Starting phenix.real_space_refine on Thu Aug 6 22:38:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r5s_53595/08_2026/9r5s_53595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r5s_53595/08_2026/9r5s_53595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r5s_53595/08_2026/9r5s_53595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r5s_53595/08_2026/9r5s_53595.map" model { file = "/net/cci-nas-00/data/ceres_data/9r5s_53595/08_2026/9r5s_53595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r5s_53595/08_2026/9r5s_53595.cif" } resolution = 3.8 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 320 5.49 5 S 27 5.16 5 C 9976 2.51 5 N 3190 2.21 5 O 3910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17423 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3262 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "J" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3298 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "A" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 749 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 734 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 794 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 746 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "H" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 5054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5054 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 23, 'TRANS': 628} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 279 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 19, 'ASP:plan': 5, 'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 6, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 187 Time building chain proxies: 3.06, per 1000 atoms: 0.18 Number of scatterers: 17423 At special positions: 0 Unit cell: (101.2, 160.05, 161.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 320 15.00 O 3910 8.00 N 3190 7.00 C 9976 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: 1.42 Conformation dependent library (CDL) restraints added in 556.8 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 12 sheets defined 62.2% alpha, 5.3% beta 151 base pairs and 272 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.149A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.661A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.859A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.878A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.866A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.580A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.571A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.969A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.984A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.607A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.705A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 98 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.639A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.604A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.523A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.798A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.861A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.569A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.986A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.507A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.635A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.630A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.876A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.619A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.542A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 4.033A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 143 through 147 Processing helix chain 'W' and resid 203 through 209 Processing helix chain 'W' and resid 229 through 234 Processing helix chain 'W' and resid 238 through 250 removed outlier: 3.571A pdb=" N LEU W 242 " --> pdb=" O GLY W 238 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN W 248 " --> pdb=" O ASN W 244 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE W 250 " --> pdb=" O CYS W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 250 through 259 Processing helix chain 'W' and resid 263 through 283 removed outlier: 3.800A pdb=" N GLU W 283 " --> pdb=" O ASP W 279 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 331 removed outlier: 3.705A pdb=" N LYS W 329 " --> pdb=" O THR W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 331 through 343 removed outlier: 3.655A pdb=" N VAL W 335 " --> pdb=" O ALA W 331 " (cutoff:3.500A) Processing helix chain 'W' and resid 347 through 351 removed outlier: 3.942A pdb=" N SER W 351 " --> pdb=" O PRO W 348 " (cutoff:3.500A) Processing helix chain 'W' and resid 377 through 394 removed outlier: 3.732A pdb=" N GLY W 383 " --> pdb=" O PHE W 379 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE W 384 " --> pdb=" O GLN W 380 " (cutoff:3.500A) Processing helix chain 'W' and resid 406 through 421 removed outlier: 3.652A pdb=" N GLN W 410 " --> pdb=" O GLY W 406 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR W 411 " --> pdb=" O LYS W 407 " (cutoff:3.500A) Processing helix chain 'W' and resid 433 through 435 No H-bonds generated for 'chain 'W' and resid 433 through 435' Processing helix chain 'W' and resid 436 through 447 Processing helix chain 'W' and resid 459 through 471 removed outlier: 3.564A pdb=" N ILE W 466 " --> pdb=" O SER W 462 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE W 471 " --> pdb=" O ARG W 467 " (cutoff:3.500A) Processing helix chain 'W' and resid 492 through 498 removed outlier: 3.532A pdb=" N LEU W 496 " --> pdb=" O TYR W 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 498 through 504 removed outlier: 3.702A pdb=" N SER W 504 " --> pdb=" O ALA W 500 " (cutoff:3.500A) Processing helix chain 'W' and resid 515 through 519 Processing helix chain 'W' and resid 523 through 531 removed outlier: 3.891A pdb=" N SER W 531 " --> pdb=" O GLU W 527 " (cutoff:3.500A) Processing helix chain 'W' and resid 549 through 560 Processing helix chain 'W' and resid 576 through 590 Processing helix