Starting phenix.real_space_refine on Sat Jul 4 02:33:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r5s_53595/07_2026/9r5s_53595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r5s_53595/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9r5s_53595/07_2026/9r5s_53595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r5s_53595/07_2026/9r5s_53595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r5s_53595/07_2026/9r5s_53595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r5s_53595/07_2026/9r5s_53595.map" } 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-dev-6108/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: 3.79, per 1000 atoms: 0.22 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: 1.31 Conformation dependent library (CDL) restraints added in 778.4 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: 2.23 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: 4.50 Time building geometry restraints manager: 1.86 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: 25562 2.76 - 5.52: 685 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: 15.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.490 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- 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 : 0.954 13.806 26260 Z= 0.820 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 0.95414 / 0.82 (26260) hydrogen bonds : bond 0.16049 / 17.89 ( 960) hydrogen bonds : angle 6.02584 / 7.94 ( 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 : 0.414 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: 0.8184 (p) REVERT: E 59 GLU cc_start: 0.6908 (pm20) cc_final: 0.6427 (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: 0.7397 (m-30) REVERT: W 146 LEU cc_start: 0.8497 (mt) cc_final: 0.8019 (mp) REVERT: W 225 ASN cc_start: 0.6347 (m-40) cc_final: 0.6119 (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: 0.6975 (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: 0.1319 time to fit residues: 47.3723 Evaluate side-chains 201 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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... 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 = 0.171487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141442 restraints weight = 32599.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.145379 restraints weight = 14932.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147941 restraints weight = 8475.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.149449 restraints weight = 5693.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.150547 restraints weight = 4430.163| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 18402 Z= 0.207 Angle : 0.800 11.110 26260 Z= 0.462 Chirality : 0.057 0.248 2960 Planarity : 0.005 0.039 2245 Dihedral : 28.357 90.424 5011 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.54 % Allowed : 8.61 % Favored : 89.85 % 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: 0.06 (0.22), residues: 1364 helix: 1.19 (0.18), residues: 793 sheet: -0.86 (0.60), residues: 68 loop : -1.72 (0.25), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG W 596 TYR 0.029 0.002 TYR W1192 PHE 0.018 0.002 PHE W 593 TRP 0.024 0.002 TRP W 386 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.21 (18402) covalent geometry : angle 0.80036 / 0.46 (26260) hydrogen bonds : bond 0.08201 / 9.19 ( 960) hydrogen bonds : angle 3.94882 / 5.22 ( 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 219 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8493 (t0) cc_final: 0.8233 (t0) REVERT: A 113 HIS cc_start: 0.7963 (t70) cc_final: 0.7660 (t70) REVERT: B 84 MET cc_start: 0.6213 (tpt) cc_final: 0.5896 (tpt) REVERT: E 57 SER cc_start: 0.7912 (p) cc_final: 0.7249 (p) REVERT: E 59 GLU cc_start: 0.7308 (pm20) cc_final: 0.6388 (pm20) REVERT: F 92 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7714 (ttp80) REVERT: G 39 TYR cc_start: 0.7841 (m-80) cc_final: 0.7565 (m-10) REVERT: G 75 LYS cc_start: 0.7214 (mtpp) cc_final: 0.6954 (mtpp) REVERT: H 56 MET cc_start: 0.6993 (mmp) cc_final: 0.6691 (tpp) REVERT: W 137 TYR cc_start: 0.7893 (m-80) cc_final: 0.7638 (m-10) REVERT: W 141 TYR cc_start: 0.8205 (p90) cc_final: 0.7774 (p90) REVERT: W 216 LYS cc_start: 0.6768 (tmtt) cc_final: 0.6325 (tttp) REVERT: W 228 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6752 (mm-30) REVERT: W 242 LEU cc_start: 0.8644 (tp) cc_final: 0.8424 (tp) REVERT: W 245 TYR cc_start: 0.8347 (t80) cc_final: 0.8084 (t80) REVERT: W 