Starting phenix.real_space_refine on Thu Feb 5 13:08:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r5s_53595/02_2026/9r5s_53595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r5s_53595/02_2026/9r5s_53595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9r5s_53595/02_2026/9r5s_53595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r5s_53595/02_2026/9r5s_53595.map" model { file = "/net/cci-nas-00/data/ceres_data/9r5s_53595/02_2026/9r5s_53595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r5s_53595/02_2026/9r5s_53595.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 320 5.49 5 S 27 5.16 5 C 9976 2.51 5 N 3190 2.21 5 O 3910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 3.38, per 1000 atoms: 0.19 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: 1.34 Conformation dependent library (CDL) restraints added in 537.5 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: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.149A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.661A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.859A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.878A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.866A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.580A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.571A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.969A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.984A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.607A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.705A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 98 Processing helix chain 'D' and resid 102 through 120 removed outlier: 3.639A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 removed outlier: 3.604A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.523A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.798A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.861A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.569A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 42 " --> pdb=" O ALA F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.986A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.507A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.635A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.630A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.876A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.619A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.542A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 removed outlier: 4.033A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 143 through 147 Processing helix chain 'W' and resid 203 through 209 Processing helix chain 'W' and resid 229 through 234 Processing helix chain 'W' and resid 238 through 250 removed outlier: 3.571A pdb=" N LEU W 242 " --> pdb=" O GLY W 238 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN W 248 " --> pdb=" O ASN W 244 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE W 250 " --> pdb=" O CYS W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 250 through 259 Processing helix chain 'W' and resid 263 through 283 removed outlier: 3.800A pdb=" N GLU W 283 " --> pdb=" O ASP W 279 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 331 removed outlier: 3.705A pdb=" N LYS W 329 " --> pdb=" O THR W 325 " (cutoff:3.500A) Processing helix chain 'W' and resid 331 through 343 removed outlier: 3.655A pdb=" N VAL W 335 " --> pdb=" O ALA W 331 " (cutoff:3.500A) Processing helix chain 'W' and resid 347 through 351 removed outlier: 3.942A pdb=" N SER W 351 " --> pdb=" O PRO W 348 " (cutoff:3.500A) Processing helix chain 'W' and resid 377 through 394 removed outlier: 3.732A pdb=" N GLY W 383 " --> pdb=" O PHE W 379 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE W 384 " --> pdb=" O GLN W 380 " (cutoff:3.500A) Processing helix chain 'W' and resid 406 through 421 removed outlier: 3.652A pdb=" N GLN W 410 " --> pdb=" O GLY W 406 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR W 411 " --> pdb=" O LYS W 407 " (cutoff:3.500A) Processing helix chain 'W' and resid 433 through 435 No H-bonds generated for 'chain 'W' and resid 433 through 435' Processing helix chain 'W' and resid 436 through 447 Processing helix chain 'W' and resid 459 through 471 removed outlier: 3.564A pdb=" N ILE W 466 " --> pdb=" O SER W 462 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE W 471 " --> pdb=" O ARG W 467 " (cutoff:3.500A) Processing helix chain 'W' and resid 492 through 498 removed outlier: 3.532A pdb=" N LEU W 496 " --> pdb=" O TYR W 492 " (cutoff:3.500A) Processing helix chain 'W' and resid 498 through 504 removed outlier: 3.702A pdb=" N SER W 504 " --> pdb=" O ALA W 500 " (cutoff:3.500A) Processing helix chain 'W' and resid 515 through 519 Processing helix chain 'W' and resid 523 through 531 removed outlier: 3.891A pdb=" N SER W 531 " --> pdb=" O GLU W 527 " (cutoff:3.500A) Processing helix chain 'W' and resid 549 through 560 Processing helix chain 'W' and resid 576 through 590 Processing helix chain 'W' and resid 591 through 594 removed outlier: 3.617A pdb=" N ILE W 594 " --> pdb=" O GLN W 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 591 through 594' Processing helix chain 'W' and resid 1011 through 1023 Processing helix chain 'W' and resid 1028 through 1030 No H-bonds generated for 'chain 'W' and resid 1028 through 1030' Processing helix chain 'W' and resid 1031 through 1038 removed outlier: 3.855A pdb=" N LEU W1035 " --> pdb=" O ILE W1031 " (cutoff:3.500A) Processing helix chain 