 through 92 and (name N or name CA or name C or name O or name CB )) or res \ id 93 through 119 or (resid 120 and (name N or name CA or name C or name O or na \ me CB )) or resid 121 through 134 or (resid 135 and (name N or name CA or name C \ or name O or name CB )) or resid 136 through 166)) } ncs_group { reference = (chain 'K' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 6 or (resid 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 55 or (res \ id 56 through 57 and (name N or name CA or name C or name O or name CB )) or res \ id 58 through 76 or (resid 77 and (name N or name CA or name C or name O or name \ CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C or n \ ame O or name CB )) or resid 81 through 94 or (resid 95 through 96 and (name N o \ r name CA or name C or name O or name CB )) or resid 97 or (resid 98 through 107 \ and (name N or name CA or name C or name O or name CB )) or resid 108 or (resid \ 109 through 110 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'L' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 6 or (resid 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 55 or (res \ id 56 through 57 and (name N or name CA or name C or name O or name CB )) or res \ id 58 through 76 or (resid 77 and (name N or name CA or name C or name O or name \ CB )) or resid 78 through 79 or (resid 80 and (name N or name CA or name C or n \ ame O or name CB )) or resid 81 through 95 or (resid 96 and (name N or name CA o \ r name C or name O or name CB )) or resid 97 or (resid 98 through 107 and (name \ N or name CA or name C or name O or name CB )) or resid 108 through 110)) selection = (chain 'M' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 6 or (resid 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 76 or (resid 77 and (na \ me N or name CA or name C or name O or name CB )) or resid 78 through 79 or (res \ id 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 95 or (resid 96 and (name N or name CA or name C or name O or name CB )) or r \ esid 97 or (resid 98 through 107 and (name N or name CA or name C or name O or n \ ame CB )) or resid 108 or (resid 109 through 110 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'N' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 6 or (resid 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 56 or (resid 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 76 or (res \ id 77 and (name N or name CA or name C or name O or name CB )) or resid 78 throu \ gh 79 or (resid 80 and (name N or name CA or name C or name O or name CB )) or r \ esid 81 through 94 or (resid 95 through 96 and (name N or name CA or name C or n \ ame O or name CB )) or resid 97 or (resid 98 through 107 and (name N or name CA \ or name C or name O or name CB )) or resid 108 or (resid 109 through 110 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'O' and (resid 3 through 46 or (resid 47 and (name N or name CA or name C \ or name O or name CB )) or resid 48 through 79 or (resid 80 and (name N or name \ CA or name C or name O or name CB )) or resid 81 through 95 or (resid 96 and (n \ ame N or name CA or name C or name O or name CB )) or resid 97 or (resid 98 thro \ ugh 107 and (name N or name CA or name C or name O or name CB )) or resid 108 or \ (resid 109 through 110 and (name N or name CA or name C or name O or name CB )) \ )) selection = (chain 'P' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 6 or (resid 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 76 or (resid 77 and (na \ me N or name CA or name C or name O or name CB )) or resid 78 through 108 or (re \ sid 109 through 110 and (name N or name CA or name C or name O or name CB )))) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.220 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: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 55.380 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 : 0.004 0.071 22532 Z= 0.244 Angle : 0.840 13.762 30695 Z= 0.515 Chirality : 0.046 0.275 3601 Planarity : 0.011 0.441 3971 Dihedral : 17.050 89.808 7955 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 1.03 % Allowed : 8.82 % Favored : 90.15 % Rotamer: Outliers : 1.22 % Allowed : 30.74 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.15), residues: 2913 helix: 1.48 (0.20), residues: 692 sheet: -1.13 (0.22), residues: 569 loop : -2.42 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 65 HIS 0.011 0.001 HIS I 14 PHE 0.021 0.001 PHE K 72 TYR 0.030 0.001 TYR B 347 ARG 0.015 0.001 ARG A 74 Details of bonding type rmsd hydrogen bonds : bond 0.25629 ( 809) hydrogen bonds : angle 8.29333 ( 2304) SS BOND : bond 0.00285 ( 1) SS BOND : angle 0.85210 ( 2) covalent geometry : bond 0.00426 (22531) covalent geometry : angle 0.83975 (30693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 856 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8282 (mm-40) REVERT: A 233 VAL cc_start: 0.9187 (t) cc_final: 0.8931 (m) REVERT: A 454 PRO cc_start: 0.7969 (OUTLIER) cc_final: 0.7722 (Cg_exo) REVERT: B 49 GLN cc_start: 0.8684 (mt0) cc_final: 0.8326 (pt0) REVERT: B 89 GLU cc_start: 0.7678 (pp20) cc_final: 0.6788 (tp30) REVERT: B 139 SER cc_start: 0.7396 (OUTLIER) cc_final: 0.6645 (p) REVERT: B 233 VAL cc_start: 0.9169 (t) cc_final: 0.8911 (m) REVERT: B 297 ASP cc_start: 0.8409 (t0) cc_final: 0.8058 (t0) REVERT: B 452 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7623 (pt) REVERT: C 129 ARG cc_start: 0.7477 (ptp90) cc_final: 0.7052 (ptp90) REVERT: D 130 TYR cc_start: 0.7406 (t80) cc_final: 0.6493 (m-80) REVERT: G 91 ILE cc_start: 0.8063 (pt) cc_final: 0.7563 (pt) REVERT: H 133 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8137 (mt-10) REVERT: H 399 ARG cc_start: 0.8008 (ttm170) cc_final: 0.7786 (ttm170) REVERT: I 65 ILE cc_start: 0.7667 (mt) cc_final: 0.7428 (mt) REVERT: P 37 VAL cc_start: 0.8356 (m) cc_final: 0.8105 (p) outliers start: 28 outliers final: 4 residues processed: 872 average time/residue: 0.3212 time to fit residues: 434.9358 Evaluate side-chains 588 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 581 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 454 PRO Chi-restraints excluded: chain B residue 103 HIS Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain J residue 152 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 0.8980 chunk 217 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 74 optimal weight: 0.4980 chunk 146 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 260 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 GLN B 387 ASN B 394 HIS D 39 GLN H 306 ASN H 324 ASN H 370 GLN I 63 GLN I 70 ASN I 147 ASN L 39 GLN L 91 GLN P 10 ASN P 50 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.103119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.085863 restraints weight = 58905.590| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.72 r_work: 0.3120 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22532 Z= 0.159 Angle : 0.705 10.993 30695 Z= 0.370 Chirality : 0.047 0.293 3601 Planarity : 0.006 0.117 3971 Dihedral : 4.836 47.350 3138 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.10 % Favored : 91.18 % Rotamer: Outliers : 4.76 % Allowed : 28.25 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.15), residues: 2913 helix: 1.33 (0.19), residues: 705 sheet: -0.99 (0.22), residues: 532 loop : -2.39 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 65 HIS 0.009 0.001 HIS I 14 PHE 0.025 0.002 PHE H 211 TYR 0.016 0.001 TYR O 99 ARG 0.006 0.001 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 809) hydrogen bonds : angle 6.05348 ( 2304) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.76513 ( 2) covalent geometry : bond 0.00358 (22531) covalent geometry : angle 0.70474 (30693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 625 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.7734 (pm20) cc_final: 0.7468 (tt0) REVERT: A 48 PHE cc_start: 0.7913 (m-10) cc_final: 0.7485 (m-80) REVERT: A 49 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8454 (mm-40) REVERT: A 233 VAL cc_start: 0.9173 (t) cc_final: 0.8856 (m) REVERT: A 263 ASP cc_start: 0.8688 (p0) cc_final: 0.8324 (p0) REVERT: A 370 GLN cc_start: 0.8776 (tp40) cc_final: 0.8569 (tp40) REVERT: B 33 GLU cc_start: 0.8274 (tp30) cc_final: 0.7779 (tt0) REVERT: B 89 GLU cc_start: 0.7877 (pp20) cc_final: 0.7158 (tp30) REVERT: B 233 VAL cc_start: 0.9416 (t) cc_final: 0.9008 (m) REVERT: B 297 ASP cc_start: 0.8451 (t0) cc_final: 0.8141 (t0) REVERT: B 323 ILE cc_start: 0.8524 (mm) cc_final: 0.8293 (mm) REVERT: B 352 LEU cc_start: 0.7516 (mt) cc_final: 0.6848 (mt) REVERT: B 370 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 23 ASP cc_start: 0.8495 (t0) cc_final: 0.8215 (t0) REVERT: C 129 ARG cc_start: 0.7735 (ptp90) cc_final: 0.7446 (ptp90) REVERT: D 130 TYR cc_start: 0.7595 (t80) cc_final: 0.6583 (m-80) REVERT: E 50 VAL cc_start: 0.9259 (t) cc_final: 0.8975 (t) REVERT: E 67 THR cc_start: 0.9308 (m) cc_final: 0.9042 (p) REVERT: E 104 ASP cc_start: 0.7638 (p0) cc_final: 0.7429 (p0) REVERT: F 71 ASP cc_start: 0.7704 (p0) cc_final: 0.7456 (p0) REVERT: H 78 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7004 (ptt90) REVERT: H 133 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8224 (mt-10) REVERT: I 166 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7822 (p0) REVERT: J 143 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: L 19 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7962 (p) REVERT: L 49 ASN cc_start: 0.8547 (t0) cc_final: 0.8301 (t0) REVERT: L 69 VAL cc_start: 0.8848 (m) cc_final: 0.8453 (p) REVERT: P 61 ILE cc_start: 0.9182 (mp) cc_final: 0.8713 (tt) outliers start: 109 outliers final: 43 residues processed: 690 average time/residue: 0.2963 time to fit residues: 327.3848 Evaluate side-chains 611 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 564 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 335 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain O residue 87 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 13 optimal weight: 0.0020 chunk 124 optimal weight: 9.9990 chunk 60 optimal weight: 0.1980 chunk 174 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 168 optimal weight: 0.0030 chunk 226 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 HIS C 9 ASN D 39 GLN F 99 HIS G 125 GLN ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 GLN ** H 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 ASN ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN P 50 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.101442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.084120 restraints weight = 58981.637| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.72 r_work: 0.3078 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 22532 Z= 0.184 Angle : 0.682 12.326 30695 Z= 0.356 Chirality : 0.047 0.293 3601 Planarity : 0.005 0.119 3971 Dihedral : 4.572 37.786 3126 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.72 % Allowed : 8.24 % Favored : 91.04 % Rotamer: Outliers : 5.28 % Allowed : 27.69 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 2913 helix: 1.30 (0.20), residues: 708 sheet: -0.85 (0.22), residues: 508 loop : -2.25 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 65 HIS 0.010 0.001 HIS B 103 PHE 0.024 0.002 PHE P 72 TYR 0.014 0.001 TYR B 384 ARG 0.007 0.001 ARG H 364 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 809) hydrogen bonds : angle 5.56490 ( 2304) SS BOND : bond 0.00196 ( 1) SS BOND : angle 0.58682 ( 2) covalent geometry : bond 