chain 'W' and resid 591 through 594 removed outlier: 3.617A pdb=" N ILE W 594 " --> pdb=" O GLN W 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 591 through 594' Processing helix chain 'W' and resid 1011 through 1023 Processing helix chain 'W' and resid 1028 through 1030 No H-bonds generated for 'chain 'W' and resid 1028 through 1030' Processing helix chain 'W' and resid 1031 through 1038 removed outlier: 3.855A pdb=" N LEU W1035 " --> pdb=" O ILE W1031 " (cutoff:3.500A) Processing helix chain 'W' and resid 1045 through 1072 Processing helix chain 'W' and resid 1129 through 1148 Processing helix chain 'W' and resid 1176 through 1191 removed outlier: 3.611A pdb=" N ASP W1180 " --> pdb=" O THR W1176 " (cutoff:3.500A) Processing helix chain 'W' and resid 1194 through 1200 Processing helix chain 'W' and resid 1249 through 1266 removed outlier: 3.505A pdb=" N GLY W1254 " --> pdb=" O ALA W1250 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER W1262 " --> pdb=" O ASP W1258 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.441A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.388A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.086A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.057A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.955A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.518A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.822A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'W' and resid 179 through 186 removed outlier: 5.695A pdb=" N VAL W 182 " --> pdb=" O LYS W 216 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS W 216 " --> pdb=" O VAL W 182 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN W 184 " --> pdb=" O LEU W 214 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU W 212 " --> pdb=" O ARG W 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR W 226 " --> pdb=" O ILE W 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 287 through 295 removed outlier: 6.597A pdb=" N LEU W 308 " --> pdb=" O ILE W 291 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER W 293 " --> pdb=" O GLN W 306 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN W 306 " --> pdb=" O SER W 293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 398 through 399 removed outlier: 6.392A pdb=" N GLN W 508 " --> pdb=" O ASN W 536 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N MET W 538 " --> pdb=" O GLN W 508 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET W 510 " --> pdb=" O MET W 538 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE W 540 " --> pdb=" O MET W 510 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL W 512 " --> pdb=" O ILE W 540 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 388 hydrogen bonds 776 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2929 1.33 - 1.45: 5958 1.45 - 1.57: 8828 1.57 - 1.69: 638 1.69 - 1.81: 49 Bond restraints: 18402 Sorted by residual: bond pdb=" N3 DC I 17 " pdb=" C4 DC I 17 " ideal model delta sigma weight residual 1.335 1.285 0.050 7.00e-03 2.04e+04 5.07e+01 bond pdb=" C1' DC J -3 " pdb=" N1 DC J -3 " ideal model delta sigma weight residual 1.468 1.562 -0.094 1.40e-02 5.10e+03 4.49e+01 bond pdb=" C1' DC I -80 " pdb=" N1 DC I -80 " ideal model delta sigma weight residual 1.468 1.561 -0.093 1.40e-02 5.10e+03 4.43e+01 bond pdb=" C1' DC J 39 " pdb=" N1 DC J 39 " ideal model delta sigma weight residual 1.468 1.559 -0.091 1.40e-02 5.10e+03 4.25e+01 bond pdb=" C1' DC I -79 " pdb=" N1 DC I -79 " ideal model delta sigma weight residual 1.468 1.557 -0.089 1.40e-02 5.10e+03 4.07e+01 ... (remaining 18397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 25544 2.76 - 5.52: 703 5.52 - 8.28: 8 8.28 - 11.05: 3 11.05 - 13.81: 2 Bond angle restraints: 26260 Sorted by residual: angle pdb=" O4' DT I 78 " pdb=" C1' DT I 78 " pdb=" N1 DT I 78 " ideal model delta sigma weight residual 108.00 112.89 -4.89 7.00e-01 2.04e+00 4.88e+01 angle pdb=" O4' DA J -25 " pdb=" C1' DA J -25 " pdb=" N9 DA J -25 " ideal model delta sigma weight residual 108.00 112.20 -4.20 7.00e-01 2.04e+00 3.60e+01 angle pdb=" O5' DA J -23 " pdb=" C5' DA J -23 " pdb=" C4' DA J -23 " ideal model delta sigma weight residual 109.40 114.12 -4.72 8.00e-01 1.56e+00 3.49e+01 angle pdb=" O4' DA I 67 " pdb=" C4' DA I 67 " pdb=" C3' DA I 67 " ideal model delta sigma weight residual 106.00 102.50 3.50 6.00e-01 2.78e+00 3.40e+01 angle pdb=" O4' DG I -72 " pdb=" C1' DG I -72 " pdb=" N9 DG I -72 " ideal model delta sigma weight residual 108.00 111.97 -3.97 7.00e-01 2.04e+00 3.21e+01 ... (remaining 26255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7628 17.99 - 35.99: 1277 35.99 - 53.98: 941 53.98 - 71.97: 333 71.97 - 89.96: 13 Dihedral angle restraints: 10192 sinusoidal: 6151 harmonic: 4041 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PRO H 47 " pdb=" C PRO H 47 " pdb=" N ASP H 48 " pdb=" CA ASP H 48 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 10189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2637 0.084 - 0.168: 310 0.168 - 0.252: 11 0.252 - 0.336: 0 0.336 - 0.420: 2 Chirality restraints: 2960 Sorted by residual: chirality pdb=" P DG J -79 " pdb=" OP1 DG J -79 " pdb=" OP2 DG J -79 " pdb=" O5' DG J -79 " both_signs ideal model delta sigma weight residual True 2.34 -2.75 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA TRP W1171 " pdb=" N TRP W1171 " pdb=" C TRP W1171 " pdb=" CB TRP W1171 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" P DC I 46 " pdb=" OP1 DC I 46 " pdb=" OP2 DC I 46 " pdb=" O5' DC I 46 " both_signs ideal model delta sigma weight residual True 2.34 -2.55 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2957 not shown) Planarity restraints: 2245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU W 220 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C GLU W 220 " 0.073 2.00e-02 2.50e+03 pdb=" O GLU W 220 " -0.027 2.00e-02 2.50e+03 pdb=" N SER W 221 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -39 " 0.049 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" N9 DG I -39 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DG I -39 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DG