'W' and resid 1045 through 1072 Processing helix chain 'W' and resid 1129 through 1148 Processing helix chain 'W' and resid 1176 through 1191 removed outlier: 3.611A pdb=" N ASP W1180 " --> pdb=" O THR W1176 " (cutoff:3.500A) Processing helix chain 'W' and resid 1194 through 1200 Processing helix chain 'W' and resid 1249 through 1266 removed outlier: 3.505A pdb=" N GLY W1254 " --> pdb=" O ALA W1250 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER W1262 " --> pdb=" O ASP W1258 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.441A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.388A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.086A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.057A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.955A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.518A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.822A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'W' and resid 179 through 186 removed outlier: 5.695A pdb=" N VAL W 182 " --> pdb=" O LYS W 216 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS W 216 " --> pdb=" O VAL W 182 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN W 184 " --> pdb=" O LEU W 214 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU W 212 " --> pdb=" O ARG W 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR W 226 " --> pdb=" O ILE W 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 287 through 295 removed outlier: 6.597A pdb=" N LEU W 308 " --> pdb=" O ILE W 291 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER W 293 " --> pdb=" O GLN W 306 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN W 306 " --> pdb=" O SER W 293 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 398 through 399 removed outlier: 6.392A pdb=" N GLN W 508 " --> pdb=" O ASN W 536 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N MET W 538 " --> pdb=" O GLN W 508 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET W 510 " --> pdb=" O MET W 538 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE W 540 " --> pdb=" O MET W 510 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL W 512 " --> pdb=" O ILE W 540 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 388 hydrogen bonds 776 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 272 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 1.80 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=" C ASN W1170 " pdb=" N TRP W1171 " ideal model delta sigma weight residual 1.332 1.377 -0.044 1.40e-02 5.10e+03 9.98e+00 bond pdb=" N3 DC I 17 " pdb=" C4 DC I 17 " ideal model delta sigma weight residual 1.334 1.285 0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" CA PRO W 368 " pdb=" C PRO W 368 " ideal model delta sigma weight residual 1.514 1.528 -0.013 5.50e-03 3.31e+04 5.78e+00 bond pdb=" C1' DC J -3 " pdb=" N1 DC J -3 " ideal model delta sigma weight residual 1.490 1.562 -0.072 3.00e-02 1.11e+03 5.73e+00 bond pdb=" C1' DC I -80 " pdb=" N1 DC I -80 " ideal model delta sigma weight residual 1.490 1.561 -0.071 3.00e-02 1.11e+03 5.62e+00 ... (remaining 18397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 25841 2.76 - 5.52: 407 5.52 - 8.28: 7 8.28 - 11.05: 3 11.05 - 13.81: 2 Bond angle restraints: 26260 Sorted by residual: angle pdb=" O3' DG I 7 " pdb=" P DC I 8 " pdb=" OP2 DC I 8 " ideal model delta sigma weight residual 108.00 94.19 13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" O3' DG I 7 " pdb=" P DC I 8 " pdb=" OP1 DC I 8 " ideal model delta sigma weight residual 108.00 120.73 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" N SER W 221 " pdb=" CA SER W 221 " pdb=" C SER W 221 " ideal model delta sigma weight residual 110.41 115.12 -4.71 1.18e+00 7.18e-01 1.59e+01 angle pdb=" C3' DG J -14 " pdb=" C2' DG J -14 " pdb=" C1' DG J -14 " ideal model delta sigma weight residual 101.60 95.87 5.73 1.50e+00 4.44e-01 1.46e+01 angle pdb=" OP1 DG J -79 " pdb=" P DG J -79 " pdb=" OP2 DG J -79 " ideal model delta sigma weight residual 120.00 109.23 10.77 3.00e+00 1.11e-01 1.29e+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 - 0.082: 2775 0.082 - 0.164: 175 0.164 - 0.246: 8 0.246 - 0.327: 0 0.327 - 0.409: 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 2.35 -2.75 -0.41 2.00e-01 2.50e+01 4.19e+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 2.35 -2.55 -0.20 2.00e-01 2.50e+01 1.03e+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: 13.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.470 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5993 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 18402 Z= 0.266 Angle : 0.849 13.806 26260 Z= 0.520 Chirality : 0.043 0.409 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 covalent geometry : bond 0.00582 (18402) covalent geometry : angle 0.84858 (26260) hydrogen bonds : bond 0.16049 ( 960) hydrogen bonds : angle 6.02584 ( 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 : 0.477 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: 0.1466 time to fit residues: 51.6365 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 : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 44 GLN E 68 GLN F 75 HIS G 24 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN W 184 ASN W 210 ASN ** W 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.169849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139245 restraints weight = 32409.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142897 restraints weight = 15543.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.145306 restraints weight = 9177.