0.00427 (22531) covalent geometry : angle 0.68217 (30693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 566 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLN cc_start: 0.8008 (pm20) cc_final: 0.7703 (tt0) REVERT: A 49 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8605 (mm-40) REVERT: A 263 ASP cc_start: 0.8875 (p0) cc_final: 0.8603 (p0) REVERT: B 89 GLU cc_start: 0.7981 (pp20) cc_final: 0.7265 (tp30) REVERT: B 94 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: B 101 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.6719 (ttt) REVERT: B 267 GLU cc_start: 0.5681 (tt0) cc_final: 0.5364 (tt0) REVERT: B 297 ASP cc_start: 0.8640 (t0) cc_final: 0.8309 (t0) REVERT: B 352 LEU cc_start: 0.7894 (mt) cc_final: 0.7197 (mt) REVERT: B 370 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7991 (tm-30) REVERT: B 396 GLU cc_start: 0.6344 (tp30) cc_final: 0.6091 (tp30) REVERT: B 425 VAL cc_start: 0.7982 (t) cc_final: 0.7777 (t) REVERT: C 21 ASP cc_start: 0.8768 (t0) cc_final: 0.8414 (t0) REVERT: C 23 ASP cc_start: 0.8785 (t0) cc_final: 0.8489 (t0) REVERT: C 53 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9344 (tp) REVERT: C 72 TYR cc_start: 0.8341 (t80) cc_final: 0.7840 (t80) REVERT: C 75 ASN cc_start: 0.7997 (m110) cc_final: 0.7769 (m-40) REVERT: C 78 ARG cc_start: 0.5358 (tpt170) cc_final: 0.3480 (mmt180) REVERT: C 88 ASP cc_start: 0.8828 (t0) cc_final: 0.8560 (t70) REVERT: C 129 ARG cc_start: 0.8084 (ptp90) cc_final: 0.7703 (ptp90) REVERT: D 59 GLN cc_start: 0.9144 (tp40) cc_final: 0.8807 (tp40) REVERT: D 130 TYR cc_start: 0.7806 (t80) cc_final: 0.6631 (m-80) REVERT: E 84 TRP cc_start: 0.8518 (OUTLIER) cc_final: 0.8262 (t-100) REVERT: E 104 ASP cc_start: 0.7995 (p0) cc_final: 0.7719 (p0) REVERT: F 134 ASN cc_start: 0.8278 (p0) cc_final: 0.8034 (p0) REVERT: F 169 ARG cc_start: 0.8894 (ttt180) cc_final: 0.8646 (ttt180) REVERT: H 13 ASN cc_start: 0.8412 (t0) cc_final: 0.8197 (t0) REVERT: I 166 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8081 (p0) REVERT: J 39 TYR cc_start: 0.8503 (p90) cc_final: 0.8264 (p90) REVERT: J 71 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: J 74 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8409 (mtmt) REVERT: J 83 LEU cc_start: 0.9058 (tp) cc_final: 0.8812 (tt) REVERT: J 91 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8089 (mm-30) REVERT: L 49 ASN cc_start: 0.8810 (t0) cc_final: 0.8556 (t0) REVERT: M 98 ILE cc_start: 0.9520 (mm) cc_final: 0.9308 (mm) REVERT: P 61 ILE cc_start: 0.9150 (mp) cc_final: 0.8705 (tt) outliers start: 121 outliers final: 71 residues processed: 641 average time/residue: 0.3003 time to fit residues: 308.5434 Evaluate side-chains 593 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 515 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 94 PHE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 335 VAL Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 380 THR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 101 ILE Chi-restraints excluded: chain P residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 88 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 128 optimal weight: 0.0870 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 166 optimal weight: 40.0000 chunk 171 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 252 optimal weight: 20.0000 chunk 213 optimal weight: 0.3980 overall best weight: 2.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 394 HIS ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 306 ASN I 70 ASN ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 109 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.083391 restraints weight = 61142.608| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.78 r_work: 0.3073 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 22532 Z= 0.191 Angle : 0.670 11.752 30695 Z= 0.349 Chirality : 0.047 0.304 3601 Planarity : 0.005 0.124 3971 Dihedral : 4.606 39.348 3126 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.62 % Favored : 91.76 % Rotamer: Outliers : 5.98 % Allowed : 27.03 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 2913 helix: 1.39 (0.20), residues: 708 sheet: -0.70 (0.23), residues: 518 loop : -2.18 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 148 HIS 0.009 0.001 HIS K 71 PHE 0.054 0.002 PHE O 93 TYR 0.017 0.001 TYR C 72 ARG 0.015 0.001 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 809) hydrogen bonds : angle 5.32498 ( 2304) SS BOND : bond 0.00190 ( 1) SS BOND : angle 0.64886 ( 2) covalent geometry : bond 0.00426 (22531) covalent geometry : angle 0.67018 (30693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 545 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 GLU cc_start: 0.9271 (pp20) cc_final: 0.8877 (pp20) REVERT: B 89 GLU cc_start: 0.8123 (pp20) cc_final: 0.7356 (tp30) REVERT: B 101 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.6905 (ttt) REVERT: B 267 GLU cc_start: 0.5909 (tt0) cc_final: 0.5556 (tt0) REVERT: B 320 THR cc_start: 0.8742 (m) cc_final: 0.8364 (p) REVERT: B 370 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8307 (tm-30) REVERT: C 13 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: C 23 ASP cc_start: 0.8970 (t0) cc_final: 0.8670 (t0) REVERT: C 59 GLN cc_start: 0.9252 (mm-40) cc_final: 0.8990 (mm110) REVERT: C 78 ARG cc_start: 0.5660 (tpt170) cc_final: 0.3392 (mmt180) REVERT: C 126 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8405 (t70) REVERT: D 59 GLN cc_start: 0.9203 (tp40) cc_final: 0.8882 (tp40) REVERT: D 130 TYR cc_start: 0.8035 (t80) cc_final: 0.6655 (m-80) REVERT: E 3 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9093 (tt) REVERT: E 36 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7888 (pt) REVERT: E 104 ASP cc_start: 0.8071 (p0) cc_final: 