I -39 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -39 " -0.012 2.00e-02 2.50e+03 pdb=" O6 DG I -39 " 0.027 2.00e-02 2.50e+03 pdb=" N1 DG I -39 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DG I -39 " -0.007 2.00e-02 2.50e+03 pdb=" N2 DG I -39 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -39 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG I -39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -17 " -0.030 2.00e-02 2.50e+03 1.95e-02 1.14e+01 pdb=" N9 DG J -17 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DG J -17 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG J -17 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG J -17 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -17 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG J -17 " 0.005 2.00e-02 2.50e+03 pdb=" N1 DG J -17 " -0.047 2.00e-02 2.50e+03 pdb=" C2 DG J -17 " 0.017 2.00e-02 2.50e+03 pdb=" N2 DG J -17 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DG J -17 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG J -17 " -0.001 2.00e-02 2.50e+03 ... (remaining 2242 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2314 2.76 - 3.29: 15568 3.29 - 3.83: 30159 3.83 - 4.36: 36507 4.36 - 4.90: 53983 Nonbonded interactions: 138531 Sorted by model distance: nonbonded pdb=" OG SER W 351 " pdb=" O ARG W 423 " model vdw 2.222 3.040 nonbonded pdb=" O ASN D 64 " pdb=" OE1 GLU D 68 " model vdw 2.248 3.040 nonbonded pdb=" O VAL F 70 " pdb=" OE1 GLU F 74 " model vdw 2.276 3.040 nonbonded pdb=" O VAL A 101 " pdb=" OE1 GLU A 105 " model vdw 2.277 3.040 nonbonded pdb=" OP1 DG I -44 " pdb=" NH1 ARG C 32 " model vdw 2.283 3.120 ... (remaining 138526 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 43 through 133 or (resid 134 and (name N or name CA or nam \ e C or name O or name CB )))) selection = (chain 'E' and resid 43 through 134) } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 102)) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 109) selection = (chain 'G' and resid 14 through 109) } ncs_group { reference = (chain 'D' and (resid 30 through 120 or (resid 121 and (name N or name CA or nam \ e C or name O )))) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 18.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 18402 Z= 0.691 Angle : 0.963 13.806 26260 Z= 0.831 Chirality : 0.052 0.420 2960 Planarity : 0.006 0.086 2245 Dihedral : 23.912 89.964 7580 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.35 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.21), residues: 1364 helix: 0.54 (0.18), residues: 745 sheet: -1.50 (0.57), residues: 63 loop : -1.63 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 96 TYR 0.013 0.001 TYR W 141 PHE 0.018 0.001 PHE W1211 TRP 0.008 0.001 TRP W 311 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00745 / 0.69 (18402) covalent geometry : angle 0.96342 / 0.83 (26260) hydrogen bonds : bond 0.16049 / 17.97 ( 960) hydrogen bonds : angle 6.02584 / 7.95 ( 2468) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8172 (ttm170) cc_final: 0.7871 (ttm110) REVERT: B 84 MET cc_start: 0.5980 (tpt) cc_final: 0.5415 (tpt) REVERT: E 58 THR cc_start: 0.8473 (p) cc_final: 0.8185 (p) REVERT: E 59 GLU cc_start: 0.6908 (pm20) cc_final: 0.6426 (pm20) REVERT: F 72 TYR cc_start: 0.7985 (m-10) cc_final: 0.7173 (m-80) REVERT: G 41 GLU cc_start: 0.7315 (tt0) cc_final: 0.7092 (tt0) REVERT: G 75 LYS cc_start: 0.7351 (mtpp) cc_final: 0.7044 (mtpp) REVERT: W 144 ASP cc_start: 0.7623 (m-30) cc_final: 0.7398 (m-30) REVERT: W 146 LEU cc_start: 0.8497 (mt) cc_final: 0.8020 (mp) REVERT: W 225 ASN cc_start: 0.6347 (m-40) cc_final: 0.6120 (m-40) REVERT: W 245 TYR cc_start: 0.8170 (t80) cc_final: 0.7812 (t80) REVERT: W 524 SER cc_start: 0.7185 (m) cc_final: 0.6732 (t) REVERT: W 530 ASN cc_start: 0.6929 (m-40) cc_final: 0.6594 (t0) REVERT: W 533 LYS cc_start: 0.7181 (mtpp) cc_final: 0.6976 (mtpp) REVERT: W 1057 MET cc_start: 0.7288 (ptt) cc_final: 0.7020 (ptt) REVERT: W 1263 PHE cc_start: 0.6815 (t80) cc_final: 0.6589 (t80) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1503 time to fit residues: 53.6076 Evaluate side-chains 202 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN F 75 HIS G 24 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 184 ASN W 210 ASN ** W 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W1145 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.171460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141409 restraints weight = 32591.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.145361 restraints weight = 14974.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147916 restraints weight = 8495.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.149511 restraints weight = 5705.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.150503 restraints weight = 4404.091| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 18402 Z= 0.214 Angle : 0.829 12.124 26260 Z= 0.475 Chirality : 0.058 0.254 2960 Planarity : 0.005 0.041 2245 Dihedral : 28.255 85.256 5011 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.54 % Allowed : 8.70 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.08 (0.22), residues: 1364 helix: 1.21 (0.18), residues: 793 sheet: -0.88 (0.59), residues: 68 loop : -1.72 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG W 596 TYR 0.028 0.002 TYR W1192 PHE 0.018 0.002 PHE W 593 TRP 0.026 0.003 TRP W 386 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.21 (18402) covalent geometry : angle 0.82912 / 0.48 (26260) hydrogen bonds : bond 0.08082 / 9.10 ( 960) hydrogen bonds : angle 3.94494 / 5.23 ( 2468) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8488 (t0) cc_final: 0.8228 (t0) REVERT: B 84 MET cc_start: 0.6221 (tpt) cc_final: 0.5901 (tpt) REVERT: F 92 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7711 (ttp80) REVERT: G 39 TYR cc_start: 0.7840 (m-80) cc_final: 0.7559 (m-10) REVERT: G 75 LYS cc_start: 0.7213 (mtpp) cc_final: 0.6950 (mtpp) REVERT: H 56 MET cc_start: 0.7016 (mmp) cc_final: 0.6706 (tpp) REVERT: W 137 TYR cc_start: 0.7892 (m-80) cc_final: 0.7657 (m-10) REVERT: W 141 TYR cc_start: 0.8204 (p90) cc_final: 