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.146865 restraints weight = 6367.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147814 restraints weight = 5010.894| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 18402 Z= 0.238 Angle : 0.688 8.776 26260 Z= 0.411 Chirality : 0.043 0.221 2960 Planarity : 0.004 0.045 2245 Dihedral : 28.007 81.629 5011 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.81 % Allowed : 8.52 % Favored : 89.66 % 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: 0.32 (0.22), residues: 1364 helix: 1.43 (0.18), residues: 788 sheet: -0.71 (0.60), residues: 68 loop : -1.66 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG W 596 TYR 0.024 0.002 TYR W1192 PHE 0.024 0.002 PHE W 444 TRP 0.019 0.003 TRP W 386 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00513 (18402) covalent geometry : angle 0.68777 (26260) hydrogen bonds : bond 0.06955 ( 960) hydrogen bonds : angle 3.67813 ( 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 239 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8528 (t0) cc_final: 0.8312 (t0) REVERT: B 84 MET cc_start: 0.6565 (tpt) cc_final: 0.6302 (tpt) REVERT: C 75 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7754 (mtmm) REVERT: D 56 MET cc_start: 0.8021 (tpp) cc_final: 0.7209 (tpp) REVERT: F 92 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7666 (ttp80) REVERT: G 39 TYR cc_start: 0.7835 (m-80) cc_final: 0.7506 (m-10) REVERT: G 75 LYS cc_start: 0.7271 (mtpp) cc_final: 0.7019 (mtpp) REVERT: G 107 VAL cc_start: 0.7727 (OUTLIER) cc_final: 0.7526 (t) REVERT: G 108 LEU cc_start: 0.8341 (mt) cc_final: 0.7999 (mt) REVERT: H 42 LEU cc_start: 0.7642 (tp) cc_final: 0.7434 (tp) REVERT: H 59 MET cc_start: 0.7673 (mmm) cc_final: 0.7412 (mmt) REVERT: W 228 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6817 (mm-30) REVERT: W 245 TYR cc_start: 0.8383 (t80) cc_final: 0.8138 (t80) REVERT: W 283 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6446 (mp0) REVERT: W 387 MET cc_start: 0.6835 (ttm) cc_final: 0.6524 (ttm) REVERT: W 393 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7958 (mtpp) REVERT: W 457 MET cc_start: 0.6692 (ppp) cc_final: 0.6482 (ppp) REVERT: W 461 LYS cc_start: 0.7763 (tttt) cc_final: 0.7262 (ttmm) REVERT: W 524 SER cc_start: 0.7753 (m) cc_final: 0.7136 (t) REVERT: W 530 ASN cc_start: 0.7818 (m-40) cc_final: 0.7563 (t0) REVERT: W 560 MET cc_start: 0.6534 (tpp) cc_final: 0.5711 (tmm) REVERT: W 1057 MET cc_start: 0.7653 (ptt) cc_final: 0.7399 (ptt) REVERT: W 1263 PHE cc_start: 0.7171 (t80) cc_final: 0.6776 (t80) outliers start: 20 outliers final: 14 residues processed: 228 average time/residue: 0.1401 time to fit residues: 46.1056 Evaluate side-chains 222 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 117 VAL 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 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 232 SER Chi-restraints excluded: chain W residue 466 ILE Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 1185 ILE Chi-restraints excluded: chain W residue 1196 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN F 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS W 138 ASN W 185 HIS W 315 ASN ** W 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 349 GLN ** W 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.165786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132298 restraints weight = 32127.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136314 restraints weight = 15135.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138935 restraints weight = 8933.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140627 restraints weight = 6221.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141640 restraints weight = 4910.601| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18402 Z= 0.223 Angle : 0.634 6.318 26260 Z= 0.382 Chirality : 0.040 0.168 2960 Planarity : 0.004 0.043 2245 Dihedral : 27.618 77.709 5011 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.81 % Allowed : 13.69 % Favored : 83.50 % 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: 0.64 (0.22), residues: 1364 helix: 1.75 (0.18), residues: 792 sheet: -0.53 (0.58), residues: 70 loop : -1.67 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 35 TYR 0.027 0.002 TYR W1192 PHE 0.028 0.002 PHE W 444 TRP 0.044 0.002 TRP W 386 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00483 (18402) covalent geometry : angle 0.63401 (26260) hydrogen bonds : bond 0.06674 ( 960) hydrogen bonds : angle 3.44397 ( 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 255 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8728 (t0) cc_final: 0.8497 (t0) REVERT: B 84 MET cc_start: 0.7130 (tpt) cc_final: 0.6781 (tpt) REVERT: C 75 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7606 (mtmm) REVERT: D 56 MET cc_start: 0.7945 (tpp) cc_final: 0.7262 (tpp) REVERT: D 82 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7618 (mtmm) REVERT: F 92 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7692 (ttp80) REVERT: G 15 LYS cc_start: 0.7675 (mtpp) cc_final: 0.7297 (mtpp) REVERT: G 23 LEU cc_start: 0.8241 (mp) cc_final: 0.7972 (mp) REVERT: G 75 LYS cc_start: 0.7327 (mtpp) cc_final: 0.7080 (mtpp) REVERT: G 107 VAL cc_start: 0.8034 (OUTLIER) cc_final: 0.7820 (t) REVERT: W 137 TYR cc_start: 0.7962 (m-10) cc_final: 0.7710 (m-10) REVERT: W 294 GLN cc_start: 0.7437 (pt0) cc_final: 0.7210 (pt0) REVERT: W 315 ASN cc_start: 0.7105 (m110) cc_final: 0.6827 (m-40) REVERT: W 393 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7925 (mtpp) REVERT: W 403 MET cc_start: 0.4955 (tpp) cc_final: 0.4718 (tpt) REVERT: W 407 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7481 (mtmm) REVERT: W 461 LYS cc_start: 0.7701 (tttt) cc_final: 0.7204 (ttmm) REVERT: W 524 SER cc_start: 0.8017 (m) cc_final: 0.7604 (t) REVERT: W 560 MET cc_start: 0.6490 (tpp) cc_final: 0.5796 (tmm) REVERT: W 1055 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8525 (tm-30) REVERT: W 1058 GLU cc_start: 0.7197 (tp30) cc_final: 0.6478 (tp30) outliers start: 31 outliers final: 16 residues processed: 237 average time/residue: 0.1499 time to fit residues: 50.8203 Evaluate side-chains 232 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 82 LYS 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 H residue 79 HIS Chi-restraints excluded: chain W residue 138 ASN Chi-restraints excluded: chain W residue 223 LEU Chi-restraints excluded: chain W residue 232 SER Chi-restraints excluded: chain W residue 455 CYS 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 502 LEU Chi-restraints excluded: chain W residue 1185 ILE Chi-restraints excluded: chain W residue 1196 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 162 optimal weight: 0.0370 chunk 131 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 113 optimal weight: 0.0770 chunk 42 optimal weight: 0.8980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS G 24 GLN G 73 ASN H 79 HIS W 138 ASN W 323 ASN W 349 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.168917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136413 restraints weight = 32112.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140307 restraints weight = 15557.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.142826 restraints weight = 9277.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.144455 restraints weight = 6498.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.145486 restraints weight = 5156.934| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18402 Z= 0.159 Angle : 0.573 7.750 26260 Z= 0.345 Chirality : 0.037 0.159 2960 Planarity : 0.004 0.039 2245 Dihedral : 27.570 77.767 5011 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.45 % Allowed : 15.87 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.23), residues: 1364 helix: 2.06 (0.19), residues: 786 sheet: -0.65 (0.56), residues: 70 loop : -1.46 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 129 TYR 0.020 0.001 TYR W 245 PHE 0.026 0.002 PHE W1188 TRP 0.044 0.002 TRP W 386 HIS 0.018 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00332 (18402) covalent geometry : angle 0.57255 (26260) hydrogen bonds : bond 0.05295 ( 960) hydrogen bonds : angle 3.07189 ( 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 239 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: B 84 MET cc_start: 0.7084 (tpt) cc_final: 0.6777 (tpt) REVERT: C 75 LYS cc_start: 0.7800 (mtmm) cc_final: 0.7427 (mtmm) REVERT: D 56 MET cc_start: 0.7799 (tpp) cc_final: 0.7197 (tpp) REVERT: D 82 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7472 (mtmm) REVERT: F 92 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7965 (ttp80) REVERT: G 15 LYS cc_start: 0.7643 (mtpp) cc_final: 0.7307 (mtpp) REVERT: G 23 LEU cc_start: 0.8103 (mp) cc_final: 0.7881 (mp) REVERT: G 39 TYR cc_start: 0.7879 (m-10) cc_final: 0.7607 (m-10) REVERT: G 75 LYS cc_start: 0.7263 (mtpp) cc_final: 0.6991 (mtpp) REVERT: W 137 TYR cc_start: 0.7943 (m-10) cc_final: 0.7642 (m-10) REVERT: W 228 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6789 (mm-30) REVERT: W 315 ASN cc_start: 0.7220 (m110) cc_final: 0.6701 (m-40) REVERT: W 387 MET cc_start: 0.6781 (ttm) cc_final: 0.6543 (ttm) REVERT: W 393 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7885 (mtpp) REVERT: W 403 MET cc_start: 0.5170 (tpp) cc_final: 0.4907 (tpt) REVERT: W 407 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7278 (mtmm) REVERT: W 441 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7862 (tt) REVERT: W 461 LYS cc_start: 0.7509 (tttt) cc_final: 0.7288 (mttt) REVERT: W 524 SER cc_start: 0.7998 (m) cc_final: 0.7551 (t) REVERT: W 560 MET cc_start: 0.6393 (tpp) cc_final: 0.5812 (tmm) REVERT: W 1057 MET cc_start: 0.7379 (ptt) cc_final: 0.7148 (ptt) REVERT: W 1058 GLU cc_start: 0.7208 (tp30) cc_final: 0.6505 (tp30) outliers start: 27 outliers final: 13 residues processed: 225 average time/residue: 0.1532 time to fit residues: 49.0008 Evaluate side-chains 214 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 232 SER Chi-restraints excluded: chain W residue 441 LEU Chi-restraints excluded: chain W residue 497 LYS Chi-restraints excluded: chain W residue 502 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS H 79 HIS W 349 GLN ** W 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 428 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.165096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131860 restraints weight = 31676.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135852 restraints weight = 15158.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.138463 restraints weight = 9013.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140150 restraints weight = 6292.