0.7818 (p0) REVERT: G 123 ARG cc_start: 0.8857 (ttp-110) cc_final: 0.7493 (mpt180) REVERT: H 273 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7824 (pm20) REVERT: I 119 LYS cc_start: 0.9392 (ttmm) cc_final: 0.9119 (ttmm) REVERT: I 145 ILE cc_start: 0.9260 (mm) cc_final: 0.9048 (mm) REVERT: J 74 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8772 (mtmm) REVERT: J 125 GLU cc_start: 0.8129 (pm20) cc_final: 0.7746 (pm20) REVERT: L 49 ASN cc_start: 0.8928 (t0) cc_final: 0.8685 (t0) REVERT: N 107 ASP cc_start: 0.8233 (t0) cc_final: 0.7975 (t0) REVERT: N 109 ASN cc_start: 0.8907 (m110) cc_final: 0.8572 (m110) outliers start: 137 outliers final: 87 residues processed: 631 average time/residue: 0.3063 time to fit residues: 303.8967 Evaluate side-chains 576 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 482 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 335 VAL Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain I residue 166 ASN Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain O residue 6 ILE Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain O residue 101 ILE Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 128 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 282 optimal weight: 50.0000 chunk 198 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 GLN C 39 GLN D 39 GLN ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.098089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.080709 restraints weight = 60991.301| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.75 r_work: 0.3022 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.6367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 22532 Z= 0.215 Angle : 0.694 12.631 30695 Z= 0.358 Chirality : 0.047 0.299 3601 Planarity : 0.005 0.127 3971 Dihedral : 4.758 41.609 3126 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.07 % Favored : 91.31 % Rotamer: Outliers : 5.98 % Allowed : 27.07 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 2913 helix: 1.35 (0.20), residues: 709 sheet: -0.64 (0.22), residues: 546 loop : -2.13 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 65 HIS 0.005 0.001 HIS H 431 PHE 0.019 0.002 PHE C 79 TYR 0.028 0.002 TYR J 39 ARG 0.009 0.001 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 809) hydrogen bonds : angle 5.31958 ( 2304) SS BOND : bond 0.00168 ( 1) SS BOND : angle 0.55373 ( 2) covalent geometry : bond 0.00507 (22531) covalent geometry : angle 0.69436 (30693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 529 time to evaluate : 2.573 Fit side-chains revert: symmetry clash REVERT: B 89 GLU cc_start: 0.8223 (pp20) cc_final: 0.7559 (tp30) REVERT: B 212 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 267 GLU cc_start: 0.5908 (tt0) cc_final: 0.5588 (tt0) REVERT: B 384 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.7344 (m-10) REVERT: B 434 ARG cc_start: 0.8722 (mtp-110) cc_final: 0.5811 (mtt90) REVERT: C 13 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: C 23 ASP cc_start: 0.9046 (t0) cc_final: 0.8773 (t0) REVERT: C 123 GLU cc_start: 0.8754 (pm20) cc_final: 0.8404 (pm20) REVERT: C 126 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8764 (t70) REVERT: D 44 ASP cc_start: 0.9096 (t0) cc_final: 0.8891 (t70) REVERT: D 59 GLN cc_start: 0.9238 (tp40) cc_final: 0.8910 (tp40) REVERT: D 88 ASP cc_start: 0.8627 (t0) cc_final: 0.8293 (t0) REVERT: E 3 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9138 (tt) REVERT: E 81 ASP cc_start: 0.9384 (p0) cc_final: 0.9112 (p0) REVERT: E 84 TRP cc_start: 0.9126 (OUTLIER) cc_final: 0.7733 (m-90) REVERT: E 104 ASP cc_start: 0.8419 (p0) cc_final: 0.8200 (p0) REVERT: F 135 ASP cc_start: 0.8566 (m-30) cc_final: 0.8349 (m-30) REVERT: G 53 ARG cc_start: 0.6105 (pmt-80) cc_final: 0.5886 (pmt-80) REVERT: G 83 ASP cc_start: 0.8822 (t70) cc_final: 0.8505 (t0) REVERT: G 88 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8662 (mp0) REVERT: G 123 ARG cc_start: 0.9027 (ttp-110) cc_final: 0.7647 (mpt180) REVERT: H 65 TRP cc_start: 0.8473 (OUTLIER) cc_final: 0.8134 (t60) REVERT: H 273 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: H 284 ASP cc_start: 0.8305 (t0) cc_final: 0.8061 (t70) REVERT: J 74 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8979 (mtmm) REVERT: J 125 GLU cc_start: 0.8478 (pm20) cc_final: 0.7992 (pm20) REVERT: J 145 ILE cc_start: 0.9505 (mm) cc_final: 0.9291 (mt) REVERT: K 91 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8562 (mm110) REVERT: L 49 ASN cc_start: 0.9009 (t0) cc_final: 0.8785 (t0) REVERT: N 107 ASP cc_start: 0.8203 (t0) cc_final: 0.7897 (t0) REVERT: N 109 ASN cc_start: 0.8942 (m110) cc_final: 0.8468 (m110) REVERT: O 12 ILE cc_start: 0.9067 (mm) cc_final: 0.8807 (pt) REVERT: O 47 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9014 (mm-30) REVERT: P 39 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7819 (tm-30) outliers start: 137 outliers final: 90 residues processed: 622 average time/residue: 0.3095 time to fit residues: 305.6231 Evaluate side-chains 589 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 491 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 196 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 273 GLU Chi-restraints excluded: chain H residue 335 VAL Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 162 LYS Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 101 ILE Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 16 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 192 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 12 optimal weight: 30.0000 chunk 235 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.097613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.080249 restraints weight = 61118.247| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.74 