0.7774 (p90) REVERT: W 216 LYS cc_start: 0.6731 (tmtt) cc_final: 0.6285 (tttp) REVERT: W 228 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6782 (mm-30) REVERT: W 242 LEU cc_start: 0.8653 (tp) cc_final: 0.8432 (tp) REVERT: W 245 TYR cc_start: 0.8348 (t80) cc_final: 0.8080 (t80) REVERT: W 283 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6369 (mp0) REVERT: W 387 MET cc_start: 0.6739 (ttm) cc_final: 0.6300 (ttm) REVERT: W 457 MET cc_start: 0.6753 (ppp) cc_final: 0.6542 (ppp) REVERT: W 461 LYS cc_start: 0.7765 (tttt) cc_final: 0.7250 (ttmm) REVERT: W 530 ASN cc_start: 0.7699 (m-40) cc_final: 0.7420 (t0) REVERT: W 560 MET cc_start: 0.6317 (tpp) cc_final: 0.5586 (tmm) REVERT: W 1183 LEU cc_start: 0.8391 (tp) cc_final: 0.8172 (mm) REVERT: W 1263 PHE cc_start: 0.7099 (t80) cc_final: 0.6728 (t80) outliers start: 17 outliers final: 10 residues processed: 206 average time/residue: 0.1431 time to fit residues: 42.8969 Evaluate side-chains 206 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 223 LEU Chi-restraints excluded: chain W residue 466 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 32 optimal weight: 0.0570 chunk 8 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 59 optimal weight: 0.0010 chunk 14 optimal weight: 9.9990 chunk 123 optimal weight: 0.0570 chunk 86 optimal weight: 0.9980 overall best weight: 0.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 75 HIS W 349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.173708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.143800 restraints weight = 32803.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147537 restraints weight = 15642.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149969 restraints weight = 9132.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.151514 restraints weight = 6279.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.152482 restraints weight = 4901.271| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18402 Z= 0.152 Angle : 0.655 9.433 26260 Z= 0.394 Chirality : 0.048 0.229 2960 Planarity : 0.004 0.032 2245 Dihedral : 28.348 82.909 5011 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.27 % Allowed : 12.06 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1364 helix: 1.91 (0.19), residues: 790 sheet: -0.72 (0.61), residues: 70 loop : -1.55 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG W 596 TYR 0.027 0.001 TYR W1192 PHE 0.022 0.002 PHE W 338 TRP 0.049 0.002 TRP W 386 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.15 (18402) covalent geometry : angle 0.65547 / 0.39 (26260) hydrogen bonds : bond 0.06267 / 7.11 ( 960) hydrogen bonds : angle 3.37612 / 4.45 ( 2468) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.6151 (mp0) REVERT: A 108 ASN cc_start: 0.8574 (t0) cc_final: 0.8341 (t0) REVERT: B 84 MET cc_start: 0.6244 (tpt) cc_final: 0.5904 (tpt) REVERT: C 39 TYR cc_start: 0.7387 (m-80) cc_final: 0.7149 (m-10) REVERT: C 75 LYS cc_start: 0.8077 (mtmm) cc_final: 0.7647 (mtmm) REVERT: D 56 MET cc_start: 0.7833 (tpp) cc_final: 0.7106 (tpp) REVERT: F 92 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7674 (ttp80) REVERT: G 39 TYR cc_start: 0.7720 (m-80) cc_final: 0.7478 (m-10) REVERT: G 75 LYS cc_start: 0.7122 (mtpp) cc_final: 0.6886 (mtpp) REVERT: H 56 MET cc_start: 0.6949 (mmp) cc_final: 0.6703 (tpp) REVERT: W 228 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6779 (mm-30) REVERT: W 242 LEU cc_start: 0.8617 (tp) cc_final: 0.8379 (tp) REVERT: W 245 TYR cc_start: 0.8360 (t80) cc_final: 0.8129 (t80) REVERT: W 283 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6364 (mp0) REVERT: W 387 MET cc_start: 0.6695 (ttm) cc_final: 0.6038 (ttm) REVERT: W 393 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7887 (mtpp) REVERT: W 407 LYS cc_start: 0.7412 (mtmm) cc_final: 0.6890 (mtmm) REVERT: W 457 MET cc_start: 0.6649 (ppp) cc_final: 0.6274 (ppp) REVERT: W 461 LYS cc_start: 0.7636 (tttt) cc_final: 0.7159 (ttmm) REVERT: W 530 ASN cc_start: 0.7695 (m-40) cc_final: 0.7390 (t0) REVERT: W 537 ARG cc_start: 0.5143 (mtt180) cc_final: 0.4774 (mtt180) REVERT: W 560 MET cc_start: 0.6353 (tpp) cc_final: 0.5479 (tmm) REVERT: W 1058 GLU cc_start: 0.7079 (tp30) cc_final: 0.6368 (tp30) REVERT: W 1263 PHE cc_start: 0.7145 (t80) cc_final: 0.6771 (t80) outliers start: 14 outliers final: 9 residues processed: 214 average time/residue: 0.1438 time to fit residues: 44.9321 Evaluate side-chains 211 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain W residue 232 SER Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 1185 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN F 75 HIS ** W 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.169159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138410 restraints weight = 32302.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142093 restraints weight = 15459.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.144487 restraints weight = 9144.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.146013 restraints weight = 6360.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.146839 restraints weight = 5032.408| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 18402 Z= 0.180 Angle : 0.675 10.158 26260 Z= 0.399 Chirality : 0.048 0.250 2960 Planarity : 0.004 0.037 2245 Dihedral : 28.254 80.537 5011 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.54 % Allowed : 13.24 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.23), residues: 1364 helix: 1.91 (0.19), residues: 786 sheet: -0.69 (0.58), residues: 70 loop : -1.51 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 35 TYR 0.026 0.002 TYR W1192 PHE 0.029 0.002 PHE W1188 TRP 0.058 0.002 TRP W 386 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 (18402) covalent geometry : angle 0.67504 / 0.40 (26260) hydrogen bonds : bond 0.06650 / 7.53 ( 960) hydrogen bonds : angle 3.35210 / 4.40 ( 2468) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8605 (t0) cc_final: 0.8377 (t0) REVERT: B 84 MET cc_start: 0.6665 (tpt) cc_final: 0.6421 (tpt) REVERT: D 56 MET cc_start: 0.7846 (tpp) cc_final: 0.7132 (tpp) REVERT: F 92 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7934 (ttp80) REVERT: G 23 LEU cc_start: 0.8169 (mp) cc_final: 0.7896 (mp) REVERT: G 75 LYS cc_start: 0.7233 (mtpp) cc_final: 0.6988 (mtpp) REVERT: G 107 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7553 (t) REVERT: G 108 LEU cc_start: 0.8334 (mt) cc_final: 0.7989 (mm) REVERT: H 42 LEU cc_start: 0.7637 (tp) cc_final: 0.7418 (tp) REVERT: W 228 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6756 (mm-30) REVERT: W 242 LEU cc_start: 0.8634 (tp) cc_final: 0.8403 (tp) REVERT: W 245 TYR cc_start: 0.8425 (t80) cc_final: 0.8203 (t80) REVERT: W 315 ASN cc_start: 0.6987 (m-40) cc_final: 0.6474 (m-40) REVERT: W 387 MET cc_start: 0.6744 (ttm) cc_final: 0.6120 (ttm) REVERT: W 393 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7958 (mtpp) REVERT: W 403 MET cc_start: 0.4960 (tpp) cc_final: 0.4655 (tpt) REVERT: W 407 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7180 (mtmm) REVERT: W 409 VAL cc_start: 0.8823 (p) cc_final: 0.8433 (t) REVERT: W 461 LYS cc_start: 0.7705 (tttt) cc_final: 0.7201 (ttmm) REVERT: W 524 SER cc_start: 0.7940 (m) cc_final: 0.7347 (t) REVERT: W 530 ASN cc_start: 0.7804 (m-40) cc_final: 0.7587 (t0) REVERT: W 560 MET cc_start: 0.6429 (tpp) cc_final: 0.5610 (tmm) REVERT: W 1058 GLU cc_start: 0.7094 (tp30) cc_final: 0.6384 (tp30) REVERT: W 1263 PHE cc_start: 0.7295 (t80) cc_final: 0.6888 (t80) outliers start: 28 outliers final: 14 residues processed: 231 average time/residue: 0.1495 time to fit residues: 50.3736 Evaluate side-chains 228 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 459 ASN Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 483 MET Chi-restraints excluded: chain W residue 514 GLU Chi-restraints excluded: chain W residue 1176 THR Chi-restraints excluded: chain W residue 1185 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 23 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 161 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS G 104 GLN H 81 ASN ** W 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 349 GLN ** 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 = 0.4150 r_free = 0.4150 target = 0.168456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137263 restraints weight = 32202.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140921 restraints weight = 15514.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.143337 restraints weight = 9218.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.144884 restraints weight = 6442.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145752 restraints weight = 5111.544| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18402 Z= 0.171 Angle : 0.643 11.908 26260 Z= 0.384 Chirality : 0.046 0.247 2960 Planarity : 0.004 0.037 2245 Dihedral : 28.141 81.392 5011 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.54 % Allowed : 15.14 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.23), residues: 1364 helix: 1.95 (0.18), residues: 786 sheet: -0.76 (0.57), residues: 70 loop : -1.47 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.041 0.002 TYR B 98 PHE 0.027 0.002 PHE W1188 TRP 0.056 0.002 TRP W 386 HIS 0.008 0.001 HIS W 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 (18402) covalent geometry : angle 0.64262 / 0.38 (26260) hydrogen bonds : bond 0.06247 / 7.07 ( 960) hydrogen bonds : angle 3.27211 / 4.24 ( 2468) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: A 108 ASN cc_start: 0.8672 (t0) cc_final: 0.8428 (t0) REVERT: B 84 MET cc_start: 0.6873 (tpt) cc_final: 0.6582 (tpt) REVERT: C 75 LYS cc_start: 0.8061 (mtmm) cc_final: 0.7648 (mtmm) REVERT: D 56 MET cc_start: 0.7857 (tpp) cc_final: 0.7180 (tpp) REVERT: F 84 MET cc_start: 0.6147 (ttm) cc_final: 0.5940 (ttm) REVERT: F 92 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7928 (ttp80) REVERT: G 23 LEU cc_start: 0.8195 (mp) cc_final: 0.7937 (mp) REVERT: G 39 TYR cc_start: 0.7963 (m-80) cc_final: 0.7694 (m-10) REVERT: G 75 LYS cc_start: 0.7237 (mtpp) cc_final: 0.7006 (mtpp) REVERT: G 107 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7706 (t) REVERT: G 108 LEU cc_start: 0.8381 (mt) cc_final: 0.7982 (mm) REVERT: H 42 LEU cc_start: 0.7741 (tp) cc_final: 0.7541 (tp) REVERT: W 141 TYR cc_start: 0.8238 (p90) cc_final: 0.7929 (p90) REVERT: W 216 LYS cc_start: 0.7504 (tttp) cc_final: 0.6887 (ptmt) REVERT: W 228 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6741 (mm-30) REVERT: W 315 ASN cc_start: 0.7014 (m-40) cc_final: 0.6464 (m-40) REVERT: W 387 MET cc_start: 0.6721 (ttm) cc_final: 0.6033 (ttm) REVERT: W 393 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7914 (mtpp) REVERT: W 403 MET cc_start: 0.4927 (tpp) cc_final: 0.4627 (tpt) REVERT: W 407 LYS cc_start: 0.7704 (mtmm) cc_final: 0.7186 (mtmm) REVERT: W 450 ASP cc_start: 0.7959 (m-30) cc_final: 0.7631 (m-30) REVERT: W 461 LYS cc_start: 0.7649 (tttt) cc_final: 0.7134 (ttmm) REVERT: W 524 SER cc_start: 0.8014 (m) cc_final: 0.7459 (t) REVERT: W 560 MET cc_start: 0.6496 (tpp) cc_final: 0.5746 (tmm) REVERT: W 1058 GLU cc_start: 0.7132 (tp30) cc_final: 0.6424 (tp30) REVERT: W 1263 PHE cc_start: 0.7242 (t80) cc_final: 0.6852 (t80) outliers start: 28 outliers final: 17 residues processed: 229 average time/residue: 0.1437 time to fit residues: 47.5069 Evaluate side-chains 232 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 232 SER Chi-restraints excluded: chain W residue 455 CYS Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 502 LEU Chi-restraints excluded: chain W residue 514 GLU Chi-restraints excluded: chain W residue 1185 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS W 138 ASN ** W 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.168127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136888 restraints weight = 32161.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.140504 restraints weight = 15599.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142910 restraints weight = 9318.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.144433 restraints weight = 6531.