Starting phenix.real_space_refine on Sun Jul 5 09:43:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zm3_60235/07_2026/8zm3_60235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zm3_60235/07_2026/8zm3_60235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zm3_60235/07_2026/8zm3_60235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zm3_60235/07_2026/8zm3_60235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zm3_60235/07_2026/8zm3_60235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zm3_60235/07_2026/8zm3_60235.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 573 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 58 5.49 5 Mg 2 5.21 5 S 117 5.16 5 C 16878 2.51 5 N 4735 2.21 5 O 5148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26938 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1258 Classifications: {'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 17, 'rna3p_pyr': 19} Link IDs: {'rna2p': 22, 'rna3p': 36} Chain breaks: 1 Chain: "C" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3476 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 29, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1352 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 156} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2799 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2833 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2781 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 13, 'TRANS': 350} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2804 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2624 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 329} Chain breaks: 5 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 1919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1919 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 240} Chain breaks: 4 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2955 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 348} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2135 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 20, 'TRANS': 247} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2398 SG CYS C 218 63.786 53.238 166.219 1.00 96.02 S ATOM 3098 SG CYS C 311 60.901 49.853 165.071 1.00 96.16 S ATOM 24137 SG CYS B 298 41.193 48.632 72.333 1.00 28.05 S ATOM 24158 SG CYS B 301 39.361 50.567 69.937 1.00 27.63 S ATOM 24371 SG CYS B 329 43.440 51.007 69.732 1.00 27.44 S ATOM 24396 SG CYS B 332 40.606 52.341 72.967 1.00 26.81 S Time building chain proxies: 5.88, per 1000 atoms: 0.22 Number of scatterers: 26938 At special positions: 0 Unit cell: (113.71, 144.42, 197.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 117 16.00 P 58 15.00 Mg 2 11.99 O 5148 8.00 N 4735 7.00 C 16878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.0 seconds 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6190 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 30 sheets defined 35.1% alpha, 17.3% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 120 through 143 removed outlier: 3.558A pdb=" N PHE C 128 " --> pdb=" O ARG C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 163 removed outlier: 4.189A pdb=" N TRP C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU C 160 " --> pdb=" O TRP C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 167 removed outlier: 3.638A pdb=" N PHE C 167 " --> pdb=" O LYS C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 164 through 167' Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.691A pdb=" N THR C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 376 removed outlier: 4.095A pdb=" N LEU C 375 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N PHE C 376 " --> pdb=" O SER C 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 372 through 376' Processing helix chain 'C' and resid 418 through 427 Processing helix chain 'C' and resid 428 through 437 Processing helix chain 'C' and resid 450 through 465 removed outlier: 3.660A pdb=" N ALA C 454 " --> pdb=" O THR C 450 " (cutoff:3.500A) Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 467 through 474 removed outlier: 3.784A pdb=" N GLU C 473 " --> pdb=" O GLY C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 484 removed outlier: 3.564A pdb=" N THR C 484 " --> pdb=" O GLN C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 498 removed outlier: 3.644A pdb=" N TYR C 495 " --> pdb=" O THR C 491 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER C 496 " --> pdb=" O LYS C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 513 Processing helix chain 'E' and resid 4 through 14 Processing helix chain 'E' and resid 16 through 26 removed outlier: 3.629A pdb=" N LEU E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 52 Proline residue: E 47 - end of helix Processing helix chain 'E' and resid 57 through 72 Processing helix chain 'E' and resid 80 through 88 removed outlier: 5.059A pdb=" N GLY E 86 " --> pdb=" O PRO E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 92 removed outlier: 3.665A pdb=" N LEU E 92 " --> pdb=" O CYS E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 96 through 107 removed outlier: 3.744A pdb=" N ARG E 100 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 111 Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.558A pdb=" N MET E 116 " --> pdb=" O ILE E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 130 Processing helix chain 'E' and resid 136 through 145 Processing helix chain 'E' and resid 149 through 155 removed outlier: 3.679A pdb=" N LYS E 153 " --> pdb=" O GLN E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 166 removed outlier: 3.725A pdb=" N ILE E 166 " --> pdb=" O LYS E 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 52 through 56 removed outlier: 4.107A pdb=" N LEU F 56 " --> pdb=" O LYS F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 78 through 89 removed outlier: 3.509A pdb=" N GLY F 89 " --> pdb=" O LEU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.744A pdb=" N ASP F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 136 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 234 through 250 removed outlier: 3.529A pdb=" N ALA F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 285 removed outlier: 3.818A pdb=" N ALA F 283 " --> pdb=" O TYR F 280 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 284 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 285' Processing helix chain 'F' and resid 295 through 313 Processing helix chain 'F' and resid 329 through 332 Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 63 through 73 removed outlier: 3.587A pdb=" N LEU H 67 " --> pdb=" O ARG H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.764A pdb=" N GLY H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 96 removed outlier: 3.547A pdb=" N ASP H 95 " --> pdb=" O ASN H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 116 Processing helix chain 'H' and resid 122 through 134 Processing helix chain 'H' and resid 139 through 146 Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 280 through 286 removed outlier: 4.417A pdb=" N ARG H 286 " --> pdb=" O ALA H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 315 Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 349 through 362 removed outlier: 3.828A pdb=" N GLY H 362 " --> pdb=" O LEU H 358 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 371 Processing helix chain 'I' and resid 38 through 49 removed outlier: 3.560A pdb=" N ILE I 42 " --> pdb=" O SER I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 53 Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 80 through 88 removed outlier: 4.901A pdb=" N ASN I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 116 removed outlier: 3.720A pdb=" N LYS I 109 " --> pdb=" O LYS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 134 removed outlier: 3.790A pdb=" N GLN I 128 " --> pdb=" O GLU I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 146 Processing helix chain 'I' and resid 223 through 230 Processing helix chain 'I' and resid 235 through 250 removed outlier: 3.782A pdb=" N HIS I 239 " --> pdb=" O ASN I 235 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL I 241 " --> pdb=" O ALA I 237 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA I 249 " --> pdb=" O LEU I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 285 removed outlier: 3.687A pdb=" N VAL I 285 " --> pdb=" O ASN I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 315 removed outlier: 3.642A pdb=" N GLN I 299 " --> pdb=" O ASP I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 329 through 332 Processing helix chain 'I' and resid 349 through 363 removed outlier: 3.540A pdb=" N GLY I 362 " --> pdb=" O LEU I 358 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 370 removed outlier: 3.627A pdb=" N GLN I 370 " --> pdb=" O TRP I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 373 No H-bonds generated for 'chain 'I' and resid 371 through 373' Processing helix chain 'J' and resid 38 through 48 Processing helix chain 'J' and resid 63 through 73 removed outlier: 4.589A pdb=" N LEU J 67 " --> pdb=" O ARG J 63 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY J 73 " --> pdb=" O GLN J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 89 removed outlier: 3.509A pdb=" N ALA J 81 " --> pdb=" O CYS J 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY J 89 " --> pdb=" O LEU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 96 removed outlier: 3.736A pdb=" N ASP J 95 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN J 96 " --> pdb=" O LYS J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 96' Processing helix chain 'J' and resid 108 through 116 Processing helix chain 'J' and resid 123 through 133 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 223 through 230 removed outlier: 3.558A pdb=" N LEU J 230 " --> pdb=" O LEU J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 250 Processing helix chain 'J' and resid 280 through 285 removed outlier: 3.580A pdb=" N PHE J 284 " --> pdb=" O ALA J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 313 Processing helix chain 'J' and resid 349 through 363 Processing helix chain 'J' and resid 365 through 370 removed outlier: 3.669A pdb=" N VAL J 369 " --> pdb=" O LYS J 365 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN J 370 " --> pdb=" O TRP J 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 365 through 370' Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 42 through 47 removed outlier: 3.958A pdb=" N ARG K 47 " --> pdb=" O LYS K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 89 removed outlier: 3.774A pdb=" N GLY K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 129 removed outlier: 3.753A pdb=" N GLN K 127 " --> pdb=" O GLU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 250 removed outlier: 3.705A pdb=" N ALA K 248 " --> pdb=" O PHE K 244 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA K 249 " --> pdb=" O LEU K 245 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS K 250 " --> pdb=" O LEU K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 313 Processing helix chain 'K' and resid 349 through 359 Processing helix chain 'K' and resid 365 through 371 Processing helix chain 'G' and resid 38 through 43 Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 234 through 250 removed outlier: 3.578A pdb=" N LYS G 250 " --> pdb=" O LEU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 285 removed outlier: 3.573A pdb=" N VAL G 285 " --> pdb=" O ASN G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 309 removed outlier: 3.816A pdb=" N TYR G 307 " --> pdb=" O GLN G 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL G 308 " --> pdb=" O LEU G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 362 Processing helix chain 'B' and resid 36 through 49 removed outlier: 3.547A pdb=" N VAL B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 removed outlier: 4.005A pdb=" N LEU B 63 " --> pdb=" O TRP B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.862A pdb=" N LYS B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.590A pdb=" N VAL B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 357 through 372 Processing helix chain 'B' and resid 373 through 378 removed outlier: 3.709A pdb=" N ARG B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 25 removed outlier: 3.818A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 37 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.783A pdb=" N ASP D 59 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE D 60 " --> pdb=" O PRO D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.523A pdb=" N CYS D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 96 " --> pdb=" O TRP D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 91 through 96' Processing helix chain 'D' and resid 99 through 103 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.548A pdb=" N LEU D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 255 through 259 Processing sheet with id=AA1, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AA3, first strand: chain 'C' and resid 248 through 252 removed outlier: 4.289A pdb=" N LYS C 389 " --> pdb=" O HIS C 252 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 388 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ASP C 404 " --> pdb=" O ALA C 396 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP C 398 " --> pdb=" O SER C 402 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 74 through 75 removed outlier: 5.378A pdb=" N GLU E 74 " --> pdb=" O LEU E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.702A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.702A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY F 268 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TRP F 326 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 58 through 61 Processing sheet with id=AA8, first strand: chain 'F' and resid 185 through 187 Processing sheet with id=AA9, first strand: chain 'H' and resid 26 through 29 removed outlier: 5.660A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 26 through 29 removed outlier: 5.660A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY H 268 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE H 323 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG H 345 " --> pdb=" O GLY H 324 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 61 Processing sheet with id=AB3, first strand: chain 'H' and resid 185 through 187 Processing sheet with id=AB4, first strand: chain 'I' and resid 26 through 29 removed outlier: 3.518A pdb=" N VAL I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER I 178 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 26 through 29 removed outlier: 3.518A pdb=" N VAL I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER I 178 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP I 326 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 185 through 187 Processing sheet with id=AB7, first strand: chain 'J' and resid 25 through 29 removed outlier: 4.161A pdb=" N LYS J 25 " --> pdb=" O ARG J 36 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER J 178 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE J 177 " --> pdb=" O TYR J 216 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 25 through 29 removed outlier: 4.161A pdb=" N LYS J 25 " --> pdb=" O ARG J 36 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER J 35 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER J 178 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE J 177 " --> pdb=" O TYR J 216 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU J 2 " --> pdb=" O PHE J 273 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE J 273 " --> pdb=" O LEU J 2 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU J 4 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL J 271 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N HIS J 6 " --> pdb=" O ILE J 269 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE J 269 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE J 8 " --> pdb=" O ASP J 267 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE J 323 " --> pdb=" O PHE J 273 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY J 324 " --> pdb=" O ARG J 345 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE J 347 " --> pdb=" O GLY J 324 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP J 326 " --> pdb=" O ILE J 347 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'K' and resid 172 through 177 removed outlier: 3.607A pdb=" N TYR K 218 " --> pdb=" O ALA K 174 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA K 176 " --> pdb=" O TYR K 216 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR K 216 " --> pdb=" O ALA K 176 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS K 217 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU K 4 " --> pdb=" O GLU K 272 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU K 272 " --> pdb=" O GLU K 4 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N HIS K 6 " --> pdb=" O LEU K 270 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU K 270 " --> pdb=" O HIS K 6 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TRP K 326 " --> pdb=" O ILE K 347 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 60 through 61 Processing sheet with id=AC3, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.767A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 26 through 29 removed outlier: 5.767A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY G 268 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG G 345 " --> pdb=" O