r_work: 0.3020 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 22532 Z= 0.208 Angle : 0.684 13.389 30695 Z= 0.350 Chirality : 0.047 0.308 3601 Planarity : 0.005 0.129 3971 Dihedral : 4.729 42.921 3126 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.10 % Favored : 91.31 % Rotamer: Outliers : 5.11 % Allowed : 28.60 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.16), residues: 2913 helix: 1.43 (0.20), residues: 709 sheet: -0.60 (0.22), residues: 555 loop : -2.07 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP H 65 HIS 0.010 0.001 HIS B 103 PHE 0.025 0.002 PHE B 115 TYR 0.028 0.001 TYR J 39 ARG 0.005 0.001 ARG D 16 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 809) hydrogen bonds : angle 5.25808 ( 2304) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.65510 ( 2) covalent geometry : bond 0.00499 (22531) covalent geometry : angle 0.68448 (30693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 513 time to evaluate : 2.539 Fit side-chains revert: symmetry clash REVERT: A 213 TYR cc_start: 0.8744 (m-10) cc_final: 0.8436 (m-80) REVERT: A 384 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.6234 (t80) REVERT: B 89 GLU cc_start: 0.8247 (pp20) cc_final: 0.7590 (tp30) REVERT: B 267 GLU cc_start: 0.5901 (tt0) cc_final: 0.5604 (tt0) REVERT: B 384 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.6902 (m-10) REVERT: B 423 MET cc_start: 0.9036 (mmm) cc_final: 0.8594 (mmt) REVERT: B 434 ARG cc_start: 0.8784 (mtp-110) cc_final: 0.8519 (mtp-110) REVERT: C 13 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: C 23 ASP cc_start: 0.9082 (t0) cc_final: 0.8840 (t0) REVERT: C 107 ASP cc_start: 0.8166 (t0) cc_final: 0.7880 (t0) REVERT: D 44 ASP cc_start: 0.9145 (t0) cc_final: 0.8936 (t70) REVERT: D 59 GLN cc_start: 0.9209 (tp40) cc_final: 0.8929 (tp40) REVERT: D 88 ASP cc_start: 0.8609 (t0) cc_final: 0.8335 (t0) REVERT: E 3 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9138 (tt) REVERT: E 31 GLN cc_start: 0.8445 (mp10) cc_final: 0.7876 (mp10) REVERT: E 104 ASP cc_start: 0.8488 (p0) cc_final: 0.8283 (p0) REVERT: G 83 ASP cc_start: 0.8863 (t70) cc_final: 0.8558 (t0) REVERT: G 88 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8766 (mp0) REVERT: G 123 ARG cc_start: 0.9038 (ttp-110) cc_final: 0.7666 (mpt180) REVERT: H 284 ASP cc_start: 0.8349 (t0) cc_final: 0.8098 (t0) REVERT: I 20 LEU cc_start: 0.8879 (tp) cc_final: 0.8666 (tp) REVERT: J 74 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.9012 (mtmm) REVERT: K 91 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8660 (mm110) REVERT: L 49 ASN cc_start: 0.8980 (t0) cc_final: 0.8768 (t0) REVERT: L 76 ASP cc_start: 0.8062 (p0) cc_final: 0.7824 (p0) REVERT: N 107 ASP cc_start: 0.8124 (t0) cc_final: 0.7823 (t0) REVERT: N 109 ASN cc_start: 0.8952 (m110) cc_final: 0.8515 (m110) REVERT: O 12 ILE cc_start: 0.9121 (mm) cc_final: 0.8838 (pt) REVERT: O 47 GLU cc_start: 0.9338 (mm-30) cc_final: 0.9025 (mm-30) REVERT: O 107 ASP cc_start: 0.6263 (t0) cc_final: 0.6046 (t0) outliers start: 117 outliers final: 90 residues processed: 592 average time/residue: 0.3099 time to fit residues: 289.9616 Evaluate side-chains 582 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 487 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 335 VAL Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 162 LYS Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 101 ILE Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 111 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 275 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN H 163 ASN ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.097722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080299 restraints weight = 59787.132| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.63 r_work: 0.3004 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 22532 Z= 0.159 Angle : 0.668 13.103 30695 Z= 0.341 Chirality : 0.046 0.315 3601 Planarity : 0.005 0.128 3971 Dihedral : 4.614 40.717 3126 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.31 % Favored : 91.21 % Rotamer: Outliers : 4.93 % Allowed : 29.26 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.16), residues: 2913 helix: 1.50 (0.20), residues: 709 sheet: -0.56 (0.22), residues: 555 loop : -1.99 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP H 65 HIS 0.005 0.001 HIS B 103 PHE 0.021 0.001 PHE P 92 TYR 0.027 0.001 TYR J 39 ARG 0.004 0.000 ARG F 14 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 809) hydrogen bonds : angle 5.14465 ( 2304) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.62849 ( 2) covalent geometry : bond 0.00380 (22531) covalent geometry : angle 0.66751 (30693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 513 time to evaluate : 2.841 Fit side-chains revert: symmetry clash REVERT: A 213 TYR cc_start: 0.8823 (m-10) cc_final: 0.8541 (m-10) REVERT: A 384 TYR cc_start: 0.6705 (OUTLIER) cc_final: 0.6347 (t80) REVERT: B 89 GLU cc_start: 0.8291 (pp20) cc_final: 0.7577 (tp30) REVERT: B 212 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8091 (tp30) REVERT: B 267 GLU cc_start: 0.6175 (tt0) cc_final: 0.5565 (tt0) REVERT: B 384 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.7040 (m-10) REVERT: B 423 MET cc_start: 0.9103 (mmm) cc_final: 0.8653 (mmt) REVERT: B 434 ARG cc_start: 0.8757 (mtp-110) cc_final: 0.8509 (mtp-110) REVERT: C 13 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: C 23 ASP cc_start: 0.9190 (t0) cc_final: 0.8895 (t0) REVERT: D 59 GLN cc_start: 0.9296 (tp40) cc_final: 0.9059 (mm-40) REVERT: D 88 ASP cc_start: 0.8882 (t0) cc_final: 0.8613 (t0) REVERT: E 3 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9190 (tt) REVERT: E 81 ASP cc_start: 0.9427 (p0) cc_final: 0.9195 (p0) REVERT: E 84 TRP