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.145360 restraints weight = 5183.428| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18402 Z= 0.163 Angle : 0.633 11.708 26260 Z= 0.378 Chirality : 0.046 0.242 2960 Planarity : 0.004 0.037 2245 Dihedral : 28.093 82.135 5011 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.54 % Allowed : 17.14 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.23), residues: 1364 helix: 2.05 (0.19), residues: 786 sheet: -0.84 (0.56), residues: 70 loop : -1.40 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 35 TYR 0.053 0.002 TYR B 98 PHE 0.041 0.002 PHE W 338 TRP 0.057 0.002 TRP W 386 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (18402) covalent geometry : angle 0.63347 / 0.38 (26260) hydrogen bonds : bond 0.06106 / 6.90 ( 960) hydrogen bonds : angle 3.21475 / 4.12 ( 2468) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: A 108 ASN cc_start: 0.8690 (t0) cc_final: 0.8446 (t0) REVERT: B 84 MET cc_start: 0.6950 (tpt) cc_final: 0.6638 (tpt) REVERT: C 75 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7535 (mtmm) REVERT: D 56 MET cc_start: 0.7856 (tpp) cc_final: 0.7157 (tpp) REVERT: D 90 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6788 (mm-30) REVERT: E 129 ARG cc_start: 0.7763 (ttt180) cc_final: 0.7481 (ttt-90) REVERT: F 84 MET cc_start: 0.6110 (ttm) cc_final: 0.5886 (ttm) REVERT: F 92 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7984 (ttp80) REVERT: G 15 LYS cc_start: 0.7600 (mtpp) cc_final: 0.7277 (mtpp) REVERT: G 23 LEU cc_start: 0.8195 (mp) cc_final: 0.7911 (mp) REVERT: G 39 TYR cc_start: 0.8072 (m-80) cc_final: 0.7753 (m-10) REVERT: G 75 LYS cc_start: 0.7275 (mtpp) cc_final: 0.7025 (mtpp) REVERT: G 107 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7708 (t) REVERT: W 141 TYR cc_start: 0.8275 (p90) cc_final: 0.7952 (p90) REVERT: W 228 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6742 (mm-30) REVERT: W 242 LEU cc_start: 0.8620 (tp) cc_final: 0.8389 (tp) REVERT: W 315 ASN cc_start: 0.7138 (m-40) cc_final: 0.6594 (m-40) REVERT: W 387 MET cc_start: 0.6703 (ttm) cc_final: 0.6006 (ttm) REVERT: W 393 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7896 (mtpp) REVERT: W 403 MET cc_start: 0.4912 (tpp) cc_final: 0.4659 (tpt) REVERT: W 407 LYS cc_start: 0.7824 (mtmm) cc_final: 0.7299 (mtmm) REVERT: W 461 LYS cc_start: 0.7603 (tttt) cc_final: 0.7369 (mttt) REVERT: W 471 PHE cc_start: 0.4084 (OUTLIER) cc_final: 0.3732 (m-80) REVERT: W 524 SER cc_start: 0.8018 (m) cc_final: 0.7492 (t) REVERT: W 560 MET cc_start: 0.6439 (tpp) cc_final: 0.5705 (tmm) REVERT: W 1058 GLU cc_start: 0.7113 (tp30) cc_final: 0.6391 (tp30) outliers start: 28 outliers final: 16 residues processed: 224 average time/residue: 0.1292 time to fit residues: 42.4965 Evaluate side-chains 230 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 138 ASN Chi-restraints excluded: chain W residue 232 SER Chi-restraints excluded: chain W residue 459 ASN Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 497 LYS Chi-restraints excluded: chain W residue 502 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 0.7980 chunk 84 optimal weight: 0.0870 chunk 147 optimal weight: 2.9990 chunk 155 optimal weight: 30.0000 chunk 17 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 88 optimal weight: 0.3980 chunk 156 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 138 ASN W 340 ASN ** W 349 GLN ** 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 = 0.4160 r_free = 0.4160 target = 0.169169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136440 restraints weight = 32148.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140484 restraints weight = 15180.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.143109 restraints weight = 8917.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144817 restraints weight = 6171.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.145766 restraints weight = 4838.622| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 18402 Z= 0.144 Angle : 0.613 12.462 26260 Z= 0.367 Chirality : 0.045 0.360 2960 Planarity : 0.004 0.036 2245 Dihedral : 28.068 82.700 5011 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.09 % Allowed : 18.31 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.23), residues: 1364 helix: 2.12 (0.19), residues: 787 sheet: -0.75 (0.57), residues: 70 loop : -1.40 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 35 TYR 0.043 0.002 TYR B 98 PHE 0.037 0.001 PHE W 338 TRP 0.045 0.002 TRP W 386 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (18402) covalent geometry : angle 0.61258 / 0.37 (26260) hydrogen bonds : bond 0.05595 / 6.32 ( 960) hydrogen bonds : angle 3.10090 / 3.97 ( 2468) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: A 108 ASN cc_start: 0.8692 (t0) cc_final: 0.8435 (t0) REVERT: B 84 MET cc_start: 0.6899 (tpt) cc_final: 0.6650 (tpt) REVERT: C 75 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7464 (mtmm) REVERT: D 56 MET cc_start: 0.7770 (tpp) cc_final: 0.7091 (tpp) REVERT: D 98 LEU cc_start: 0.7532 (mt) cc_final: 0.7324 (tp) REVERT: E 129 ARG cc_start: 0.7702 (ttt180) cc_final: 0.7401 (ttt-90) REVERT: F 92 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8059 (ttp80) REVERT: G 15 LYS cc_start: 0.7585 (mtpp) cc_final: 0.7255 (mtpp) REVERT: G 75 LYS cc_start: 0.7226 (mtpp) cc_final: 0.6975 (mtpp) REVERT: W 141 TYR cc_start: 0.8304 (p90) cc_final: 0.7877 (p90) REVERT: W 186 ARG cc_start: 0.7044 (ttm170) cc_final: 0.6323 (ttm170) REVERT: W 228 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6507 (mm-30) REVERT: W 242 LEU cc_start: 0.8622 (tp) cc_final: 0.8395 (tp) REVERT: W 315 ASN cc_start: 0.7098 (m-40) cc_final: 0.6585 (m-40) REVERT: W 387 MET cc_start: 0.6685 (ttm) cc_final: 0.6017 (ttm) REVERT: W 393 LYS cc_start: 0.8182 (mtpp) cc_final: 0.7851 (mtpp) REVERT: W 403 MET cc_start: 0.5060 (tpp) cc_final: 0.4808 (tpt) REVERT: W 407 LYS cc_start: 0.7735 (mtmm) cc_final: 0.7259 (mtmm) REVERT: W 461 LYS cc_start: 0.7465 (tttt) cc_final: 0.7246 (mttt) REVERT: W 471 PHE cc_start: 0.4081 (OUTLIER) cc_final: 0.3753 (m-80) REVERT: W 507 TRP cc_start: 0.7551 (m100) cc_final: 0.7071 (m100) REVERT: W 560 MET cc_start: 0.6410 (tpp) cc_final: 0.5712 (tmm) REVERT: W 1049 TYR cc_start: 0.6969 (m-80) cc_final: 0.6662 (m-80) REVERT: W 1058 GLU cc_start: 0.7095 (tp30) cc_final: 0.6385 (tp30) outliers start: 23 outliers final: 15 residues processed: 228 average time/residue: 0.1434 time to fit residues: 47.5414 Evaluate side-chains 231 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 138 ASN Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 459 ASN Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 497 LYS Chi-restraints excluded: chain W residue 1013 SER Chi-restraints excluded: chain W residue 1181 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 8 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 138 ASN W 349 GLN W 428 HIS W 508 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.167823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136147 restraints weight = 32148.