GLY G 324 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 7 through 17 removed outlier: 6.799A pdb=" N THR B 7 " --> pdb=" O GLN B 142 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN B 142 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE B 9 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 140 " --> pdb=" O PHE B 9 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG B 11 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 138 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU B 13 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N SER B 136 " --> pdb=" O GLU B 13 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ALA B 15 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 134 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 28 through 29 removed outlier: 7.701A pdb=" N ARG B 29 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 9.356A pdb=" N LEU B 132 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER B 136 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 69 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG B 74 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 11.649A pdb=" N ILE B 207 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 212 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG B 241 " --> pdb=" O PRO B 234 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU B 243 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AC9, first strand: chain 'B' and resid 307 through 310 removed outlier: 3.543A pdb=" N LEU B 328 " --> pdb=" O THR B 307 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 66 through 70 removed outlier: 3.613A pdb=" N GLU D 108 " --> pdb=" O ARG D 6 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 184 through 205 removed outlier: 7.728A pdb=" N GLN D 187 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N GLU D 237 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N CYS D 189 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL D 235 " --> pdb=" O CYS D 189 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU D 191 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N GLU D 233 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 193 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS D 201 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 131 through 140 removed outlier: 6.178A pdb=" N LYS D 151 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL D 140 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N THR D 149 " --> pdb=" O VAL D 140 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2694 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 11 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 5.46 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4536 1.32 - 1.45: 7677 1.45 - 1.57: 15142 1.57 - 1.70: 119 1.70 - 1.83: 175 Bond restraints: 27649 Sorted by residual: bond pdb=" CA ASN K 282 " pdb=" C ASN K 282 " ideal model delta sigma weight residual 1.521 1.472 0.048 9.90e-03 1.02e+04 2.37e+01 bond pdb=" CB MET G 209 " pdb=" CG MET G 209 " ideal model delta sigma weight residual 1.520 1.376 0.144 3.00e-02 1.11e+03 2.32e+01 bond pdb=" N TYR K 280 " pdb=" CA TYR K 280 " ideal model delta sigma weight residual 1.457 1.410 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" CA SER K 178 " pdb=" C SER K 178 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.26e-02 6.30e+03 1.62e+01 bond pdb=" CA PHE K 215 " pdb=" C PHE K 215 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.03e-02 9.43e+03 1.60e+01 ... (remaining 27644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 37198 3.49 - 6.97: 482 6.97 - 10.46: 77 10.46 - 13.94: 20 13.94 - 17.43: 2 Bond angle restraints: 37779 Sorted by residual: angle pdb=" N VAL K 129 " pdb=" CA VAL K 129 " pdb=" C VAL K 129 " ideal model delta sigma weight residual 112.96 97.21 15.75 1.00e+00 1.00e+00 2.48e+02 angle pdb=" N TYR K 280 " pdb=" CA TYR K 280 " pdb=" C TYR K 280 " ideal model delta sigma weight residual 112.57 99.51 13.06 1.13e+00 7.83e-01 1.34e+02 angle pdb=" N SER K 39 " pdb=" CA SER K 39 " pdb=" C SER K 39 " ideal model delta sigma weight residual 113.20 99.60 13.60 1.21e+00 6.83e-01 1.26e+02 angle pdb=" N ASN K 235 " pdb=" CA ASN K 235 " pdb=" C ASN K 235 " ideal model delta sigma weight residual 111.71 99.40 12.31 1.15e+00 7.56e-01 1.15e+02 angle pdb=" N ILE K 181 " pdb=" CA ILE K 181 " pdb=" C ILE K 181 " ideal model delta sigma weight residual 109.58 96.52 13.06 1.29e+00 6.01e-01 1.02e+02 ... (remaining 37774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 15758 35.82 - 71.63: 835 71.63 - 107.45: 61 107.45 - 143.27: 3 143.27 - 179.08: 4 Dihedral angle restraints: 16661 sinusoidal: 7086 harmonic: 9575 Sorted by residual: dihedral pdb=" O4' U A 34 " pdb=" C1' U A 34 " pdb=" N1 U A 34 " pdb=" C2 U A 34 " ideal model delta sinusoidal sigma weight residual 200.00 36.58 163.42 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' C A 6 " pdb=" C1' C A 6 " pdb=" N1 C A 6 " pdb=" C2 C A 6 " ideal model delta sinusoidal sigma weight residual 200.00 49.58 150.42 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" O4' U A 18 " pdb=" C1' U A 18 " pdb=" N1 U A 18 " pdb=" C2 U A 18 " ideal model delta sinusoidal sigma weight residual 200.00 62.30 137.70 1 1.50e+01 4.44e-03 7.42e+01 ... (remaining 16658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3884 0.101 - 0.201: 292 0.201 - 0.302: 29 0.302 - 0.402: 8 0.402 - 0.503: 2 Chirality restraints: 4215 Sorted by residual: chirality pdb=" CA ASP K 20 " pdb=" N ASP K 20 " pdb=" C ASP K 20 " pdb=" CB ASP K 20 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" CA TRP K 223 " pdb=" N TRP K 223 " pdb=" C TRP K 223 " pdb=" CB TRP K 223 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA ASP K 19 " pdb=" N ASP K 19 " pdb=" C ASP K 19 " pdb=" CB ASP K 19 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 4212 not shown) Planarity restraints: 4692 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 337 " 0.035 2.00e-02 2.50e+03 4.42e-02 3.92e+01 pdb=" CG TYR G 337 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 TYR G 337 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR G 337 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR G 337 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR G 337 " 0.039 2.00e-02 2.50e+03 pdb=" CZ TYR G 337 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR G 337 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA I 23 " 0.096 5.00e-02 4.00e+02 1.43e-01 3.26e+01 pdb=" N PRO I 24 " -0.247 5.00e-02 4.00e+02 pdb=" CA PRO I 24 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO I 24 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN K 252 " 0.083 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO K 253 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " 0.064 5.00e-02 4.00e+02 ... (remaining 4689 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1052 2.71 - 3.25: 24361 3.25 - 3.80: 42740 3.80 - 4.35: 52823 4.35 - 4.90: 87979 Nonbonded interactions: 208955 Sorted by model distance: nonbonded pdb=" O PHE J 29 " pdb=" NH1 ARG J 34 " model vdw 2.157 3.120 nonbonded pdb=" O ALA G 247 " pdb=" OG1 THR G 251 " model vdw 2.199 3.040 nonbonded pdb=" O ASP D 48 " pdb=" OH TYR D 94 " model vdw 2.209 3.040 nonbonded pdb=" O GLU G 185 " pdb=" CG MET G 209 " model vdw 2.230 3.440 nonbonded pdb=" ND2 ASN F 252 " pdb=" O ALA F 262 " model vdw 2.245 3.120 ... (remaining 208950 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 'F' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 78 or (resid 79 through 81 and (name N or name CA or name C or name O or name \ CB )) or resid 82 through 86 or (resid 87 and (name N or name CA or name C or na \ me O or name CB )) or resid 88 through 98 or (resid 99 and (name N or name CA or \ name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (name \ N or name CA or name C or name O or name CB )) or resid 106 through 116 or (res \ id 117 through 118 and (name N or name CA or name C or name O or name CB )) or r \ esid 119 or (resid 120 and (name N or name CA or name C or name O or name CB )) \ or resid 121 or (resid 122 through 126 and (name N or name CA or name C or name \ O or name CB )) or resid 127 through 155 or (resid 156 and (name N or name CA or \ name C or name O or name CB )) or resid 157 through 159 or (resid 160 through 1 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 162 through \ 192 or resid 208 through 225 or (resid 226 and (name N or name CA or name C or \ name O or name CB )) or resid 227 or (resid 228 and (name N or name CA or name C \ or name O or name CB )) or resid 229 through 230 or (resid 231 and (name N or n \ ame CA or name C or name O or name CB )) or resid 232 through 256 or resid 263 t \ hrough 291 or (resid 292 and (name N or name CA or name C or name O