cc_start: 0.9252 (OUTLIER) cc_final: 0.7941 (m-90) REVERT: G 40 THR cc_start: 0.9476 (OUTLIER) cc_final: 0.9234 (p) REVERT: G 66 MET cc_start: 0.9432 (mmm) cc_final: 0.9225 (mmm) REVERT: G 83 ASP cc_start: 0.9007 (t70) cc_final: 0.8618 (m-30) REVERT: G 123 ARG cc_start: 0.9158 (ttp-110) cc_final: 0.7637 (mpt180) REVERT: H 65 TRP cc_start: 0.8714 (OUTLIER) cc_final: 0.8345 (t60) REVERT: H 78 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7107 (ptp90) REVERT: H 284 ASP cc_start: 0.8597 (t0) cc_final: 0.8346 (t0) REVERT: J 74 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9057 (mtmm) REVERT: K 57 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8773 (m-30) REVERT: K 91 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8722 (mm110) REVERT: N 107 ASP cc_start: 0.8299 (t0) cc_final: 0.8025 (t0) REVERT: N 109 ASN cc_start: 0.9024 (m110) cc_final: 0.8627 (m110) REVERT: O 12 ILE cc_start: 0.9169 (mm) cc_final: 0.8919 (pt) REVERT: O 47 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9121 (mm-30) REVERT: O 107 ASP cc_start: 0.6574 (t0) cc_final: 0.6328 (t0) outliers start: 113 outliers final: 87 residues processed: 585 average time/residue: 0.3276 time to fit residues: 302.6991 Evaluate side-chains 590 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 493 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 6 ASP Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 335 VAL Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 81 CYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 162 LYS Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 101 ILE Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 249 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 275 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN E 52 ASN ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN M 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080591 restraints weight = 59735.166| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.62 r_work: 0.3004 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.7024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22532 Z= 0.159 Angle : 0.670 14.892 30695 Z= 0.342 Chirality : 0.046 0.314 3601 Planarity : 0.005 0.129 3971 Dihedral : 4.569 40.105 3126 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.17 % Favored : 91.28 % Rotamer: Outliers : 4.98 % Allowed : 28.95 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.16), residues: 2913 helix: 1.55 (0.20), residues: 708 sheet: -0.46 (0.23), residues: 535 loop : -1.96 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 65 HIS 0.006 0.001 HIS B 103 PHE 0.026 0.001 PHE P 92 TYR 0.024 0.001 TYR J 39 ARG 0.005 0.000 ARG D 16 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 809) hydrogen bonds : angle 5.08118 ( 2304) SS BOND : bond 0.00119 ( 1) SS BOND : angle 0.60261 ( 2) covalent geometry : bond 0.00379 (22531) covalent geometry : angle 0.66982 (30693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 504 time to evaluate : 2.662 Fit side-chains revert: symmetry clash REVERT: A 213 TYR cc_start: 0.8806 (m-10) cc_final: 0.8553 (m-10) REVERT: A 384 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.6264 (t80) REVERT: B 89 GLU cc_start: 0.8334 (pp20) cc_final: 0.7623 (tp30) REVERT: B 212 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8083 (tp30) REVERT: B 267 GLU cc_start: 0.6197 (tt0) cc_final: 0.5585 (tt0) REVERT: B 384 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7163 (m-10) REVERT: B 423 MET cc_start: 0.9118 (mmm) cc_final: 0.8693 (mmt) REVERT: B 434 ARG cc_start: 0.8744 (mtp-110) cc_final: 0.8495 (mtp-110) REVERT: C 13 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: C 110 MET cc_start: 0.9180 (ptp) cc_final: 0.8976 (ppp) REVERT: D 12 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8931 (mt) REVERT: D 40 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8514 (mp0) REVERT: D 59 GLN cc_start: 0.9285 (tp40) cc_final: 0.9060 (mm-40) REVERT: D 88 ASP cc_start: 0.8896 (t0) cc_final: 0.8652 (t0) REVERT: E 3 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9198 (tt) REVERT: E 31 GLN cc_start: 0.8440 (mp10) cc_final: 0.8000 (mp10) REVERT: E 81 ASP cc_start: 0.9429 (p0) cc_final: 0.9215 (p0) REVERT: E 84 TRP cc_start: 0.9252 (OUTLIER) cc_final: 0.8018 (m-90) REVERT: G 40 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.9227 (p) REVERT: G 83 ASP cc_start: 0.9009 (t70) cc_final: 0.8600 (m-30) REVERT: G 123 ARG cc_start: 0.9157 (ttp-110) cc_final: 0.7650 (mpt180) REVERT: H 65 TRP cc_start: 0.8730 (OUTLIER) cc_final: 0.8344 (t60) REVERT: H 78 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7103 (ptp90) REVERT: H 284 ASP cc_start: 0.8600 (t0) cc_final: 0.8363 (t0) REVERT: I 160 LYS cc_start: 0.9067 (tppt) cc_final: 0.8849 (tppp) REVERT: J 74 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.9064 (mtmm) REVERT: K 57 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8793 (m-30) REVERT: K 91 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8739 (mm110) REVERT: M 66 SER cc_start: 0.9327 (t) cc_final: 0.9032 (p) REVERT: N 107 ASP cc_start: 0.8234 (t0) cc_final: 0.7920 (t0) REVERT: N 109 ASN cc_start: 0.9012 (m110) cc_final: 0.8520 (m110) REVERT: O 12 ILE cc_start: 0.9172 (mm) cc_final: 0.8920 (pt) REVERT: O 47 GLU cc_start: 0.9465 (mm-30) cc_final: 0.9135 (mm-30) REVERT: O 107 ASP cc_start: 0.6677 (t0) cc_final: 0.6461 (t0) outliers start: 114 outliers final: 89 residues processed: 573 average time/residue: 0.3187 time to fit residues: 285.2532 Evaluate side-chains 602 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 502 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 335 VAL Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 81 CYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 162 