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140003 restraints weight = 15189.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.142452 restraints weight = 8901.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.144103 restraints weight = 6149.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145041 restraints weight = 4830.457| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18402 Z= 0.167 Angle : 0.623 11.332 26260 Z= 0.372 Chirality : 0.045 0.237 2960 Planarity : 0.004 0.039 2245 Dihedral : 28.016 83.888 5011 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.18 % Allowed : 18.40 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.23), residues: 1364 helix: 2.06 (0.19), residues: 787 sheet: -0.61 (0.56), residues: 68 loop : -1.46 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 35 TYR 0.043 0.002 TYR B 98 PHE 0.041 0.002 PHE W 338 TRP 0.042 0.002 TRP W 386 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.17 (18402) covalent geometry : angle 0.62303 / 0.37 (26260) hydrogen bonds : bond 0.06007 / 6.79 ( 960) hydrogen bonds : angle 3.20746 / 4.10 ( 2468) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: A 108 ASN cc_start: 0.8699 (t0) cc_final: 0.8442 (t0) REVERT: B 84 MET cc_start: 0.7018 (tpt) cc_final: 0.6747 (tpt) REVERT: C 75 LYS cc_start: 0.7911 (mtmm) cc_final: 0.7424 (mtmm) REVERT: D 56 MET cc_start: 0.7829 (tpp) cc_final: 0.7060 (tpp) REVERT: D 98 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7331 (tp) REVERT: E 129 ARG cc_start: 0.7703 (ttt180) cc_final: 0.7399 (ttt-90) REVERT: F 92 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8092 (ttp80) REVERT: G 15 LYS cc_start: 0.7638 (mtpp) cc_final: 0.7301 (mtpp) REVERT: G 75 LYS cc_start: 0.7256 (mtpp) cc_final: 0.7003 (mtpp) REVERT: W 141 TYR cc_start: 0.8322 (p90) cc_final: 0.8007 (p90) REVERT: W 228 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6769 (mm-30) REVERT: W 315 ASN cc_start: 0.7166 (m-40) cc_final: 0.6693 (m-40) REVERT: W 387 MET cc_start: 0.6743 (ttm) cc_final: 0.6090 (ttm) REVERT: W 393 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7872 (mtpp) REVERT: W 403 MET cc_start: 0.5124 (tpp) cc_final: 0.4849 (tpt) REVERT: W 407 LYS cc_start: 0.7850 (mtmm) cc_final: 0.7207 (mtmm) REVERT: W 461 LYS cc_start: 0.7496 (tttt) cc_final: 0.7269 (mttt) REVERT: W 507 TRP cc_start: 0.7692 (m100) cc_final: 0.7118 (m100) REVERT: W 524 SER cc_start: 0.8046 (m) cc_final: 0.7561 (t) REVERT: W 560 MET cc_start: 0.6437 (tpp) cc_final: 0.5767 (tmm) REVERT: W 1058 GLU cc_start: 0.7119 (tp30) cc_final: 0.6385 (tp30) outliers start: 24 outliers final: 17 residues processed: 222 average time/residue: 0.1537 time to fit residues: 48.9674 Evaluate side-chains 228 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 138 ASN Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 459 ASN Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 497 LYS Chi-restraints excluded: chain W residue 1013 SER Chi-restraints excluded: chain W residue 1181 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 114 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 138 ASN ** W 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 410 GLN ** 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 = 0.4139 r_free = 0.4139 target = 0.167615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.135876 restraints weight = 31979.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.139732 restraints weight = 15047.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.142252 restraints weight = 8800.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143822 restraints weight = 6088.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.144668 restraints weight = 4789.674| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18402 Z= 0.162 Angle : 0.621 13.002 26260 Z= 0.370 Chirality : 0.044 0.280 2960 Planarity : 0.004 0.039 2245 Dihedral : 27.989 84.416 5011 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.09 % Allowed : 18.31 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.23), residues: 1364 helix: 2.06 (0.19), residues: 787 sheet: -0.71 (0.55), residues: 68 loop : -1.47 (0.25), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 35 TYR 0.047 0.002 TYR B 98 PHE 0.036 0.002 PHE W 338 TRP 0.042 0.002 TRP W 386 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.16 (18402) covalent geometry : angle 0.62061 / 0.37 (26260) hydrogen bonds : bond 0.05916 / 6.69 ( 960) hydrogen bonds : angle 3.21367 / 4.12 ( 2468) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6281 (mp0) REVERT: A 108 ASN cc_start: 0.8673 (t0) cc_final: 0.8419 (t0) REVERT: B 84 MET cc_start: 0.7086 (tpt) cc_final: 0.6801 (tpt) REVERT: C 75 LYS cc_start: 0.7848 (mtmm) cc_final: 0.7406 (mtmm) REVERT: D 56 MET cc_start: 0.7828 (tpp) cc_final: 0.7142 (tpp) REVERT: D 98 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7267 (tp) REVERT: E 129 ARG cc_start: 0.7708 (ttt180) cc_final: 0.7465 (ttt-90) REVERT: F 92 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8089 (ttp80) REVERT: G 15 LYS cc_start: 0.7666 (mtpp) cc_final: 0.7318 (mtpp) REVERT: G 75 LYS cc_start: 0.7271 (mtpp) cc_final: 0.7018 (mtpp) REVERT: W 141 TYR cc_start: 0.8325 (p90) cc_final: 0.8032 (p90) REVERT: W 228 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6764 (mm-30) REVERT: W 242 LEU cc_start: 0.8623 (tp) cc_final: 0.8410 (tp) REVERT: W 315 ASN cc_start: 