283 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6372 (mp0) REVERT: W 387 MET cc_start: 0.6775 (ttm) cc_final: 0.6346 (ttm) REVERT: W 457 MET cc_start: 0.6757 (ppp) cc_final: 0.6538 (ppp) REVERT: W 461 LYS cc_start: 0.7760 (tttt) cc_final: 0.7248 (ttmm) REVERT: W 530 ASN cc_start: 0.7695 (m-40) cc_final: 0.7410 (t0) REVERT: W 560 MET cc_start: 0.6298 (tpp) cc_final: 0.5576 (tmm) REVERT: W 1057 MET cc_start: 0.7648 (ptt) cc_final: 0.7379 (ptt) REVERT: W 1183 LEU cc_start: 0.8398 (tp) cc_final: 0.8175 (mm) REVERT: W 1263 PHE cc_start: 0.7092 (t80) cc_final: 0.6721 (t80) outliers start: 17 outliers final: 11 residues processed: 207 average time/residue: 0.1340 time to fit residues: 40.5397 Evaluate side-chains 207 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain W residue 522 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 59 optimal weight: 0.0040 chunk 14 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 75 HIS ** G 73 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 = 0.4178 r_free = 0.4178 target = 0.170873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.140282 restraints weight = 32751.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144024 restraints weight = 15554.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.146461 restraints weight = 9104.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.148025 restraints weight = 6290.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149034 restraints weight = 4925.651| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18402 Z= 0.170 Angle : 0.671 9.280 26260 Z= 0.403 Chirality : 0.049 0.359 2960 Planarity : 0.004 0.036 2245 Dihedral : 28.369 88.047 5011 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.63 % Allowed : 11.70 % 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: 0.71 (0.23), residues: 1364 helix: 1.82 (0.19), residues: 782 sheet: -0.72 (0.60), residues: 70 loop : -1.55 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG W 596 TYR 0.036 0.002 TYR W1192 PHE 0.033 0.002 PHE W 338 TRP 0.055 0.003 TRP W 386 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.17 (18402) covalent geometry : angle 0.67061 / 0.40 (26260) hydrogen bonds : bond 0.06715 / 7.63 ( 960) hydrogen bonds : angle 3.43835 / 4.51 ( 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 231 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6196 (mp0) REVERT: A 108 ASN cc_start: 0.8605 (t0) cc_final: 0.8387 (t0) REVERT: B 84 MET cc_start: 0.6459 (tpt) cc_final: 0.6156 (tpt) REVERT: C 75 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7752 (mtmm) REVERT: D 56 MET cc_start: 0.7863 (tpp) cc_final: 0.7119 (tpp) REVERT: F 92 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7677 (ttp80) REVERT: G 23 LEU cc_start: 0.8176 (mp) cc_final: 0.7918 (mp) REVERT: G 39 TYR cc_start: 0.7914 (m-80) cc_final: 0.7561 (m-10) REVERT: G 75 LYS cc_start: 0.7234 (mtpp) cc_final: 0.6969 (mtpp) REVERT: G 108 LEU cc_start: 0.8301 (mt) cc_final: 0.7997 (mm) REVERT: H 42 LEU cc_start: 0.7634 (tp) cc_final: 0.7355 (tp) REVERT: H 56 MET cc_start: 0.7071 (mmp) cc_final: 0.6809 (tpp) REVERT: W 216 LYS cc_start: 0.7011 (tmtt) cc_final: 0.6776 (tttp) REVERT: W 228 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6750 (mm-30) REVERT: W 242 LEU cc_start: 0.8629 (tp) cc_final: 0.8397 (tp) REVERT: W 245 TYR cc_start: 0.8391 (t80) cc_final: 0.8129 (t80) REVERT: W 387 MET cc_start: 0.6716 (ttm) cc_final: 0.6075 (ttm) REVERT: W 393 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7897 (mtpp) REVERT: W 407 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7070 (mtmm) REVERT: W 457 MET cc_start: 0.6620 (ppp) cc_final: 0.6313 (ppp) REVERT: W 461 LYS cc_start: 0.7728 (tttt) cc_final: 0.7281 (ttmm) REVERT: W 524 SER cc_start: 0.7875 (m) cc_final: 0.7275 (t) REVERT: W 530 ASN cc_start: 0.7749 (m-40) cc_final: 0.7427 (t0) REVERT: W 537 ARG cc_start: 0.5452 (mtt180) cc_final: 0.5225 (mtt180) REVERT: W 560 MET cc_start: 0.6450 (tpp) cc_final: 0.5568 (tmm) REVERT: W 1058 GLU cc_start: 0.7138 (tp30) cc_final: 0.6442 (tp30) REVERT: W 1263 PHE cc_start: 0.7183 (t80) cc_final: 0.6797 (t80) outliers start: 18 outliers final: 12 residues processed: 222 average time/residue: 0.1518 time to fit residues: 49.2882 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 : 0.512 ------------------------------------------------------------------------------- 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 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 128 SER Chi-restraints excluded: chain W residue 232 SER Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 528 SER 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: 7.9990 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 111 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 113 optimal weight: 0.0060 chunk 42 optimal weight: 0.3980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS H 79 HIS ** W 340 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.172113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.141227 restraints weight = 32536.