LYS Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain O residue 101 ILE Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 252 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN M 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.079386 restraints weight = 60041.708| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.60 r_work: 0.2995 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.7192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 22532 Z= 0.197 Angle : 0.688 14.537 30695 Z= 0.352 Chirality : 0.046 0.317 3601 Planarity : 0.005 0.130 3971 Dihedral : 4.594 39.267 3126 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.38 % Favored : 91.14 % Rotamer: Outliers : 4.89 % Allowed : 29.34 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2913 helix: 1.53 (0.20), residues: 708 sheet: -0.63 (0.23), residues: 552 loop : -1.92 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP H 65 HIS 0.006 0.001 HIS B 103 PHE 0.024 0.001 PHE B 115 TYR 0.025 0.001 TYR J 39 ARG 0.005 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 809) hydrogen bonds : angle 5.11742 ( 2304) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.55022 ( 2) covalent geometry : bond 0.00470 (22531) covalent geometry : angle 0.68829 (30693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 502 time to evaluate : 2.876 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.8121 (mtt90) cc_final: 0.7907 (mtt90) REVERT: A 33 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8342 (mm-30) REVERT: A 160 ASP cc_start: 0.8520 (t0) cc_final: 0.8256 (t0) REVERT: A 213 TYR cc_start: 0.8816 (m-10) cc_final: 0.8522 (m-10) REVERT: A 384 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.5943 (t80) REVERT: B 89 GLU cc_start: 0.8420 (pp20) cc_final: 0.7698 (tp30) REVERT: B 212 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8114 (tp30) REVERT: B 267 GLU cc_start: 0.6162 (tt0) cc_final: 0.5543 (tt0) REVERT: B 297 ASP cc_start: 0.8964 (t0) cc_final: 0.8616 (t0) REVERT: B 384 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7116 (m-10) REVERT: B 423 MET cc_start: 0.9150 (mmm) cc_final: 0.8747 (mmt) REVERT: B 434 ARG cc_start: 0.8729 (mtp-110) cc_final: 0.8456 (mtp-110) REVERT: C 13 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8125 (m-30) REVERT: C 23 ASP cc_start: 0.9203 (t0) cc_final: 0.8922 (t0) REVERT: C 107 ASP cc_start: 0.8541 (t0) cc_final: 0.8286 (t0) REVERT: D 40 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8535 (mp0) REVERT: D 59 GLN cc_start: 0.9304 (tp40) cc_final: 0.9103 (mm-40) REVERT: D 72 TYR cc_start: 0.9227 (t80) cc_final: 0.8981 (t80) REVERT: D 88 ASP cc_start: 0.8921 (t0) cc_final: 0.8677 (t0) REVERT: E 3 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9214 (tt) REVERT: E 81 ASP cc_start: 0.9440 (p0) cc_final: 0.9214 (p0) REVERT: E 84 TRP cc_start: 0.9269 (OUTLIER) cc_final: 0.8030 (m-90) REVERT: G 40 THR cc_start: 0.9462 (OUTLIER) cc_final: 0.9218 (p) REVERT: G 83 ASP cc_start: 0.9012 (t70) cc_final: 0.8583 (m-30) REVERT: G 120 GLU cc_start: 0.9015 (tp30) cc_final: 0.8061 (tm-30) REVERT: G 123 ARG cc_start: 0.9175 (ttp-110) cc_final: 0.7655 (mpt180) REVERT: H 78 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7159 (ptp90) REVERT: H 284 ASP cc_start: 0.8596 (t0) cc_final: 0.8331 (t0) REVERT: J 74 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9092 (mtmm) REVERT: K 91 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8734 (mm110) REVERT: M 66 SER cc_start: 0.9366 (t) cc_final: 0.9067 (p) REVERT: M 89 SER cc_start: 0.9101 (t) cc_final: 0.8767 (p) REVERT: N 107 ASP cc_start: 0.8227 (t0) cc_final: 0.7935 (t0) REVERT: N 109 ASN cc_start: 0.9068 (m110) cc_final: 0.8589 (m110) REVERT: O 12 ILE cc_start: 0.9172 (mm) cc_final: 0.8908 (pt) REVERT: O 47 GLU cc_start: 0.9479 (mm-30) cc_final: 0.9122 (mm-30) REVERT: O 107 ASP cc_start: 0.6805 (t0) cc_final: 0.6584 (t0) outliers start: 112 outliers final: 95 residues processed: 575 average time/residue: 0.3157 time to fit residues: 285.0189 Evaluate side-chains 589 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 486 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 ASN Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 335 VAL Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 441 VAL Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 81 CYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 162 LYS Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 101 ILE Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 13 LEU Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 206 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 276 optimal weight: 0.0370 chunk 169 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 GLN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN M 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.097888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080684 restraints weight = 59819.143| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.62 r_work: 0.3020 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22532 Z= 0.144 Angle : 0.676 14.183 30695 Z= 0.344 Chirality : 0.046 0.317 3601 Planarity : 0.005 0.129 3971 Dihedral : 4.530 38.544 3126 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.20 % Favored : 91.28 % Rotamer: Outliers : 4.19 % Allowed : 30.22 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.16), residues: 2913 helix: 1.53 (0.20), residues: 710 sheet: -0.24 (0.24), residues: 514 loop : -1.91 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP H 65 HIS 0.005 0.001 HIS B 103 PHE 0.027 0.001 PHE B 115 TYR 0.023 0.001 TYR J 39 ARG 0.004 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 809) hydrogen bonds : angle 5.06710 ( 2304) SS BOND : bond 0.00103 ( 1) SS BOND : angle 0.60657 ( 2) covalent geometry : bond 0.00344 (22531) covalent geometry : angle 0.67615 (30693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5826 Ramachandran restraints generated. 