0.7176 (m-40) cc_final: 0.6725 (m-40) REVERT: W 387 MET cc_start: 0.6805 (ttm) cc_final: 0.6156 (ttm) REVERT: W 393 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7869 (mtpp) REVERT: W 403 MET cc_start: 0.5176 (tpp) cc_final: 0.4889 (tpt) REVERT: W 407 LYS cc_start: 0.7829 (mtmm) cc_final: 0.7227 (mtmm) REVERT: W 461 LYS cc_start: 0.7477 (tttt) cc_final: 0.7251 (mttt) REVERT: W 507 TRP cc_start: 0.7656 (m100) cc_final: 0.7100 (m100) REVERT: W 524 SER cc_start: 0.8069 (m) cc_final: 0.7585 (t) REVERT: W 560 MET cc_start: 0.6449 (tpp) cc_final: 0.5770 (tmm) REVERT: W 1058 GLU cc_start: 0.7120 (tp30) cc_final: 0.6394 (tp30) outliers start: 23 outliers final: 19 residues processed: 221 average time/residue: 0.1569 time to fit residues: 49.4706 Evaluate side-chains 229 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 138 ASN Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 459 ASN Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 497 LYS Chi-restraints excluded: chain W residue 1013 SER Chi-restraints excluded: chain W residue 1181 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 82 optimal weight: 0.0570 chunk 102 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.1980 chunk 157 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 349 GLN ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.168362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137070 restraints weight = 32218.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.140916 restraints weight = 15072.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.143412 restraints weight = 8774.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.145046 restraints weight = 6033.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.146076 restraints weight = 4714.156| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18402 Z= 0.151 Angle : 0.617 12.583 26260 Z= 0.368 Chirality : 0.044 0.308 2960 Planarity : 0.004 0.047 2245 Dihedral : 27.984 84.513 5011 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.90 % Allowed : 18.68 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.23), residues: 1364 helix: 2.06 (0.19), residues: 788 sheet: -0.66 (0.55), residues: 68 loop : -1.44 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 35 TYR 0.043 0.002 TYR B 98 PHE 0.034 0.002 PHE W 338 TRP 0.043 0.002 TRP W 386 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (18402) covalent geometry : angle 0.61686 / 0.37 (26260) hydrogen bonds : bond 0.05725 / 6.46 ( 960) hydrogen bonds : angle 3.18717 / 4.10 ( 2468) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6259 (mp0) REVERT: A 108 ASN cc_start: 0.8663 (t0) cc_final: 0.8413 (t0) REVERT: B 72 TYR cc_start: 0.7694 (m-80) cc_final: 0.7072 (m-80) REVERT: B 84 MET cc_start: 0.7078 (tpt) cc_final: 0.6779 (tpt) REVERT: D 56 MET cc_start: 0.7785 (tpp) cc_final: 0.7137 (tpp) REVERT: D 82 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7480 (mtmm) REVERT: G 15 LYS cc_start: 0.7666 (mtpp) cc_final: 0.7299 (mtpp) REVERT: G 75 LYS cc_start: 0.7251 (mtpp) cc_final: 0.7003 (mtpp) REVERT: W 141 TYR cc_start: 0.8322 (p90) cc_final: 0.8002 (p90) REVERT: W 228 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6749 (mm-30) REVERT: W 242 LEU cc_start: 0.8592 (tp) cc_final: 0.8379 (tp) REVERT: W 315 ASN cc_start: 0.7165 (m-40) cc_final: 0.6719 (m-40) REVERT: W 387 MET cc_start: 0.6810 (ttm) cc_final: 0.6176 (ttm) REVERT: W 393 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7849 (mtpp) REVERT: W 403 MET cc_start: 0.5173 (tpp) cc_final: 0.4900 (tpt) REVERT: W 407 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7201 (mtmm) REVERT: W 461 LYS cc_start: 0.7440 (tttt) cc_final: 0.7219 (mttt) REVERT: W 471 PHE cc_start: 0.4075 (OUTLIER) cc_final: 0.3716 (m-80) REVERT: W 507 TRP cc_start: 0.7646 (m100) cc_final: 0.7069 (m100) REVERT: W 524 SER cc_start: 0.8051 (m) cc_final: 0.7574 (t) REVERT: W 527 GLU cc_start: 0.6571 (mm-30) cc_final: 0.6347 (mm-30) REVERT: W 560 MET cc_start: 0.6404 (tpp) cc_final: 0.5770 (tmm) REVERT: W 1049 TYR cc_start: 0.7067 (m-80) cc_final: 0.6763 (m-80) REVERT: W 1058 GLU cc_start: 0.7132 (tp30) cc_final: 0.6375 (tp30) outliers start: 21 outliers final: 15 residues processed: 216 average time/residue: 0.1566 time to fit residues: 48.6523 Evaluate side-chains 224 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain W residue 128 SER Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 349 GLN Chi-restraints excluded: chain W residue 459 ASN Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 497 LYS Chi-restraints excluded: chain W residue 1181 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 142 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 78 optimal weight: 0.0050 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.168524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.137245 restraints weight = 32441.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141088 restraints weight = 15186.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143645 restraints weight = 8821.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.145145 restraints weight = 6047.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.146260 restraints weight = 4751.742| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.322 18402 Z= 0.289 Angle : 0.836 59.040 26260 Z= 0.521 Chirality : 0.052 1.276 2960 Planarity : 0.006 0.183 2245 Dihedral : 27.983 84.506 5011 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.99 % Allowed : 18.86 % Favored : 79.15 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.23), residues: 1364 helix: 2.04 (0.19), residues: 788 sheet: -0.67 (0.55), residues: 68 loop : -1.43 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.056 0.001 ARG W1016 TYR 0.039 0.002 TYR B 98 PHE 0.027 0.002 PHE W 338 TRP 0.060 0.004 TRP W 447 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.29 (18402) covalent geometry : angle 0.83643 / 0.52 (26260) hydrogen bonds : bond 0.05775 / 6.52 ( 960) hydrogen bonds : angle 3.20904 / 4.12 ( 2468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3594.71 seconds wall clock time: 62 minutes 14.61 seconds (3734.61 seconds total)