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141281 restraints weight = 4953.352| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 18402 Z= 0.215 Angle : 0.608 10.629 26260 Z= 0.365 Chirality : 0.039 0.158 2960 Planarity : 0.004 0.042 2245 Dihedral : 27.478 80.987 5011 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.90 % Allowed : 16.86 % Favored : 80.24 % 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: 0.79 (0.22), residues: 1364 helix: 1.84 (0.18), residues: 790 sheet: -0.49 (0.55), residues: 68 loop : -1.53 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.019 0.002 TYR F 98 PHE 0.025 0.002 PHE W1188 TRP 0.033 0.002 TRP W 386 HIS 0.028 0.002 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00470 (18402) covalent geometry : angle 0.60792 (26260) hydrogen bonds : bond 0.06420 ( 960) hydrogen bonds : angle 3.32352 ( 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: 32 poor density : 201 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: B 84 MET cc_start: 0.7285 (tpt) cc_final: 0.6990 (tpt) REVERT: C 75 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7390 (mtmm) REVERT: D 56 MET cc_start: 0.7885 (tpp) cc_final: 0.7235 (tpp) REVERT: D 82 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7595 (mtmm) REVERT: D 90 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6692 (mm-30) REVERT: F 92 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8002 (ttp80) REVERT: G 15 LYS cc_start: 0.7783 (mtpp) cc_final: 0.7420 (mtpp) REVERT: G 23 LEU cc_start: 0.8309 (mp) cc_final: 0.8081 (mp) REVERT: G 75 LYS cc_start: 0.7295 (mtpp) cc_final: 0.7027 (mtpp) REVERT: H 81 ASN cc_start: 0.8114 (m-40) cc_final: 0.7903 (m110) REVERT: H 82 LYS cc_start: 0.7777 (mmtt) cc_final: 0.7540 (mmtm) REVERT: W 228 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6719 (mm-30) REVERT: W 315 ASN cc_start: 0.7295 (m110) cc_final: 0.6776 (m-40) REVERT: W 387 MET cc_start: 0.6821 (ttm) cc_final: 0.6582 (ttm) REVERT: W 393 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7784 (mtpp) REVERT: W 403 MET cc_start: 0.5126 (tpp) cc_final: 0.4904 (tpt) REVERT: W 407 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7436 (mtmm) REVERT: W 440 TRP cc_start: 0.7322 (m100) cc_final: 0.7008 (m100) REVERT: W 441 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8121 (tt) REVERT: W 455 CYS cc_start: 0.6898 (p) cc_final: 0.6614 (m) REVERT: W 461 LYS cc_start: 0.7547 (tttt) cc_final: 0.7300 (mttt) REVERT: W 471 PHE cc_start: 0.4134 (OUTLIER) cc_final: 0.3738 (m-80) REVERT: W 524 SER cc_start: 0.8105 (m) cc_final: 0.7691 (t) REVERT: W 560 MET cc_start: 0.6444 (tpp) cc_final: 0.5923 (tmm) REVERT: W 1058 GLU cc_start: 0.7225 (tp30) cc_final: 0.6501 (tp30) outliers start: 32 outliers final: 20 residues processed: 223 average time/residue: 0.1612 time to fit residues: 51.3722 Evaluate side-chains 222 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain 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 232 SER Chi-restraints excluded: chain W residue 409 VAL Chi-restraints excluded: chain W residue 441 LEU Chi-restraints excluded: chain W residue 459 ASN Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 502 LEU Chi-restraints excluded: chain W residue 1185 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 166 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 84 GLN H 79 HIS W 349 GLN W 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.132704 restraints weight = 32177.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136476 restraints weight = 15150.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138897 restraints weight = 8860.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140482 restraints weight = 6106.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141517 restraints weight = 4773.190| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 18402 Z= 0.199 Angle : 0.585 6.703 26260 Z= 0.351 Chirality : 0.037 0.168 2960 Planarity : 0.004 0.039 2245 Dihedral : 27.418 79.749 5011 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.63 % Allowed : 17.41 % 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: 0.80 (0.22), residues: 1364 helix: 1.88 (0.18), residues: 793 sheet: -0.52 (0.55), residues: 68 loop : -1.61 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.027 0.002 TYR D 37 PHE 0.032 0.002 PHE W 338 TRP 0.036 0.002 TRP W 386 HIS 0.018 0.002 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00432 (18402) covalent geometry : angle 0.58526 (26260) hydrogen bonds : bond 0.05967 ( 960) hydrogen bonds : angle 3.21835 ( 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 238 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: B 84 MET cc_start: 0.7317 (tpt) cc_final: 0.6992 (tpt) REVERT: B 98 TYR cc_start: 0.8076 (m-10) cc_final: 0.7839 (m-80) REVERT: C 75 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7402 (mtmm) REVERT: D 56 MET cc_start: 0.7822 (tpp) cc_final: 0.7224 (tpp) REVERT: D 82 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7663 (mtmm) REVERT: D 117 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7908 (ttmm) REVERT: F 92 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7975 (ttp80) REVERT: G 23 LEU cc_start: 0.8354 (mp) cc_final: 0.8120 (mp) REVERT: G 75 LYS cc_start: 0.7297 (mtpp) cc_final: 0.7037 (mtpp) REVERT: W 228 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6155 (mm-30) REVERT: W 315 ASN cc_start: 0.7309 (m110) cc_final: 0.6890 (m-40) REVERT: W 387 MET cc_start: 0.6848 (ttm) cc_final: 0.6619 (ttm) REVERT: W 393 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7751 (mtpp) REVERT: W 403 MET cc_start: 0.5096 (tpp) cc_final: 0.4894 (tpt) REVERT: W 407 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7426 (mtmm) REVERT: W 440 TRP cc_start: 0.7356 (m100) cc_final: 0.7050 (m100) REVERT: W 441 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8040 (tp) REVERT: W 455 CYS cc_start: 0.6905 (p) cc_final: 0.6515 (m) REVERT: W 471 PHE cc_start: 0.4111 (OUTLIER) cc_final: 0.3773 (m-80) REVERT: W 524 SER cc_start: 0.8107 (m) cc_final: 0.7696 (t) REVERT: W 560 MET cc_start: 0.6398 (tpp) cc_final: 0.5854 (tmm) REVERT: W 561 PRO cc_start: 0.7446 (Cg_endo) cc_final: 0.7207 (Cg_exo) REVERT: W 1058 GLU cc_start: 0.7299 (tp30) cc_final: 0.6529 (tp30) REVERT: W 1126 LYS cc_start: 0.6123 (pttm) cc_final: 0.5592 (pttp) outliers start: 29 outliers final: 16 residues processed: 229 average time/residue: 0.1609 time to fit residues: 52.5061 Evaluate side-chains 225 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 232 SER Chi-restraints excluded: chain W residue 441 LEU Chi-restraints excluded: chain W residue 459 ASN Chi-restraints excluded: chain W residue 471 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 chunk 155 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 156 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 108 ASN H 79 HIS H 81 ASN W 304 GLN W 306 GLN W 349 GLN W 410 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.163960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133187 restraints weight = 32154.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136979 restraints weight = 15192.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139387 restraints weight = 8879.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.140976 restraints weight = 6137.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.142023 restraints weight = 4797.246| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18402 Z= 0.186 Angle : 0.571 6.997 26260 Z= 0.342 Chirality : 0.037 0.156 2960 Planarity : 0.004 0.042 2245 Dihedral : 27.411 80.113 5011 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.72 % Allowed : 17.77 % Favored : 79.51 % 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: 0.87 (0.22), residues: 1364 helix: 1.94 (0.18), residues: 793 sheet: -0.53 (0.56), residues: 68 loop : -1.59 (0.24), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 129 TYR 0.026 0.002 TYR D 37 PHE 0.024 0.002 PHE W 338 TRP 0.039 0.002 TRP W 386 HIS 0.024 0.002 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00404 (18402) covalent geometry : angle 0.57107 (26260) hydrogen bonds : bond 0.05768 ( 960) hydrogen bonds : angle 3.16907 ( 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 238 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: B 84 MET cc_start: 0.7331 (tpt) cc_final: 0.7003 (tpt) REVERT: B 98 TYR cc_start: 0.8082 (m-10) cc_final: 0.7837 (m-80) REVERT: C 75 LYS cc_start: 0.7648 (mtmm) cc_final: 0.7333 (mtmm) REVERT: D 56 MET cc_start: 0.7738 (tpp) cc_final: 0.7150 (tpp) REVERT: D 82 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7676 (mtmm) REVERT: D 117 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7881 (ttmm) REVERT: F 92 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8044 (ttp80) REVERT: G 23 LEU cc_start: 0.8344 (mp) cc_final: 0.8104 (mp) REVERT: G 75 LYS cc_start: 0.7308 (mtpp) cc_final: 0.7034 (mtpp) REVERT: W 228 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6196 (mm-30) REVERT: W 294 GLN cc_start: 0.7551 (pt0) cc_final: 0.7272 (pt0) REVERT: W 315 ASN cc_start: 0.7322 (m110) cc_final: 0.7013 (m-40) REVERT: W 393 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7738 (mtpp) REVERT: W 403 MET cc_start: 0.5276 (tpp) cc_final: 0.5043 (tpt) REVERT: W 407 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7388 (mtmm) REVERT: W 440 TRP cc_start: 0.7377 (m100) cc_final: 0.7059 (m100) REVERT: W 441 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8084 (tt) REVERT: W 455 CYS cc_start: 0.6878 (p) cc_final: 0.6580 (m) REVERT: W 461 LYS cc_start: 0.7524 (mttt) cc_final: 0.7146 (mptt) REVERT: W 471 PHE cc_start: 0.4000 (OUTLIER) cc_final: 0.3619 (m-80) REVERT: W 487 VAL cc_start: 0.7813 (t) cc_final: 0.7489 (m) REVERT: W 524 SER cc_start: 0.8088 (m) cc_final: 0.7666 (t) REVERT: W 533 LYS cc_start: 0.7533 (mtpp) cc_final: 0.7326 (mtpp) REVERT: W 560 MET cc_start: 0.6356 (tpp) cc_final: 0.5875 (tmm) REVERT: W 1058 GLU cc_start: 0.7324 (tp30) cc_final: 0.6541 (tp30) outliers start: 30 outliers final: 16 residues processed: 226 average time/residue: 0.1597 time to fit residues: 51.4925 Evaluate side-chains 227 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 441 LEU Chi-restraints excluded: chain W residue 459 ASN Chi-restraints excluded: chain W residue 471 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 8 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 148 optimal weight: 20.0000 chunk 107 optimal weight: 0.0870 chunk 156 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN G 24 GLN H 79 HIS W 349 GLN W 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.165009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.134452 restraints weight = 32304.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138206 restraints weight = 15251.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140631 restraints weight = 8906.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.142257 restraints weight = 6131.