2913 Oldfield, 0 Emsley, 2913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 509 time to evaluate : 2.631 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 213 TYR cc_start: 0.8789 (m-10) cc_final: 0.8546 (m-10) REVERT: A 384 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.6137 (t80) REVERT: A 423 MET cc_start: 0.4335 (mtp) cc_final: 0.3391 (ptp) REVERT: B 89 GLU cc_start: 0.8433 (pp20) cc_final: 0.7704 (tp30) REVERT: B 212 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8084 (tp30) REVERT: B 267 GLU cc_start: 0.6152 (tt0) cc_final: 0.5545 (tt0) REVERT: B 297 ASP cc_start: 0.8973 (t0) cc_final: 0.8644 (t0) REVERT: B 370 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8513 (tm-30) REVERT: B 384 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7175 (m-10) REVERT: B 423 MET cc_start: 0.9152 (mmm) cc_final: 0.8751 (mmt) REVERT: B 434 ARG cc_start: 0.8658 (mtp-110) cc_final: 0.8405 (mtp-110) REVERT: C 13 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: D 40 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8552 (mp0) REVERT: D 55 TYR cc_start: 0.9409 (t80) cc_final: 0.9177 (t80) REVERT: D 59 GLN cc_start: 0.9278 (tp40) cc_final: 0.9073 (mm-40) REVERT: D 72 TYR cc_start: 0.9205 (t80) cc_final: 0.8962 (t80) REVERT: D 88 ASP cc_start: 0.8941 (t0) cc_final: 0.8714 (t0) REVERT: E 3 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9220 (tt) REVERT: E 31 GLN cc_start: 0.8477 (mp10) cc_final: 0.8008 (mm-40) REVERT: E 51 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8579 (mtmm) REVERT: E 81 ASP cc_start: 0.9441 (p0) cc_final: 0.9222 (p0) REVERT: E 84 TRP cc_start: 0.9255 (OUTLIER) cc_final: 0.7988 (m-90) REVERT: G 40 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9200 (p) REVERT: G 83 ASP cc_start: 0.8997 (t70) cc_final: 0.8577 (m-30) REVERT: G 120 GLU cc_start: 0.9015 (tp30) cc_final: 0.8149 (tm-30) REVERT: G 123 ARG cc_start: 0.9163 (ttp-110) cc_final: 0.7699 (mpt180) REVERT: H 65 TRP cc_start: 0.8776 (OUTLIER) cc_final: 0.8414 (t60) REVERT: H 78 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7117 (ptp90) REVERT: H 133 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8644 (mt-10) REVERT: H 284 ASP cc_start: 0.8585 (t0) cc_final: 0.8357 (t0) REVERT: J 74 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.9074 (mtmm) REVERT: K 91 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8747 (mm110) REVERT: M 66 SER cc_start: 0.9353 (t) cc_final: 0.9029 (p) REVERT: M 80 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8433 (tttm) REVERT: N 107 ASP cc_start: 0.8182 (t0) cc_final: 0.7978 (t0) REVERT: N 109 ASN cc_start: 0.9063 (m110) cc_final: 0.8565 (m110) REVERT: O 47 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9113 (mm-30) REVERT: O 107 ASP cc_start: 0.6763 (t0) cc_final: 0.6557 (t0) outliers start: 96 outliers final: 81 residues processed: 568 average time/residue: 0.3079 time to fit residues: 274.6798 Evaluate side-chains 579 residues out of total 2573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 489 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 384 TYR Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 436 HIS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 78 ARG Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 259 THR Chi-restraints excluded: chain H residue 335 VAL Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 164 ARG Chi-restraints excluded: chain J residue 74 LYS Chi-restraints excluded: chain J residue 81 CYS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 162 LYS Chi-restraints excluded: chain K residue 12 ILE Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 88 SER Chi-restraints excluded: chain M residue 3 THR Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 57 ASP Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain O residue 15 THR Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 101 ILE Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain P residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 232 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 276 optimal weight: 30.0000 chunk 198 optimal weight: 0.3980 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 30.0000 chunk 79 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN E 52 ASN ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN M 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.079837 restraints weight = 59824.465| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.60 r_work: 0.2997 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.7430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22532 Z= 0.171 Angle : 0.686 14.516 30695 Z= 0.350 Chirality : 0.046 0.314 3601 Planarity : 0.005 0.129 3971 Dihedral : 4.504 38.806 3126 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.20 % Favored : 91.31 % Rotamer: Outliers : 4.41 % Allowed : 30.00 % Favored : 65.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.16), residues: 2913 helix: 1.53 (0.20), residues: 711 sheet: -0.49 (0.23), residues: 546 loop : -1.87 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP H 65 HIS 0.005 0.001 HIS I 14 PHE 0.030 0.001 PHE B 115 TYR 0.024 0.001 TYR J 39 ARG 0.004 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 809) hydrogen bonds : angle 5.04349 ( 2304) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.55368 ( 2) covalent geometry : bond 0.00413 (22531) covalent geometry : angle 0.68633 (30693) =============================================================================== Job complete usr+sys time: 14032.24 seconds wall clock time: 244 minutes 42.49 seconds (14682.49 seconds total)