or name CB ) \ ) or resid 293 through 315 or (resid 316 and (name N or name CA or name C or nam \ e O or name CB )) or resid 324 through 338 or (resid 339 and (name N or name CA \ or name C or name O or name CB )) or resid 340 or (resid 341 and (name N or name \ CA or name C or name O or name CB )) or resid 342 through 351 or (resid 352 and \ (name N or name CA or name C or name O or name CB )) or resid 353 through 359 o \ r resid 361 through 368 or (resid 369 and (name N or name CA or name C or name O \ or name CB )) or resid 370 through 372)) selection = (chain 'H' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 74 or (resi \ d 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throug \ h 79 or (resid 80 through 81 and (name N or name CA or name C or name O or name \ CB )) or resid 82 or (resid 83 and (name N or name CA or name C or name O or nam \ e CB )) or resid 84 through 90 or (resid 91 and (name N or name CA or name C or \ name O or name CB )) or resid 97 or (resid 98 through 99 and (name N or name CA \ or name C or name O or name CB )) or resid 100 through 104 or (resid 105 and (na \ me N or name CA or name C or name O or name CB )) or resid 106 through 116 or (r \ esid 117 through 118 and (name N or name CA or name C or name O or name CB )) or \ resid 119 through 121 or (resid 122 through 126 and (name N or name CA or name \ C or name O or name CB )) or resid 127 through 152 or (resid 153 through 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 or (resid 156 \ and (name N or name CA or name C or name O or name CB )) or resid 157 through 1 \ 59 or (resid 160 through 161 and (name N or name CA or name C or name O or name \ CB )) or resid 162 through 192 or resid 208 through 225 or (resid 226 and (name \ N or name CA or name C or name O or name CB )) or resid 227 or (resid 228 and (n \ ame N or name CA or name C or name O or name CB )) or resid 229 through 230 or ( \ resid 231 and (name N or name CA or name C or name O or name CB )) or resid 232 \ through 256 or resid 263 through 291 or (resid 292 and (name N or name CA or nam \ e C or name O or name CB )) or resid 293 through 311 or (resid 312 and (name N o \ r name CA or name C or name O or name CB )) or resid 313 through 316 or resid 32 \ 4 through 338 or (resid 339 and (name N or name CA or name C or name O or name C \ B )) or resid 340 or (resid 341 and (name N or name CA or name C or name O or na \ me CB )) or resid 342 through 351 or (resid 352 and (name N or name CA or name C \ or name O or name CB )) or resid 353 through 359 or resid 361 through 364 or (r \ esid 365 and (name N or name CA or name C or name O or name CB )) or resid 366 t \ hrough 367 or (resid 368 through 369 and (name N or name CA or name C or name O \ or name CB )) or resid 370 through 372)) selection = (chain 'I' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 74 or (resid 75 and (nam \ e N or name CA or name C or name O or name CB )) or resid 76 through 82 or (resi \ d 83 and (name N or name CA or name C or name O or name CB )) or resid 84 throug \ h 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or re \ sid 97 or (resid 98 through 99 and (name N or name CA or name C or name O or nam \ e CB )) or resid 100 through 104 or (resid 105 and (name N or name CA or name C \ or name O or name CB )) or resid 106 through 108 or (resid 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 119 or (resid 120 a \ nd (name N or name CA or name C or name O or name CB )) or resid 121 through 159 \ or (resid 160 through 161 and (name N or name CA or name C or name O or name CB \ )) or resid 162 through 192 or resid 208 through 225 or (resid 226 and (name N \ or name CA or name C or name O or name CB )) or resid 227 or (resid 228 and (nam \ e N or name CA or name C or name O or name CB )) or resid 229 through 256 or res \ id 263 through 311 or (resid 312 and (name N or name CA or name C or name O or n \ ame CB )) or resid 313 through 315 or (resid 316 and (name N or name CA or name \ C or name O or name CB )) or resid 324 through 338 or (resid 339 and (name N or \ name CA or name C or name O or name CB )) or resid 340 through 351 or (resid 352 \ and (name N or name CA or name C or name O or name CB )) or resid 353 through 3 \ 59 or resid 361 through 364 or (resid 365 and (name N or name CA or name C or na \ me O or name CB )) or resid 366 through 367 or (resid 368 through 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 or (resid 371 and (n \ ame N or name CA or name C or name O or name CB )) or resid 372)) selection = (chain 'J' and (resid 1 through 52 or (resid 53 through 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 69 or (resid 70 and (nam \ e N or name CA or name C or name O or name CB )) or resid 71 through 79 or (resi \ d 80 through 81 and (name N or name CA or name C or name O or name CB )) or resi \ d 82 through 86 or (resid 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 90 or (resid 91 and (name N or name CA or name C or na \ me O or name CB )) or resid 97 or (resid 98 through 99 and (name N or name CA or \ name C or name O or name CB )) or resid 100 through 108 or (resid 109 and (name \ N or name CA or name C or name O or name CB )) or resid 110 through 116 or (res \ id 117 through 118 and (name N or name CA or name C or name O or name CB )) or r \ esid 119 through 121 or (resid 122 through 126 and (name N or name CA or name C \ or name O or name CB )) or resid 127 through 152 or (resid 153 through 154 and ( \ name N or name CA or name C or name O or name CB )) or resid 155 or (resid 156 a \ nd (name N or name CA or name C or name O or name CB )) or resid 157 or (resid 1 \ 58 through 161 and (name N or name CA or name C or name O or name CB )) or resid \ 162 through 192 or resid 208 through 225 or (resid 226 and (name N or name CA o \ r name C or name O or name CB )) or resid 227 through 230 or (resid 231 and (nam \ e N or name CA or name C or name O or name CB )) or resid 232 through 256 or res \ id 263 through 311 or (resid 312 and (name N or name CA or name C or name O or n \ ame CB )) or resid 313 through 315 or (resid 316 and (name N or name CA or name \ C or name O or name CB )) or resid 324 through 351 or (resid 352 and (name N or \ name CA or name C or name O or name CB )) or resid 353 through 359 or resid 361 \ through 367 or (resid 368 through 369 and (name N or name CA or name C or name O \ or name CB )) or resid 370 or (resid 371 and (name N or name CA or name C or na \ me O or name CB )) or resid 372)) selection = (chain 'K' and (resid 1 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 78 or (resid 79 throug \ h 81 and (name N or name CA or name C or name O or name CB )) or resid 82 or (re \ sid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 thro \ ugh 86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or \ resid 88 through 90 or (resid 91 and (name N or name CA or name C or name O or n \ ame CB )) or resid 97 or (resid 98 through 99 and (name N or name CA or name C o \ r name O or name CB )) or resid 100 through 104 or (resid 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 through 108 or (resid 109 an \ d (name N or name CA or name C or name O or name CB )) or resid 110 through 116 \ or (resid 117 through 118 and (name N or name CA or name C or name O or name CB \ )) or resid 119 or (resid 120 and (name N or name CA or name C or name O or name \ CB )) or resid 121 or (resid 122 through 126 and (name N or name CA or name C o \ r name O or name CB )) or resid 127 through 152 or (resid 153 through 154 and (n \ ame N or name CA or name C or name O or name CB )) or resid 155 or (resid 156 an \ d (name N or name CA or name C or name O or name CB )) or resid 157 through 159 \ or (resid 160 through 161 and (name N or name CA or name C or name O or name CB \ )) or resid 162 through 227 or (resid 228 and (name N or name CA or name C or na \ me O or name CB )) or resid 229 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 through 311 or (resid 312 and (n \ ame N or name CA or name C or name O or name CB )) or resid 313 through 338 or ( \ resid 339 and (name N or name CA or name C or name O or name CB )) or resid 340 \ or (resid 341 and (name N or name CA or name C or name O or name CB )) or resid \ 342 through 367 or (resid 368 through 369 and (name N or name CA or name C or na \ me O or name CB )) or resid 370 through 372)) } 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.590 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 27649 Z= 0.307 Angle : 1.027 17.429 37779 Z= 0.620 Chirality : 0.058 0.503 4215 Planarity : 0.008 0.143 4692 Dihedral : 19.992 179.084 10471 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.03 % Favored : 89.39 % Rotamer: Outliers : 4.62 % Allowed : 26.01 % Favored : 69.37 