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.145148 restraints weight = 15057.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147661 restraints weight = 8673.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.149296 restraints weight = 5921.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.150365 restraints weight = 4601.568| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18402 Z= 0.146 Angle : 0.630 10.979 26260 Z= 0.377 Chirality : 0.046 0.236 2960 Planarity : 0.004 0.035 2245 Dihedral : 28.384 79.983 5011 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.09 % Allowed : 14.14 % Favored : 83.77 % 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: 0.94 (0.23), residues: 1364 helix: 2.03 (0.19), residues: 780 sheet: -0.62 (0.60), residues: 70 loop : -1.49 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.029 0.001 TYR B 98 PHE 0.027 0.001 PHE W1188 TRP 0.049 0.002 TRP W 386 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.15 (18402) covalent geometry : angle 0.62960 / 0.38 (26260) hydrogen bonds : bond 0.05754 / 6.43 ( 960) hydrogen bonds : angle 3.16237 / 4.13 ( 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 242 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6137 (mp0) REVERT: A 108 ASN cc_start: 0.8567 (t0) cc_final: 0.8322 (t0) REVERT: B 84 MET cc_start: 0.6516 (tpt) cc_final: 0.6298 (tpt) REVERT: C 75 LYS cc_start: 0.8070 (mtmm) cc_final: 0.7628 (mtmm) REVERT: D 56 MET cc_start: 0.7742 (tpp) cc_final: 0.7108 (tpp) REVERT: F 92 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7963 (ttp80) REVERT: G 39 TYR cc_start: 0.7854 (m-80) cc_final: 0.7646 (m-10) REVERT: G 75 LYS cc_start: 0.7115 (mtpp) cc_final: 0.6887 (mtpp) REVERT: W 228 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6759 (mm-30) REVERT: W 242 LEU cc_start: 0.8603 (tp) cc_final: 0.8377 (tp) REVERT: W 245 TYR cc_start: 0.8400 (t80) cc_final: 0.8180 (t80) REVERT: W 387 MET cc_start: 0.6708 (ttm) cc_final: 0.6211 (ttm) REVERT: W 393 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7887 (mtpp) REVERT: W 403 MET cc_start: 0.4953 (tpp) cc_final: 0.4658 (tpt) REVERT: W 407 LYS cc_start: 0.7672 (mtmm) cc_final: 0.7141 (mtmm) REVERT: W 450 ASP cc_start: 0.7939 (m-30) cc_final: 0.7646 (m-30) REVERT: W 461 LYS cc_start: 0.7609 (tttt) cc_final: 0.7060 (ttmm) REVERT: W 524 SER cc_start: 0.7900 (m) cc_final: 0.7300 (t) REVERT: W 530 ASN cc_start: 0.7807 (m-40) cc_final: 0.7586 (t0) REVERT: W 537 ARG cc_start: 0.5413 (mtt180) cc_final: 0.5126 (mtt-85) REVERT: W 560 MET cc_start: 0.6313 (tpp) cc_final: 0.5555 (tmm) REVERT: W 1058 GLU cc_start: 0.7110 (tp30) cc_final: 0.6388 (tp30) REVERT: W 1263 PHE cc_start: 0.7217 (t80) cc_final: 0.6820 (t80) outliers start: 23 outliers final: 10 residues processed: 227 average time/residue: 0.1518 time to fit residues: 50.0832 Evaluate side-chains 219 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 117 VAL 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 H residue 79 HIS 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 497 LYS Chi-restraints excluded: chain W residue 1198 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: 0.6980 chunk 97 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 161 optimal weight: 0.0170 chunk 114 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 98 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 10.0000 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN W 138 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 = 0.4175 r_free = 0.4175 target = 0.170561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.139763 restraints weight = 32314.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.143408 restraints weight = 15659.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145718 restraints weight = 9301.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.147320 restraints weight = 6517.