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143246 restraints weight = 4771.674| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18402 Z= 0.172 Angle : 0.558 7.923 26260 Z= 0.335 Chirality : 0.036 0.158 2960 Planarity : 0.004 0.069 2245 Dihedral : 27.412 80.078 5011 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.54 % Allowed : 18.13 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1364 helix: 2.00 (0.19), residues: 794 sheet: -0.59 (0.57), residues: 68 loop : -1.55 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.026 0.001 TYR D 37 PHE 0.030 0.002 PHE W 338 TRP 0.031 0.002 TRP W 386 HIS 0.013 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00367 (18402) covalent geometry : angle 0.55815 (26260) hydrogen bonds : bond 0.05441 ( 960) hydrogen bonds : angle 3.10969 ( 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 222 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6308 (mp0) REVERT: B 84 MET cc_start: 0.7330 (tpt) cc_final: 0.7002 (tpt) REVERT: B 98 TYR cc_start: 0.8108 (m-10) cc_final: 0.7864 (m-80) REVERT: C 75 LYS cc_start: 0.7542 (mtmm) cc_final: 0.7221 (mtmm) REVERT: D 40 LYS cc_start: 0.7231 (mttp) cc_final: 0.6948 (mttp) REVERT: D 56 MET cc_start: 0.7694 (tpp) cc_final: 0.7107 (tpp) REVERT: D 82 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7679 (mtmm) REVERT: F 92 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8046 (ttp80) REVERT: G 23 LEU cc_start: 0.8329 (mp) cc_final: 0.8106 (mp) REVERT: G 75 LYS cc_start: 0.7294 (mtpp) cc_final: 0.7032 (mtpp) REVERT: W 294 GLN cc_start: 0.7473 (pt0) cc_final: 0.7229 (pt0) REVERT: W 315 ASN cc_start: 0.7335 (m110) cc_final: 0.7012 (m-40) REVERT: W 390 LEU cc_start: 0.8366 (mp) cc_final: 0.8122 (mp) REVERT: W 403 MET cc_start: 0.5297 (tpp) cc_final: 0.5049 (tpt) REVERT: W 407 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7350 (mtmm) REVERT: W 440 TRP cc_start: 0.7362 (m100) cc_final: 0.7034 (m100) REVERT: W 444 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: W 455 CYS cc_start: 0.6850 (p) cc_final: 0.6500 (m) REVERT: W 459 ASN cc_start: 0.6878 (OUTLIER) cc_final: 0.6417 (p0) REVERT: W 461 LYS cc_start: 0.7481 (mttt) cc_final: 0.7103 (mptt) REVERT: W 471 PHE cc_start: 0.4009 (OUTLIER) cc_final: 0.3703 (m-80) REVERT: W 524 SER cc_start: 0.8091 (m) cc_final: 0.7677 (t) REVERT: W 560 MET cc_start: 0.6347 (tpp) cc_final: 0.5849 (tmm) REVERT: W 1058 GLU cc_start: 0.7328 (tp30) cc_final: 0.6542 (tp30) outliers start: 28 outliers final: 20 residues processed: 213 average time/residue: 0.1576 time to fit residues: 48.0098 Evaluate side-chains 220 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 459 ASN Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 538 MET Chi-restraints excluded: chain W residue 1168 VAL Chi-restraints excluded: chain W residue 1196 THR 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: 0.7980 chunk 72 optimal weight: 0.3980 chunk 130 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN G 24 GLN H 79 HIS W 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.164347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133357 restraints weight = 32349.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137168 restraints weight = 15166.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.139666 restraints weight = 8869.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.141285 restraints weight = 6083.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.142232 restraints weight = 4747.569| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18402 Z= 0.180 Angle : 0.568 8.472 26260 Z= 0.339 Chirality : 0.036 0.220 2960 Planarity : 0.004 0.094 2245 Dihedral : 27.396 80.432 5011 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.72 % Allowed : 18.31 % Favored : 78.97 % 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: 0.95 (0.23), residues: 1364 helix: 1.97 (0.19), residues: 797 sheet: -0.46 (0.59), residues: 67 loop : -1.51 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 129 TYR 0.026 0.002 TYR D 37 PHE 0.025 0.002 PHE W 338 TRP 0.028 0.002 TRP W 386 HIS 0.011 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00390 (18402) covalent geometry : angle 0.56761 (26260) hydrogen bonds : bond 0.05555 ( 960) hydrogen bonds : angle 3.14860 ( 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 228 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: B 84 MET cc_start: 0.7359 (tpt) cc_final: 0.7028 (tpt) REVERT: B 98 TYR cc_start: 0.8100 (m-10) cc_final: 0.7838 (m-80) REVERT: C 75 LYS cc_start: 0.7455 (mtmm) cc_final: 0.7180 (mtmm) REVERT: D 40 LYS cc_start: 0.7238 (mttp) cc_final: 0.6954 (mttp) REVERT: D 56 MET cc_start: 0.7700 (tpp) cc_final: 0.7119 (tpp) REVERT: D 82 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7678 (mtmm) REVERT: E 50 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: G 23 LEU cc_start: 0.8365 (mp) cc_final: 0.8137 (mp) REVERT: G 75 LYS cc_start: 0.7294 (mtpp) cc_final: 0.7042 (mtpp) REVERT: W 294 GLN cc_start: 0.7489 (pt0) cc_final: 0.7242 (pt0) REVERT: W 315 ASN cc_start: 0.7355 (m110) cc_final: 0.7099 (m-40) REVERT: W 390 LEU cc_start: 0.8382 (mp) cc_final: 0.8130 (mp) REVERT: W 403 MET cc_start: 0.5312 (tpp) cc_final: 0.5059 (tpt) REVERT: W 407 LYS cc_start: 0.7911 (mtmm) cc_final: 0.7369 (mtmm) REVERT: W 440 TRP cc_start: 0.7393 (m100) cc_final: 0.7063 (m100) REVERT: W 444 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: W 455 CYS cc_start: 0.6847 (p) cc_final: 0.6573 (m) REVERT: W 461 LYS cc_start: 0.7469 (mttt) cc_final: 0.7135 (mptt) REVERT: W 471 PHE cc_start: 0.4016 (OUTLIER) cc_final: 0.3657 (m-80) REVERT: W 487 VAL cc_start: 0.7815 (t) cc_final: 0.7487 (m) REVERT: W 524 SER cc_start: 0.8127 (m) cc_final: 0.7716 (t) REVERT: W 560 MET cc_start: 0.6358 (tpp) cc_final: 0.5842 (tmm) REVERT: W 1058 GLU cc_start: 0.7349 (tp30) cc_final: 0.6548 (tp30) outliers start: 30 outliers final: 19 residues processed: 217 average time/residue: 0.1663 time to fit residues: 51.3924 Evaluate side-chains 220 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 502 LEU Chi-restraints excluded: chain W residue 1185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 0.0570 chunk 111 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 82 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.0570 chunk 157 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN W 410 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.165382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134804 restraints weight = 32109.