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.13), residues: 3260 helix: -1.17 (0.14), residues: 1094 sheet: 0.34 (0.22), residues: 511 loop : -2.36 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 62 TYR 0.101 0.002 TYR G 337 PHE 0.036 0.002 PHE C 128 TRP 0.036 0.002 TRP B 59 HIS 0.007 0.001 HIS I 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.31 (27649) covalent geometry : angle 1.02671 / 0.62 (37779) hydrogen bonds : bond 0.19523 / 19.45 ( 945) hydrogen bonds : angle 7.39904 / 8.33 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 313 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 HIS cc_start: 0.5472 (OUTLIER) cc_final: 0.3753 (m-70) REVERT: K 21 LEU cc_start: 0.3686 (OUTLIER) cc_final: 0.3469 (mp) REVERT: K 33 LEU cc_start: 0.4317 (OUTLIER) cc_final: 0.3992 (tp) REVERT: K 44 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.5999 (ttt-90) REVERT: K 78 TRP cc_start: 0.4807 (OUTLIER) cc_final: 0.4521 (t60) REVERT: K 280 TYR cc_start: 0.5487 (OUTLIER) cc_final: 0.4254 (m-80) REVERT: K 295 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6778 (t0) REVERT: K 298 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5918 (mt-10) REVERT: K 299 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6406 (mp-120) outliers start: 124 outliers final: 49 residues processed: 401 average time/residue: 0.1918 time to fit residues: 120.7660 Evaluate side-chains 361 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 303 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 10 ASN Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 44 ARG Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 78 TRP Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 88 CYS Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain K residue 131 ASN Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 165 THR Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 172 GLN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 217 LYS Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 233 ASP Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 295 ASP Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain D residue 41 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 6.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 501 GLN E 50 GLN F 239 HIS ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 GLN ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 264 ASN K 10 ASN K 17 ASN K 131 ASN K 135 GLN ** K 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN ** K 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 235 ASN K 239 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS D 135 HIS D 193 GLN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.223972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.209985 restraints weight = 59206.452| |-----------------------------------------------------------------------------| r_work (start): 0.4753 rms_B_bonded: 2.39 r_work: 0.4690 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4873 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27649 Z= 0.135 Angle : 0.640 11.081 37779 Z= 0.337 Chirality : 0.043 0.264 4215 Planarity : 0.005 0.070 4692 Dihedral : 15.130 179.122 4606 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.01 % Favored : 91.84 % Rotamer: Outliers : 3.95 % Allowed : 25.82 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3260 helix: -0.29 (0.15), residues: 1100 sheet: 0.37 (0.22), residues: 520 loop : -2.15 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 47 TYR 0.033 0.001 TYR G 337 PHE 0.030 0.002 PHE C 376 TRP 0.024 0.001 TRP E 156 HIS 0.005 0.001 HIS K 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (27649) covalent geometry : angle 0.63975 / 0.34 (37779) hydrogen bonds : bond 0.04418 / 4.15 ( 945) hydrogen bonds : angle 5.42415 / 6.19 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 322 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 SER cc_start: 0.6532 (OUTLIER) cc_final: 0.6102 (p) REVERT: C 424 GLN cc_start: 0.5644 (mm110) cc_final: 0.5316 (mt0) REVERT: H 33 LEU cc_start: 0.4898 (OUTLIER) cc_final: 0.4687 (mp) REVERT: J 5 ILE cc_start: 0.3511 (mm) cc_final: 0.3289 (mm) REVERT: K 42 ILE cc_start: 0.7122 (pt) cc_final: 0.6858 (pt) REVERT: K 46 ILE cc_start: 0.4877 (OUTLIER) cc_final: 0.4236 (tt) REVERT: K 51 ASP cc_start: 0.5184 (OUTLIER) cc_final: 0.4853 (p0) REVERT: K 78 TRP cc_start: 0.4939 (OUTLIER) cc_final: 0.4573 (t60) REVERT: K 114 ILE cc_start: 0.6133 (OUTLIER) cc_final: 0.5805 (tp) REVERT: K 256 LYS cc_start: 0.2202 (OUTLIER) cc_final: 0.0851 (tttm) REVERT: K 298 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6183 (mt-10) REVERT: B 95 GLU cc_start: 0.0626 (OUTLIER) cc_final: -0.2286 (tm-30) outliers start: 106 outliers final: 54 residues processed: 400 average time/residue: 0.1916 time to fit residues: 119.8470 Evaluate side-chains 367 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 304 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 501 GLN Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 158 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 43 LYS Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 78 TRP Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 172 GLN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 217 LYS Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 228 LYS Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain D residue 41 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 172 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 288 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 191 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 184 optimal weight: 0.6980 chunk 173 optimal weight: 0.4980 chunk 199 optimal weight: 0.8980 chunk 197 optimal weight: 0.3980 chunk 246 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 141 ASN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN I 264 ASN ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 172 GLN ** K 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 370 GLN B 242 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.223322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.209329 restraints weight = 59632.716| |-----------------------------------------------------------------------------| r_work (start): 0.4745 rms_B_bonded: 2.40 r_work: 0.4682 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.4682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4902 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 27649 Z= 0.125 Angle : 0.601 11.583 37779 Z= 0.314 Chirality : 0.042 0.259 4215 Planarity : 0.004 0.057 4692 Dihedral : 14.680 179.665 4566 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.25 % Favored : 91.63 % Rotamer: Outliers : 4.02 % Allowed : 25.75 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3260 helix: 0.12 (0.16), residues: 1094 sheet: 0.55 (0.21), residues: 526 loop : -2.09 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 36 TYR 0.016 0.001 TYR I 28 PHE 0.023 0.001 PHE J 102 TRP 0.026 0.001 TRP E 156 HIS 0.005 0.001 HIS C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (27649) covalent geometry : angle 0.60065 / 0.31 (37779) hydrogen bonds : bond 0.03996 / 3.73 ( 945) hydrogen bonds : angle 5.08474 / 5.88 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 333 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 327 ILE cc_start: -0.1946 (OUTLIER) cc_final: -0.2451 (pt) REVERT: C 422 LEU cc_start: 0.6386 (tp) cc_final: 0.6120 (mt) REVERT: C 424 GLN cc_start: 0.5711 (mm110) cc_final: 0.5208 (mt0) REVERT: C 485 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6783 (tp30) REVERT: K 33 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.5259 (mp) REVERT: K 46 ILE cc_start: 0.4635 (OUTLIER) cc_final: 0.4081 (tt) REVERT: K 51 ASP cc_start: 0.5250 (OUTLIER) cc_final: 0.4903 (p0) REVERT: K 78 TRP cc_start: 0.4938 (OUTLIER) cc_final: 0.4546 (t60) REVERT: K 114 ILE cc_start: 0.6153 (OUTLIER) cc_final: 0.5821 (tp) REVERT: K 256 LYS cc_start: 0.2548 (OUTLIER) cc_final: 0.1782 (tttm) REVERT: B 95 GLU cc_start: 0.0961 (OUTLIER) cc_final: -0.2021 (tm-30) outliers start: 108 outliers final: 60 residues processed: 413 average time/residue: 0.1898 time to fit residues: 123.3049 Evaluate side-chains 377 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 309 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 99 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 28 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 78 TRP Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 220 SER Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 318 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 301 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 69 GLN ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 ASN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 