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.148187 restraints weight = 5137.624| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18402 Z= 0.152 Angle : 0.610 9.042 26260 Z= 0.370 Chirality : 0.045 0.252 2960 Planarity : 0.004 0.035 2245 Dihedral : 28.280 82.004 5011 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.36 % Allowed : 15.87 % Favored : 81.78 % 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: 0.97 (0.23), residues: 1364 helix: 2.06 (0.19), residues: 780 sheet: -0.77 (0.57), residues: 70 loop : -1.45 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 35 TYR 0.039 0.002 TYR B 98 PHE 0.026 0.001 PHE W1188 TRP 0.055 0.002 TRP W 386 HIS 0.021 0.002 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.15 (18402) covalent geometry : angle 0.61005 / 0.37 (26260) hydrogen bonds : bond 0.05808 / 6.54 ( 960) hydrogen bonds : angle 3.16270 / 4.09 ( 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 233 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6228 (mp0) REVERT: A 108 ASN cc_start: 0.8632 (t0) cc_final: 0.8388 (t0) REVERT: B 84 MET cc_start: 0.6690 (tpt) cc_final: 0.6439 (tpt) REVERT: C 75 LYS cc_start: 0.8039 (mtmm) cc_final: 0.7574 (mtmm) REVERT: D 56 MET cc_start: 0.7763 (tpp) cc_final: 0.7034 (tpp) REVERT: F 92 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8014 (ttp80) REVERT: G 39 TYR cc_start: 0.7953 (m-80) cc_final: 0.7714 (m-10) REVERT: G 75 LYS cc_start: 0.7147 (mtpp) cc_final: 0.6930 (mtpp) REVERT: H 59 MET cc_start: 0.7638 (mmm) cc_final: 0.7437 (mmm) REVERT: W 141 TYR cc_start: 0.8236 (p90) cc_final: 0.7729 (p90) REVERT: W 216 LYS cc_start: 0.7230 (tmtt) cc_final: 0.6769 (ptmt) REVERT: W 228 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6728 (mm-30) REVERT: W 242 LEU cc_start: 0.8621 (tp) cc_final: 0.8398 (tp) REVERT: W 245 TYR cc_start: 0.8438 (t80) cc_final: 0.8234 (t80) REVERT: W 315 ASN cc_start: 0.7061 (m-40) cc_final: 0.6297 (m-40) REVERT: W 387 MET cc_start: 0.6756 (ttm) cc_final: 0.6401 (ttm) REVERT: W 393 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7888 (mtpp) REVERT: W 403 MET cc_start: 0.4914 (tpp) cc_final: 0.4611 (tpt) REVERT: W 407 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7294 (mtmm) REVERT: W 450 ASP cc_start: 0.7944 (m-30) cc_final: 0.7634 (m-30) REVERT: W 461 LYS cc_start: 0.7590 (tttt) cc_final: 0.7076 (ttmm) REVERT: W 524 SER cc_start: 0.8000 (m) cc_final: 0.7425 (t) REVERT: W 528 SER cc_start: 0.7153 (OUTLIER) cc_final: 0.6857 (t) REVERT: W 530 ASN cc_start: 0.7821 (m-40) cc_final: 0.7607 (t0) REVERT: W 560 MET cc_start: 0.6413 (tpp) cc_final: 0.5661 (tmm) REVERT: W 1058 GLU cc_start: 0.7158 (tp30) cc_final: 0.6424 (tp30) REVERT: W 1263 PHE cc_start: 0.7223 (t80) cc_final: 0.6833 (t80) outliers start: 26 outliers final: 14 residues processed: 217 average time/residue: 0.1649 time to fit residues: 51.4082 Evaluate side-chains 222 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 82 LEU 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 G residue 63 LEU Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 138 ASN 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 497 LYS Chi-restraints excluded: chain W residue 528 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 104 GLN H 79 HIS H 81 ASN W 138 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.169500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.136775 restraints weight = 32189.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.140779 restraints weight = 15182.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.143399 restraints weight = 8939.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145125 restraints weight = 6198.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.146057 restraints weight = 4856.047| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3811 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= 0.162 Angle : 0.619 11.584 26260 Z= 0.372 Chirality : 0.045 0.239 2960 Planarity : 0.004 0.036 2245 Dihedral : 28.198 82.880 5011 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.99 % Allowed : 17.50 % Favored : 80.51 % 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: 1.03 (0.23), residues: 1364 helix: 2.10 (0.19), residues: 787 sheet: -0.87 (0.56), residues: 70 loop : -1.43 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 35 TYR 0.053 0.002 TYR B 98 PHE 0.022 0.002 PHE W 338 TRP 0.064 0.002 TRP W 386 HIS 0.011 0.001 HIS W 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (18402) covalent geometry : angle 0.61921 / 0.37 (26260) hydrogen bonds : bond 0.05873 / 6.60 ( 960) hydrogen bonds : angle 3.12877 / 4.00 ( 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 232 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8689 (t0) cc_final: 0.8459 (t0) REVERT: B 84 MET cc_start: 0.6852 (tpt) cc_final: 0.6595 (tpt) REVERT: C 75 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7526 (mtmm) REVERT: D 56 MET cc_start: 0.7796 (tpp) cc_final: 0.7028 (tpp) REVERT: E 129 ARG cc_start: 0.7713 (ttt180) cc_final: 0.7437 (ttt-90) REVERT: F 92 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8030 (ttp80) REVERT: G 15 LYS cc_start: 0.7525 (mtpp) cc_final: 0.7210 (mtpp) REVERT: G 39 TYR cc_start: 0.8047 (m-80) cc_final: 0.7806 (m-10) REVERT: G 75 LYS cc_start: 0.7189 (mtpp) cc_final: 0.6965 (mtpp) REVERT: H 42 LEU cc_start: 0.7783 (tp) cc_final: 0.7564 (tp) REVERT: W 216 LYS cc_start: 0.7514 (tmtt) cc_final: 0.7093 (ptmt) REVERT: W 228 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6772 (mm-30) REVERT: W 242 LEU cc_start: 0.8618 (tp) cc_final: 0.8391 (tp) REVERT: W 315 ASN cc_start: 0.7102 (m-40) cc_final: 0.6390 (m-40) REVERT: W 387 MET cc_start: 0.6765 (ttm) cc_final: 0.6373 (ttm) REVERT: W 393 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7882 (mtpp) REVERT: W 403 MET cc_start: 0.4939 (tpp) cc_final: 0.4644 (tpt) REVERT: W 407 LYS cc_start: 0.7808 (mtmm) cc_final: 0.7287 (mtmm) REVERT: W 450 ASP cc_start: 0.7936 (m-30) cc_final: 0.7608 (m-30) REVERT: W 461 LYS cc_start: 0.7535 (tttt) cc_final: 0.7063 (ttmm) REVERT: W 524 SER cc_start: 0.8038 (m) cc_final: 0.7488 (t) REVERT: W 528 SER cc_start: 0.7201 (OUTLIER) cc_final: 0.6892 (t) REVERT: W 560 MET cc_start: 0.6388 (tpp) cc_final: 0.5697 (tmm) REVERT: W 1058 GLU cc_start: 0.7132 (tp30) cc_final: 0.6408 (tp30) outliers start: 22 outliers final: 14 residues processed: 221 average time/residue: 0.1634 time to fit residues: 52.2596 Evaluate side-chains 221 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 73 ASN 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 459 ASN Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 497 LYS Chi-restraints excluded: chain W residue 528 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 0.0040 chunk 123 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS 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 = 0.4155 r_free = 0.4155 target = 0.168790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136456 restraints weight = 32204.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140296 restraints weight = 15640.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142815 restraints weight = 9347.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144438 restraints weight = 6540.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145384 restraints weight = 5181.094| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18402 Z= 0.159 Angle : 0.614 12.031 26260 Z= 0.369 Chirality : 0.045 0.311 2960 Planarity : 0.004 0.037 2245 Dihedral : 28.145 83.436 5011 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.36 % Allowed : 17.68 % Favored : 79.96 % 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: 1.04 (0.23), residues: 1364 helix: 2.09 (0.19), residues: 786 sheet: -0.86 (0.56), residues: 70 loop : -1.41 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 35 TYR 0.045 0.002 TYR B 98 PHE 0.028 0.002 PHE W 338 TRP 0.051 0.002 TRP W 386 HIS 0.020 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (18402) covalent geometry : angle 0.61399 / 0.37 (26260) hydrogen bonds : bond 0.05806 / 6.54 ( 960) hydrogen bonds : angle 3.13541 / 3.99 ( 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 236 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: A 108 ASN cc_start: 0.8632 (t0) cc_final: 0.8385 (t0) REVERT: B 84 MET cc_start: 0.6950 (tpt) cc_final: 0.6671 (tpt) REVERT: C 75 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7472 (mtmm) REVERT: D 56 MET cc_start: 0.7806 (tpp) cc_final: 0.7032 (tpp) REVERT: E 129 ARG cc_start: 0.7771 (ttt180) cc_final: 0.7464 (ttt-90) REVERT: F 24 ASP cc_start: 0.7147 (m-30) cc_final: 0.6945 (m-30) REVERT: F 92 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8075 (ttp80) REVERT: G 15 LYS cc_start: 0.7583 (mtpp) cc_final: 0.7260 (mtpp) REVERT: G 39 TYR cc_start: 0.8079 (m-80) cc_final: 0.7872 (m-10) REVERT: G 75 LYS cc_start: 0.7272 (mtpp) cc_final: 0.7029 (mtpp) REVERT: H 42 LEU cc_start: 0.7767 (tp) cc_final: 0.7563 (tp) REVERT: W 186 ARG cc_start: 0.7075 (ttm170) cc_final: 0.6325 (ttm170) REVERT: W 216 LYS cc_start: 0.7533 (tmtt) cc_final: 0.7178 (ptmt) REVERT: W 228 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6553 (mm-30) REVERT: W 242 LEU cc_start: 0.8648 (tp) cc_final: 0.8418 (tp) REVERT: W 315 ASN cc_start: 0.7136 (m-40) cc_final: 0.6484 (m-40) REVERT: W 387 MET cc_start: 0.6751 (ttm) cc_final: 0.6363 (ttm) REVERT: W 393 LYS cc_start: 0.8220 (mtpp) cc_final: 0.7887 (mtpp) REVERT: W 403 MET cc_start: 0.5133 (tpp) cc_final: 0.4838 (tpt) REVERT: W 407 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7326 (mtmm) REVERT: W 409 VAL cc_start: 0.8944 (m) cc_final: 0.8337 (t) REVERT: W 461 LYS cc_start: 0.7524 (tttt) cc_final: 0.7283 (mttt) REVERT: W 528 SER cc_start: 0.7145 (OUTLIER) cc_final: 0.6872 (t) REVERT: W 560 MET cc_start: 0.6422 (tpp) cc_final: 0.5728 (tmm) REVERT: W 1049 TYR cc_start: 0.6904 (m-80) cc_final: 0.6578 (m-80) REVERT: W 1058 GLU cc_start: 0.7150 (tp30) cc_final: 0.6424 (tp30) outliers start: 26 outliers final: 16 residues processed: 223 average time/residue: 0.1568 time to fit residues: 50.4560 Evaluate side-chains 226 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 C residue 51 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 63 LEU 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 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 528 SER 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: 0.8980 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 107 optimal weight: 0.0570 chunk 156 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 73 ASN H 79 HIS H 81 ASN W 340 ASN ** W 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 428 HIS W 508 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.168876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136106 restraints weight = 32238.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140160 restraints weight = 15188.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.142802 restraints weight = 8906.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.144523 restraints weight = 6150.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145454 restraints weight = 4816.675| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18402 Z= 0.154 Angle : 0.606 11.203 26260 Z= 0.365 Chirality : 0.044 0.236 2960 Planarity : 0.004 0.036 2245 Dihedral : 28.101 83.984 5011 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.36 % Allowed : 17.77 % Favored : 79.87 % 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: 1.06 (0.23), residues: 1364 helix: 2.11 (0.19), residues: 787 sheet: -0.87 (0.56), residues: 70 loop : -1.40 (0.25), residues: 507 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 0.022 0.002 PHE W 338 TRP 0.045 0.002 TRP W 386 HIS 0.026 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (18402) covalent geometry : angle 0.60565 / 0.37 (26260) hydrogen bonds : bond 0.05723 / 6.45 ( 960) hydrogen bonds : angle 3.12807 / 4.00 ( 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 231 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: A 108 ASN cc_start: 0.8690 (t0) cc_final: 0.8428 (t0) REVERT: B 84 MET cc_start: 0.6964 (tpt) cc_final: 0.6679 (tpt) REVERT: C 75 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7447 (mtmm) REVERT: D 56 MET cc_start: 0.7788 (tpp) cc_final: 0.7061 (tpp) REVERT: E 129 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7411 (ttt-90) REVERT: F 92 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8092 (ttp80) REVERT: G 15 LYS cc_start: 0.7611 (mtpp) cc_final: 0.7286 (mtpp) REVERT: W 216 LYS cc_start: 0.7633 (tmtt) cc_final: 0.7343 (ptmt) REVERT: W 228 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6569 (mm-30) REVERT: W 242 LEU cc_start: 0.8635 (tp) cc_final: 0.8412 (tp) REVERT: W 315 ASN cc_start: 0.7116 (m-40) cc_final: 0.6565 (m-40) REVERT: W 387 MET cc_start: 0.6729 (ttm) cc_final: 0.6289 (ttm) REVERT: W 393 LYS cc_start: 0.8200 (mtpp) cc_final: 0.7854 (mtpp) REVERT: W 403 MET cc_start: 0.5093 (tpp) cc_final: 0.4818 (tpt) REVERT: W 407 LYS cc_start: 0.7840 (mtmm) cc_final: 0.7229 (mtmm) REVERT: W 461 LYS cc_start: 0.7440 (tttt) cc_final: 0.7212 (mttt) REVERT: W 507 TRP cc_start: 0.7644 (m100) cc_final: 0.7197 (m100) REVERT: W 560 MET cc_start: 0.6386 (tpp) cc_final: 0.5748 (tmm) REVERT: W 1058 GLU cc_start: 0.7165 (tp30) cc_final: 0.6426 (tp30) outliers start: 26 outliers final: 19 residues processed: 217 average time/residue: 0.1537 time to fit residues: 48.2254 Evaluate side-chains 222 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 C residue 51 