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138593 restraints weight = 15149.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141048 restraints weight = 8851.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142714 restraints weight = 6074.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.143497 restraints weight = 4708.189| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18402 Z= 0.167 Angle : 0.564 9.145 26260 Z= 0.335 Chirality : 0.036 0.175 2960 Planarity : 0.004 0.075 2245 Dihedral : 27.392 80.292 5011 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.27 % Allowed : 18.95 % Favored : 78.79 % 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: 2.05 (0.19), residues: 795 sheet: -0.26 (0.60), residues: 65 loop : -1.49 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 129 TYR 0.027 0.001 TYR D 37 PHE 0.027 0.002 PHE W1263 TRP 0.026 0.002 TRP W 386 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00358 (18402) covalent geometry : angle 0.56410 (26260) hydrogen bonds : bond 0.05314 ( 960) hydrogen bonds : angle 3.10185 ( 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 223 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6259 (mp0) REVERT: B 72 TYR cc_start: 0.7899 (m-80) cc_final: 0.7388 (m-80) REVERT: B 84 MET cc_start: 0.7347 (tpt) cc_final: 0.7011 (tpt) REVERT: B 98 TYR cc_start: 0.8102 (m-10) cc_final: 0.7839 (m-80) REVERT: C 75 LYS cc_start: 0.7431 (mtmm) cc_final: 0.7150 (mtmm) REVERT: D 56 MET cc_start: 0.7661 (tpp) cc_final: 0.7114 (tpp) REVERT: D 82 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7664 (mtmm) REVERT: E 50 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: G 23 LEU cc_start: 0.8352 (mp) cc_final: 0.8117 (mp) REVERT: G 75 LYS cc_start: 0.7261 (mtpp) cc_final: 0.7018 (mtpp) REVERT: W 294 GLN cc_start: 0.7501 (pt0) cc_final: 0.7227 (pt0) REVERT: W 315 ASN cc_start: 0.7339 (m110) cc_final: 0.7084 (m-40) REVERT: W 390 LEU cc_start: 0.8363 (mp) cc_final: 0.8121 (mp) REVERT: W 403 MET cc_start: 0.5332 (tpp) cc_final: 0.5076 (tpt) REVERT: W 407 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7356 (mtmm) REVERT: W 440 TRP cc_start: 0.7374 (m100) cc_final: 0.7036 (m100) REVERT: W 444 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: W 455 CYS cc_start: 0.6813 (p) cc_final: 0.6460 (m) REVERT: W 461 LYS cc_start: 0.7438 (mttt) cc_final: 0.7080 (mptt) REVERT: W 467 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7209 (mtm180) REVERT: W 471 PHE cc_start: 0.3952 (OUTLIER) cc_final: 0.3661 (m-80) REVERT: W 501 GLU cc_start: 0.7506 (mp0) cc_final: 0.7075 (mp0) REVERT: W 524 SER cc_start: 0.8129 (m) cc_final: 0.7703 (t) REVERT: W 560 MET cc_start: 0.6318 (tpp) cc_final: 0.5745 (tmm) REVERT: W 561 PRO cc_start: 0.7405 (Cg_endo) cc_final: 0.7136 (Cg_exo) REVERT: W 1058 GLU cc_start: 0.7341 (tp30) cc_final: 0.6538 (tp30) outliers start: 25 outliers final: 19 residues processed: 215 average time/residue: 0.1669 time to fit residues: 50.8209 Evaluate side-chains 220 residues out of total 1202 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR 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 A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain W residue 134 THR Chi-restraints excluded: chain W residue 229 THR Chi-restraints excluded: chain W residue 444 PHE Chi-restraints excluded: chain W residue 471 PHE Chi-restraints excluded: chain W residue 502 LEU Chi-restraints excluded: chain W residue 1196 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 142 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 0.0980 chunk 116 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN G 24 GLN H 79 HIS W 410 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.163929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.133317 restraints weight = 32281.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137063 restraints weight = 15283.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139554 restraints weight = 8958.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141138 restraints weight = 6162.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142125 restraints weight = 4812.960| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18402 Z= 0.200 Angle : 0.592 8.763 26260 Z= 0.351 Chirality : 0.037 0.170 2960 Planarity : 0.004 0.072 2245 Dihedral : 27.383 81.234 5011 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.54 % Allowed : 18.77 % Favored : 78.69 % 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: 0.93 (0.23), residues: 1364 helix: 1.94 (0.19), residues: 792 sheet: -0.09 (0.59), residues: 64 loop : -1.49 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 129 TYR 0.027 0.002 TYR D 37 PHE 0.026 0.002 PHE W1263 TRP 0.027 0.002 TRP W 386 HIS 0.005 0.001 HIS W 222 Details of bonding type rmsd covalent geometry : bond 0.00436 (18402) covalent geometry : angle 0.59212 (26260) hydrogen bonds : bond 0.05980 ( 960) hydrogen bonds : angle 3.26499 ( 2468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3791.45 seconds wall clock time: 65 minutes 41.88 seconds (3941.88 seconds total)