ASN K 239 HIS K 263 HIS K 351 ASN G 17 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.217192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.202608 restraints weight = 57275.911| |-----------------------------------------------------------------------------| r_work (start): 0.4677 rms_B_bonded: 2.38 r_work: 0.4611 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5185 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 27649 Z= 0.200 Angle : 0.721 10.002 37779 Z= 0.378 Chirality : 0.046 0.346 4215 Planarity : 0.006 0.066 4692 Dihedral : 14.651 178.470 4544 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.29 % Favored : 90.55 % Rotamer: Outliers : 5.51 % Allowed : 25.30 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3260 helix: -0.30 (0.15), residues: 1119 sheet: 0.31 (0.22), residues: 512 loop : -2.23 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 33 TYR 0.032 0.002 TYR I 28 PHE 0.036 0.002 PHE G 273 TRP 0.024 0.002 TRP J 223 HIS 0.012 0.002 HIS F 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (27649) covalent geometry : angle 0.72080 / 0.38 (37779) hydrogen bonds : bond 0.04591 / 4.18 ( 945) hydrogen bonds : angle 5.30902 / 6.10 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 340 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 SER cc_start: 0.6404 (OUTLIER) cc_final: 0.6052 (p) REVERT: C 422 LEU cc_start: 0.7283 (tp) cc_final: 0.6976 (tt) REVERT: C 424 GLN cc_start: 0.5957 (mm110) cc_final: 0.5547 (mt0) REVERT: H 33 LEU cc_start: 0.4813 (OUTLIER) cc_final: 0.4470 (mp) REVERT: H 338 LYS cc_start: 0.3849 (OUTLIER) cc_final: 0.3052 (pttm) REVERT: J 149 LEU cc_start: 0.3683 (OUTLIER) cc_final: 0.3470 (tp) REVERT: J 209 MET cc_start: 0.2704 (OUTLIER) cc_final: 0.1078 (mmt) REVERT: J 296 LEU cc_start: 0.1861 (OUTLIER) cc_final: 0.0776 (tt) REVERT: K 28 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: K 33 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.5253 (mp) REVERT: K 46 ILE cc_start: 0.4540 (OUTLIER) cc_final: 0.3947 (tt) REVERT: K 256 LYS cc_start: 0.3245 (OUTLIER) cc_final: 0.2196 (tptm) REVERT: K 299 GLN cc_start: 0.6259 (OUTLIER) cc_final: 0.6002 (mp-120) REVERT: G 148 MET cc_start: 0.5977 (OUTLIER) cc_final: 0.4208 (tpt) REVERT: B 95 GLU cc_start: 0.0996 (OUTLIER) cc_final: -0.1928 (tm-30) REVERT: B 148 VAL cc_start: 0.6135 (t) cc_final: 0.5849 (p) outliers start: 148 outliers final: 84 residues processed: 449 average time/residue: 0.1904 time to fit residues: 135.8448 Evaluate side-chains 415 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 318 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain E residue 14 ASN Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 214 CYS Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 296 LEU Chi-restraints excluded: chain K residue 11 HIS Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 28 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 172 GLN Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 144 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 326 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 303 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN J 92 ASN ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN D 154 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.217444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.202978 restraints weight = 57397.107| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 2.37 r_work: 0.4616 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5172 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 27649 Z= 0.139 Angle : 0.629 11.244 37779 Z= 0.326 Chirality : 0.043 0.252 4215 Planarity : 0.005 0.061 4692 Dihedral : 14.467 178.786 4534 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.25 % Favored : 91.60 % Rotamer: Outliers : 4.55 % Allowed : 26.64 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.14), residues: 3260 helix: -0.08 (0.16), residues: 1126 sheet: 0.45 (0.22), residues: 499 loop : -2.19 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 36 TYR 0.031 0.001 TYR G 337 PHE 0.019 0.002 PHE C 229 TRP 0.022 0.001 TRP E 156 HIS 0.006 0.001 HIS C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (27649) covalent geometry : angle 0.62882 / 0.33 (37779) hydrogen bonds : bond 0.03844 / 3.55 ( 945) hydrogen bonds : angle 5.03456 / 5.82 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 324 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 LEU cc_start: -0.0018 (OUTLIER) cc_final: -0.0281 (tp) REVERT: C 377 SER cc_start: 0.5819 (OUTLIER) cc_final: 0.5493 (p) REVERT: C 422 LEU cc_start: 0.7079 (tp) cc_final: 0.6798 (tt) REVERT: C 424 GLN cc_start: 0.5839 (mm110) cc_final: 0.5224 (mt0) REVERT: C 477 TYR cc_start: 0.6177 (t80) cc_final: 0.5774 (t80) REVERT: H 33 LEU cc_start: 0.4635 (OUTLIER) cc_final: 0.4250 (mp) REVERT: I 330 ASN cc_start: 0.7496 (t0) cc_final: 0.7157 (t0) REVERT: J 209 MET cc_start: 0.2839 (OUTLIER) cc_final: 0.1184 (mmt) REVERT: K 28 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.6062 (m-80) REVERT: K 33 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5247 (mp) REVERT: K 46 ILE cc_start: 0.4698 (OUTLIER) cc_final: 0.4125 (tt) REVERT: K 141 ASP cc_start: 0.4428 (OUTLIER) cc_final: 0.3253 (m-30) REVERT: K 256 LYS cc_start: 0.3034 (OUTLIER) cc_final: 0.2132 (tptm) REVERT: K 299 GLN cc_start: 0.6150 (OUTLIER) cc_final: 0.5926 (mp-120) REVERT: K 370 GLN cc_start: 0.2976 (tp-100) cc_final: 0.2765 (tp40) REVERT: G 148 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.4202 (tpt) REVERT: B 95 GLU cc_start: 0.1025 (OUTLIER) cc_final: -0.1819 (tm-30) REVERT: B 148 VAL cc_start: 0.6188 (t) cc_final: 0.5879 (p) REVERT: B 164 LEU cc_start: 0.7144 (mp) cc_final: 0.6827 (mt) outliers start: 122 outliers final: 75 residues processed: 410 average time/residue: 0.1683 time to fit residues: 111.3174 Evaluate side-chains 398 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 311 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 99 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 28 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 301 ILE Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 280 optimal weight: 1.9990 chunk 200 optimal weight: 0.0670 chunk 274 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 37 optimal weight: 0.0050 chunk 139 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 208 optimal weight: 0.7980 chunk 286 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 overall best weight: 0.4932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 263 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.218036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.203568 restraints weight = 57561.153| |-----------------------------------------------------------------------------| r_work (start): 0.4686 rms_B_bonded: 2.37 r_work: 0.4621 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5147 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27649 Z= 0.115 Angle : 0.592 12.327 37779 Z= 0.306 Chirality : 0.042 0.236 4215 Planarity : 0.004 0.055 4692 Dihedral : 14.302 179.676 4531 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.88 % Favored : 91.99 % Rotamer: Outliers : 4.36 % Allowed : 26.79 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3260 helix: 0.17 (0.16), residues: 1122 sheet: 0.54 (0.22), residues: 506 loop : -2.09 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 36 TYR 0.029 0.001 TYR B 341 PHE 0.016 0.001 PHE C 229 TRP 0.020 0.001 TRP E 156 HIS 0.007 0.001 HIS C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (27649) covalent geometry : angle 0.59179 / 0.31 (37779) hydrogen bonds : bond 0.03486 / 3.21 ( 945) hydrogen bonds : angle 4.82845 / 5.61 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 328 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 LEU cc_start: 0.0519 (OUTLIER) cc_final: 0.0246 (tp) REVERT: C 292 MET cc_start: 0.3177 (OUTLIER) cc_final: 0.2959 (tpp) REVERT: C 424 GLN cc_start: 0.5964 (mm110) cc_final: 0.5309 (mt0) REVERT: C 477 TYR cc_start: 0.6156 (t80) cc_final: 0.5744 (t80) REVERT: E 85 MET cc_start: 0.1451 (mmp) cc_final: 0.0866 (mmp) REVERT: E 102 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6550 (mp) REVERT: H 338 LYS cc_start: 0.3925 (OUTLIER) cc_final: 0.3091 (pttm) REVERT: I 330 ASN cc_start: 0.7515 (t0) cc_final: 0.7182 (t0) REVERT: J 61 THR cc_start: 0.2565 (OUTLIER) cc_final: 0.2258 (p) REVERT: J 209 MET cc_start: 0.2788 (OUTLIER) cc_final: 0.2135 (mpp) REVERT: K 28 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: K 33 LEU cc_start: 0.5474 (OUTLIER) cc_final: 0.5240 (mp) REVERT: K 46 ILE cc_start: 0.4737 (OUTLIER) cc_final: 0.4185 (tt) REVERT: K 141 ASP cc_start: 0.4439 (OUTLIER) cc_final: 0.3009 (m-30) REVERT: K 256 LYS cc_start: 0.3072 (OUTLIER) cc_final: 0.2324 (tptm) REVERT: K 299 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.6069 (mp-120) REVERT: B 91 MET cc_start: 0.5272 (mmm) cc_final: 0.4832 (mmm) REVERT: B 95 GLU cc_start: 0.0889 (OUTLIER) cc_final: -0.1970 (tm-30) REVERT: B 148 VAL cc_start: 0.6191 (t) cc_final: 0.5891 (p) REVERT: D 201 LYS cc_start: 0.6405 (ttmm) cc_final: 0.5764 (tttt) outliers start: 117 outliers final: 78 residues processed: 410 average time/residue: 0.1873 time to fit residues: 121.8612 Evaluate side-chains 405 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 314 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 28 TYR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 301 ILE Chi-restraints excluded: chain K residue 367 GLU Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 161 TRP Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 31 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 253 optimal weight: 3.9990 chunk 283 optimal weight: 3.9990 chunk 275 optimal weight: 0.0170 chunk 71 optimal weight: 0.8980 chunk 161 optimal weight: 0.0170 chunk 174 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.217636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.203231 restraints weight = 57096.029| |-----------------------------------------------------------------------------| r_work (start): 0.4687 rms_B_bonded: 2.36 r_work: 0.4623 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.4623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5151 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27649 Z= 0.113 Angle : 0.586 9.909 37779 Z= 0.303 Chirality : 0.041 0.226 4215 Planarity : 0.004 0.052 4692 Dihedral : 14.236 179.652 4531 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.39 % Favored : 92.48 % Rotamer: Outliers : 4.81 % Allowed : 26.01 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.15), residues: 3260 helix: 0.29 (0.16), residues: 1122 sheet: 0.60 (0.22), residues: 504 loop : -2.06 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 113 TYR 0.021 0.001 TYR J 315 PHE 0.022 0.001 PHE C 229 TRP 0.025 0.001 TRP C 391 HIS 0.006 0.001 HIS C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (27649) covalent geometry : angle 0.58623 / 0.30 (37779) hydrogen bonds : bond 0.03466 / 3.20 ( 945) hydrogen bonds : angle 4.77675 / 5.57 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 326 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASN cc_start: 0.2560 (OUTLIER) cc_final: 0.2087 (p0) REVERT: C 288 LEU cc_start: 0.0190 (OUTLIER) cc_final: -0.0063 (tp) REVERT: C 424 GLN cc_start: 0.5877 (mm110) cc_final: 0.5318 (mt0) REVERT: C 477 TYR cc_start: 0.6150 (t80) cc_final: 0.5716 (t80) REVERT: E 102 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6632 (mp) REVERT: F 80 LYS cc_start: 0.1943 (tttt) cc_final: 0.1070 (ptmt) REVERT: H 338 LYS cc_start: 0.3923 (OUTLIER) cc_final: 0.3110 (pttm) REVERT: I 246 LEU cc_start: 0.6012 (tp) cc_final: 0.5768 (tp) REVERT: J 61 THR cc_start: 0.2616 (OUTLIER) cc_final: 0.2294 (p) REVERT: J 209 MET cc_start: 0.2506 (OUTLIER) cc_final: 0.1852 (mpp) REVERT: K 33 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.5333 (mp) REVERT: K 46 ILE cc_start: 0.4795 (OUTLIER) cc_final: 0.4264 (tt) REVERT: K 141 ASP cc_start: 0.4486 (OUTLIER) cc_final: 0.2163 (p0) REVERT: K 299 GLN cc_start: 0.6285 (OUTLIER) cc_final: 0.6027 (mp-120) REVERT: G 148 MET cc_start: 0.5838 (OUTLIER) cc_final: 0.4073 (tpt) REVERT: B 91 MET cc_start: 0.5083 (mmm) cc_final: 0.4761 (mmm) REVERT: B 95 GLU cc_start: 0.0753 (OUTLIER) cc_final: -0.2033 (tm-30) REVERT: B 148 VAL cc_start: 0.6315 (t) cc_final: 0.6012 (p) REVERT: D 201 LYS cc_start: 0.6444 (ttmm) cc_final: 0.5875 (tttt) outliers start: 129 outliers final: 86 residues processed: 415 average time/residue: 0.1831 time to fit residues: 121.5316 Evaluate side-chains 408 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 310 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 26 THR Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 347 ILE Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 99 MET Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 299 GLN Chi-restraints excluded: chain K residue 301 ILE Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 161 TRP Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 50 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 197 optimal weight: 0.0980 chunk 80 optimal weight: 0.9990 chunk 306 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 248 optimal weight: 0.3980 chunk 283 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 169 optimal weight: 0.0040 chunk 46 optimal weight: 3.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN H 10 ASN ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 ASN ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 172 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.217747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.203382 restraints weight = 57906.151| |-----------------------------------------------------------------------------| r_work (start): 0.4690 rms_B_bonded: 2.38 r_work: 0.4626 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5143 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 27649 Z= 0.107 Angle : 0.576 10.053 37779 Z= 0.298 Chirality : 0.041 0.252 4215 Planarity : 0.004 0.054 4692 Dihedral : 14.163 179.086 4530 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.39 % Favored : 92.48 % Rotamer: Outliers : 4.17 % Allowed : 26.49 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 3260 helix: 0.41 (0.16), residues: 1121 sheet: 0.65 (0.22), residues: 498 loop : -1.98 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG H 113 TYR 0.023 0.001 TYR G 265 PHE 0.021 0.001 PHE C 229 TRP 0.022 0.001 TRP E 156 HIS 0.007 0.001 HIS C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (27649) covalent geometry : angle 0.57584 / 0.30 (37779) hydrogen bonds : bond 0.03314 / 3.04 ( 945) hydrogen bonds : angle 4.63853 / 5.47 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 317 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASN cc_start: 0.2428 (OUTLIER) cc_final: 0.1941 (p0) REVERT: C 288 LEU cc_start: 0.0507 (OUTLIER) cc_final: 0.0222 (tp) REVERT: C 424 GLN cc_start: 0.5711 (mm110) cc_final: 0.5296 (mt0) REVERT: C 477 TYR cc_start: 0.6056 (t80) cc_final: 0.5611 (t80) REVERT: E 102 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6692 (mp) REVERT: F 80 LYS cc_start: 0.1828 (tttt) cc_final: 0.1002 (ptmt) REVERT: H 338 LYS cc_start: 0.3923 (OUTLIER) cc_final: 0.3090 (pttm) REVERT: J 61 THR cc_start: 0.2589 (OUTLIER) cc_final: 0.2280 (p) REVERT: J 209 MET cc_start: 0.2640 (OUTLIER) cc_final: 0.2058 (mpp) REVERT: K 141 ASP cc_start: 0.4384 (OUTLIER) cc_final: 0.2082 (p0) REVERT: K 256 LYS cc_start: 0.3033 (OUTLIER) cc_final: 0.2324 (tptm) REVERT: K 280 TYR cc_start: 0.5658 (OUTLIER) cc_final: 0.4514 (m-80) REVERT: G 148 MET cc_start: 0.5881 (OUTLIER) cc_final: 0.4137 (tpt) REVERT: G 265 TYR cc_start: 0.5850 (OUTLIER) cc_final: 0.5288 (m-10) REVERT: B 91 MET cc_start: 0.5105 (mmm) cc_final: 0.4873 (mmm) REVERT: B 95 GLU cc_start: 0.0783 (OUTLIER) cc_final: -0.2010 (tm-30) REVERT: B 164 LEU cc_start: 0.7193 (mp) cc_final: 0.6912 (mt) outliers start: 112 outliers final: 75 residues processed: 398 average time/residue: 0.1838 time to fit residues: 117.5281 Evaluate side-chains 399 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 312 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 216 TYR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 110 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 301 ILE Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 161 TRP Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 184 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 238 optimal weight: 0.0770 chunk 308 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 216 optimal weight: 0.0670 chunk 37 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.217806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.203441 restraints weight = 58403.487| |-----------------------------------------------------------------------------| r_work (start): 0.4689 rms_B_bonded: 2.37 r_work: 0.4625 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5144 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 27649 Z= 0.106 Angle : 0.569 9.805 37779 Z= 0.294 Chirality : 0.041 0.204 4215 Planarity : 0.004 0.052 4692 Dihedral : 14.041 178.795 4523 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.12 % Favored : 92.76 % Rotamer: Outliers : 3.69 % Allowed : 27.12 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 3260 helix: 0.47 (0.16), residues: 1127 sheet: 0.65 (0.22), residues: 498 loop : -1.95 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 36 TYR 0.020 0.001 TYR I 28 PHE 0.025 0.001 PHE C 229 TRP 0.018 0.001 TRP E 