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 82 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 73 ASN 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 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 502 LEU Chi-restraints excluded: chain W residue 1013 SER Chi-restraints excluded: chain W residue 1047 GLU 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: 8.9990 chunk 75 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 H 79 HIS ** W 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 349 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 = 0.4083 r_free = 0.4083 target = 0.163006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131077 restraints weight = 31936.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134851 restraints weight = 15102.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137270 restraints weight = 8937.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138883 restraints weight = 6246.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139785 restraints weight = 4929.151| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 18402 Z= 0.283 Angle : 0.752 12.480 26260 Z= 0.440 Chirality : 0.050 0.248 2960 Planarity : 0.005 0.045 2245 Dihedral : 28.040 86.398 5011 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.81 % Allowed : 18.59 % 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: 0.40 (0.22), residues: 1364 helix: 1.48 (0.18), residues: 792 sheet: -0.87 (0.54), residues: 68 loop : -1.59 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W1016 TYR 0.056 0.003 TYR B 98 PHE 0.041 0.003 PHE W 444 TRP 0.045 0.003 TRP W 386 HIS 0.048 0.003 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.28 (18402) covalent geometry : angle 0.75226 / 0.44 (26260) hydrogen bonds : bond 0.08056 / 9.07 ( 960) hydrogen bonds : angle 3.71879 / 4.77 ( 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 219 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6342 (mp0) REVERT: A 108 ASN cc_start: 0.8733 (t0) cc_final: 0.8486 (t0) REVERT: B 84 MET cc_start: 0.7262 (tpt) cc_final: 0.6955 (tpt) REVERT: D 56 MET cc_start: 0.7998 (tpp) cc_final: 0.7234 (tpp) REVERT: D 82 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7573 (mtmm) REVERT: E 129 ARG cc_start: 0.7758 (ttt180) cc_final: 0.7447 (ttt-90) REVERT: F 92 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8043 (ttp80) REVERT: G 15 LYS cc_start: 0.7736 (mtpp) cc_final: 0.7385 (mtpp) REVERT: G 38 ASN cc_start: 0.8353 (m-40) cc_final: 0.8149 (m-40) REVERT: W 216 LYS cc_start: 0.7958 (tmtt) cc_final: 0.6862 (ptmt) REVERT: W 228 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6730 (mm-30) REVERT: W 315 ASN cc_start: 0.7276 (m-40) cc_final: 0.6810 (m-40) REVERT: W 387 MET cc_start: 0.6855 (ttm) cc_final: 0.6226 (ttm) REVERT: W 393 LYS cc_start: 0.8294 (mtpp) cc_final: 0.7944 (mtpp) REVERT: W 403 MET cc_start: 0.5135 (tpp) cc_final: 0.4894 (tpt) REVERT: W 407 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7456 (mtmm) REVERT: W 437 MET cc_start: 0.7199 (ttt) cc_final: 0.6944 (ttt) REVERT: W 440 TRP cc_start: 0.7338 (m100) cc_final: 0.7063 (m100) REVERT: W 455 CYS cc_start: 0.6911 (p) cc_final: 0.6690 (m) REVERT: W 471 PHE cc_start: 0.4202 (OUTLIER) cc_final: 0.3622 (m-80) REVERT: W 524 SER cc_start: 0.8162 (m) cc_final: 0.7767 (t) REVERT: W 560 MET cc_start: 0.6574 (tpp) cc_final: 0.5886 (tmm) REVERT: W 1058 GLU cc_start: 0.7205 (tp30) cc_final: 0.6457 (tp30) REVERT: W 1212 LEU cc_start: 0.7616 (mp) cc_final: 0.7413 (tt) outliers start: 20 outliers final: 13 residues processed: 209 average time/residue: 0.1539 time to fit residues: 46.1220 Evaluate side-chains 212 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 195 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 82 LYS 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 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 502 LEU Chi-restraints excluded: chain W residue 514 GLU Chi-restraints excluded: chain W residue 1013 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 0.8980 chunk 111 optimal weight: 0.4980 chunk 146 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.166736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135218 restraints weight = 31933.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138982 restraints weight = 15026.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141490 restraints weight = 8815.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.142952 restraints weight = 6096.