156 HIS 0.006 0.001 HIS C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (27649) covalent geometry : angle 0.56858 / 0.29 (37779) hydrogen bonds : bond 0.03230 / 2.97 ( 945) hydrogen bonds : angle 4.58116 / 5.42 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 317 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASN cc_start: 0.2442 (OUTLIER) cc_final: 0.1925 (p0) REVERT: C 288 LEU cc_start: 0.0733 (OUTLIER) cc_final: 0.0442 (tp) REVERT: C 377 SER cc_start: 0.4722 (OUTLIER) cc_final: 0.4251 (p) REVERT: C 422 LEU cc_start: 0.7398 (tp) cc_final: 0.7057 (tp) REVERT: C 424 GLN cc_start: 0.5318 (mm110) cc_final: 0.5079 (mt0) REVERT: E 102 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6631 (mp) REVERT: F 80 LYS cc_start: 0.1919 (tttt) cc_final: 0.1118 (ptmt) REVERT: H 338 LYS cc_start: 0.3931 (OUTLIER) cc_final: 0.3105 (pttm) REVERT: I 330 ASN cc_start: 0.7518 (t0) cc_final: 0.7132 (t0) REVERT: J 61 THR cc_start: 0.2669 (OUTLIER) cc_final: 0.2341 (p) REVERT: J 167 VAL cc_start: 0.1438 (OUTLIER) cc_final: 0.1179 (p) REVERT: J 209 MET cc_start: 0.2720 (OUTLIER) cc_final: 0.2134 (mpp) REVERT: K 141 ASP cc_start: 0.4351 (OUTLIER) cc_final: 0.2021 (p0) REVERT: K 256 LYS cc_start: 0.2996 (OUTLIER) cc_final: 0.2264 (tptm) REVERT: K 280 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.4589 (m-80) REVERT: G 148 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.4198 (tpt) REVERT: G 265 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5524 (m-10) REVERT: B 91 MET cc_start: 0.5074 (mmm) cc_final: 0.4856 (mmm) REVERT: B 95 GLU cc_start: 0.0641 (OUTLIER) cc_final: -0.2011 (tm-30) outliers start: 99 outliers final: 74 residues processed: 386 average time/residue: 0.1620 time to fit residues: 101.2862 Evaluate side-chains 400 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 312 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 14 ASN Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 99 MET Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 276 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 216 TYR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 168 GLU Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 301 ILE Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 161 TRP Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 26 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 17 optimal weight: 0.0970 chunk 291 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 169 optimal weight: 0.0170 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 384 ASN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.217056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.202910 restraints weight = 58045.729| |-----------------------------------------------------------------------------| r_work (start): 0.4683 rms_B_bonded: 2.32 r_work: 0.4620 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5170 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27649 Z= 0.111 Angle : 0.582 10.126 37779 Z= 0.299 Chirality : 0.041 0.220 4215 Planarity : 0.004 0.057 4692 Dihedral : 14.015 178.722 4521 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.24 % Favored : 92.64 % Rotamer: Outliers : 3.61 % Allowed : 26.97 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.15), residues: 3260 helix: 0.54 (0.16), residues: 1123 sheet: 0.66 (0.22), residues: 493 loop : -1.94 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 18 TYR 0.021 0.001 TYR I 28 PHE 0.024 0.001 PHE C 229 TRP 0.019 0.001 TRP E 156 HIS 0.007 0.001 HIS C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (27649) covalent geometry : angle 0.58192 / 0.30 (37779) hydrogen bonds : bond 0.03254 / 3.00 ( 945) hydrogen bonds : angle 4.56318 / 5.42 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6520 Ramachandran restraints generated. 3260 Oldfield, 0 Emsley, 3260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 316 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 ASN cc_start: 0.2606 (OUTLIER) cc_final: 0.2063 (p0) REVERT: C 288 LEU cc_start: 0.0939 (OUTLIER) cc_final: 0.0641 (tp) REVERT: C 419 ASP cc_start: 0.4319 (OUTLIER) cc_final: 0.3917 (m-30) REVERT: E 102 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6592 (mp) REVERT: F 80 LYS cc_start: 0.1848 (tttt) cc_final: 0.1206 (ptmt) REVERT: F 226 LEU cc_start: 0.2090 (OUTLIER) cc_final: 0.1331 (tp) REVERT: H 338 LYS cc_start: 0.3943 (OUTLIER) cc_final: 0.3083 (pttm) REVERT: H 347 ILE cc_start: 0.7740 (tp) cc_final: 0.7474 (tt) REVERT: I 335 LEU cc_start: 0.5684 (tp) cc_final: 0.5251 (tp) REVERT: J 61 THR cc_start: 0.2708 (OUTLIER) cc_final: 0.2373 (p) REVERT: J 167 VAL cc_start: 0.1412 (OUTLIER) cc_final: 0.1148 (p) REVERT: J 181 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7993 (tt) REVERT: J 209 MET cc_start: 0.2741 (OUTLIER) cc_final: 0.2186 (mpp) REVERT: K 141 ASP cc_start: 0.4238 (OUTLIER) cc_final: 0.2460 (p0) REVERT: K 256 LYS cc_start: 0.3161 (OUTLIER) cc_final: 0.2366 (tptm) REVERT: K 280 TYR cc_start: 0.5910 (OUTLIER) cc_final: 0.4589 (m-80) REVERT: G 148 MET cc_start: 0.5954 (OUTLIER) cc_final: 0.4164 (tpt) REVERT: G 265 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.5521 (m-10) REVERT: B 91 MET cc_start: 0.5029 (mmm) cc_final: 0.4824 (mmm) REVERT: B 95 GLU cc_start: 0.0682 (OUTLIER) cc_final: -0.1961 (tm-30) REVERT: B 164 LEU cc_start: 0.7289 (mp) cc_final: 0.7032 (mt) outliers start: 97 outliers final: 70 residues processed: 390 average time/residue: 0.1761 time to fit residues: 111.0599 Evaluate side-chains 400 residues out of total 2793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 314 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 252 HIS Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 14 ASN Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 198 GLU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 316 TYR Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 209 MET Chi-restraints excluded: chain J residue 216 TYR Chi-restraints excluded: chain J residue 221 ILE Chi-restraints excluded: chain J residue 271 VAL Chi-restraints excluded: chain J residue 311 ILE Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 141 ASP Chi-restraints excluded: chain K residue 154 LYS Chi-restraints excluded: chain K residue 161 LYS Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain K residue 210 PHE Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 271 VAL Chi-restraints excluded: chain K residue 280 TYR Chi-restraints excluded: chain K residue 285 VAL Chi-restraints excluded: chain K residue 301 ILE Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 265 TYR Chi-restraints excluded: chain G residue 278 ILE Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain B residue 22 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 135 HIS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 161 TRP Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 143 optimal weight: 0.1980 chunk 139 optimal weight: 0.0670 chunk 72 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 309 optimal weight: 0.9980 chunk 181 optimal weight: 0.0670 chunk 279 optimal weight: 0.7980 chunk 286 optimal weight: 2.9990 chunk 153 optimal weight: 0.0270 chunk 232 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 overall best weight: 0.2314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 424 GLN C 467 ASN ** F 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 ASN ** H 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 HIS ** K 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.217931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.204128 restraints weight = 58134.886| |-----------------------------------------------------------------------------| r_work (start): 0.4697 rms_B_bonded: 2.24 r_work: 0.4636 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.4636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5116 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27649 Z= 0.101 Angle : 0.567 10.053 37779 Z= 0.292 Chirality : 0.041 0.193 4215 Planarity : 0.004 0.053 4692 Dihedral : 13.885 178.391 4516 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.72 % Favored : 93.16 % Rotamer: Outliers : 3.09 % Allowed : 27.27 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 3260 helix: 0.68 (0.17), residues: 1118 sheet: 0.73 (0.23), residues: 484 loop : -1.89 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 18 TYR 0.017 0.001 TYR I 28 PHE 0.025 0.001 PHE C 229 TRP 0.020 0.001 TRP E 156 HIS 0.006 0.001 HIS C 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (27649) covalent geometry : angle 0.56718 / 0.29 (37779) hydrogen bonds : bond 0.03130 / 2.88 ( 945) hydrogen bonds : angle 4.47900 / 5.34 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6680.43 seconds wall clock time: 115 minutes 28.77 seconds (6928.77 seconds total)