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.143985 restraints weight = 4829.307| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18402 Z= 0.166 Angle : 0.641 12.625 26260 Z= 0.383 Chirality : 0.045 0.264 2960 Planarity : 0.004 0.039 2245 Dihedral : 28.060 84.990 5011 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.81 % Allowed : 18.95 % Favored : 79.24 % 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: 0.75 (0.22), residues: 1364 helix: 1.81 (0.19), residues: 788 sheet: -0.74 (0.56), residues: 68 loop : -1.51 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 35 TYR 0.048 0.002 TYR B 98 PHE 0.024 0.002 PHE W 338 TRP 0.047 0.002 TRP W 386 HIS 0.014 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.17 (18402) covalent geometry : angle 0.64119 / 0.38 (26260) hydrogen bonds : bond 0.06311 / 7.11 ( 960) hydrogen bonds : angle 3.35526 / 4.28 ( 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 222 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: A 108 ASN cc_start: 0.8681 (t0) cc_final: 0.8433 (t0) REVERT: B 84 MET cc_start: 0.7154 (tpt) cc_final: 0.6857 (tpt) REVERT: C 75 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7458 (mtmm) REVERT: D 56 MET cc_start: 0.7882 (tpp) cc_final: 0.7273 (tpp) REVERT: D 82 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7627 (mtmm) REVERT: E 129 ARG cc_start: 0.7719 (ttt180) cc_final: 0.7470 (ttt-90) REVERT: F 92 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7990 (ttp80) REVERT: G 15 LYS cc_start: 0.7710 (mtpp) cc_final: 0.7360 (mtpp) REVERT: G 38 ASN cc_start: 0.8367 (m-40) cc_final: 0.8163 (m-40) REVERT: W 216 LYS cc_start: 0.7731 (tmtt) cc_final: 0.7014 (tttt) REVERT: W 228 GLU cc_start: 0.6995 (mm-30) cc_final: 0.6696 (mm-30) REVERT: W 242 LEU cc_start: 0.8614 (tp) cc_final: 0.8404 (tp) REVERT: W 315 ASN cc_start: 0.7188 (m-40) cc_final: 0.6748 (m110) REVERT: W 387 MET cc_start: 0.6879 (ttm) cc_final: 0.6275 (ttm) REVERT: W 393 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7865 (mtpp) REVERT: W 403 MET cc_start: 0.5166 (tpp) cc_final: 0.4902 (tpt) REVERT: W 407 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7384 (mtmm) REVERT: W 440 TRP cc_start: 0.7215 (m100) cc_final: 0.6954 (m100) REVERT: W 461 LYS cc_start: 0.7605 (mttt) cc_final: 0.7192 (mptt) REVERT: W 524 SER cc_start: 0.8078 (m) cc_final: 0.7623 (t) REVERT: W 560 MET cc_start: 0.6476 (tpp) cc_final: 0.5855 (tmm) REVERT: W 1058 GLU cc_start: 0.7184 (tp30) cc_final: 0.6425 (tp30) outliers start: 20 outliers final: 14 residues processed: 213 average time/residue: 0.1589 time to fit residues: 48.6542 Evaluate side-chains 219 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 C residue 51 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 82 LYS 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 W residue 128 SER Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 325 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 142 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 64 optimal weight: 0.0670 chunk 42 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS W 184 ASN W 349 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.167153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135874 restraints weight = 32248.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.139652 restraints weight = 15110.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142161 restraints weight = 8853.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143745 restraints weight = 6090.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.144434 restraints weight = 4788.217| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 18402 Z= 0.157 Angle : 0.629 12.402 26260 Z= 0.376 Chirality : 0.044 0.237 2960 Planarity : 0.004 0.038 2245 Dihedral : 28.069 85.568 5011 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.72 % Allowed : 19.67 % Favored : 78.60 % 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: 0.83 (0.23), residues: 1364 helix: 1.87 (0.19), residues: 787 sheet: -0.72 (0.56), residues: 68 loop : -1.44 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 35 TYR 0.044 0.002 TYR B 98 PHE 0.022 0.002 PHE W 338 TRP 0.046 0.002 TRP W 386 HIS 0.007 0.001 HIS H 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (18402) covalent geometry : angle 0.62942 / 0.38 (26260) hydrogen bonds : bond 0.05915 / 6.69 ( 960) hydrogen bonds : angle 3.28436 / 4.17 ( 2468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3694.44 seconds wall clock time: 64 minutes 0.20 seconds (3840.20 seconds total)