Starting phenix.real_space_refine on Tue Jul 29 16:19:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lhg_23339/07_2025/7lhg_23339.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lhg_23339/07_2025/7lhg_23339.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/7lhg_23339/07_2025/7lhg_23339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lhg_23339/07_2025/7lhg_23339.map" model { file = "/net/cci-nas-00/data/ceres_data/7lhg_23339/07_2025/7lhg_23339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lhg_23339/07_2025/7lhg_23339.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 7299 2.51 5 N 2024 2.21 5 O 2237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11592 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 6217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6217 Classifications: {'peptide': 805} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 31, 'TRANS': 773} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1702 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain: "K" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1177 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 146} 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: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2496 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 299} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 7.44, per 1000 atoms: 0.64 Number of scatterers: 11592 At special positions: 0 Unit cell: (99.813, 96.726, 171.843, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 2237 8.00 N 2024 7.00 C 7299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.8 seconds 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2700 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 28 sheets defined 4.2% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 72 through 78 removed outlier: 3.587A pdb=" N VAL C 76 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.658A pdb=" N LEU C 126 " --> pdb=" O GLN C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 459 removed outlier: 4.111A pdb=" N TYR C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.632A pdb=" N ASP D 130 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 158 Processing helix chain 'G' and resid 194 through 200 Processing helix chain 'G' and resid 232 through 237 Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 32 removed outlier: 3.730A pdb=" N TYR C 32 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 50 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL C 53 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN C 68 " --> pdb=" O VAL C 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42 removed outlier: 6.609A pdb=" N ASP C 35 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE C 119 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE C 37 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 116 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 111 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG C 118 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 107 " --> pdb=" O ASN C 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 467 through 469 removed outlier: 6.727A pdb=" N THR C 494 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 473 " --> pdb=" O TYR C 490 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR C 471 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR C 472 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA C 439 " --> pdb=" O THR C 472 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR C 474 " --> pdb=" O THR C 437 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 410 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR C 398 " --> pdb=" O SER C 426 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLY C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 393 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 382 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 343 " --> pdb=" O PHE C 357 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR C 338 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP C 239 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 231 " --> pdb=" O TRP C 239 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR C 241 " --> pdb=" O ASN C 229 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN C 229 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 217 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE C 211 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 9.024A pdb=" N ASN C 230 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 14.993A pdb=" N SER C 209 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 192 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 205 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP C 186 " --> pdb=" O SER C 209 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE C 211 " --> pdb=" O ARG C 184 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG C 184 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 213 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG C 182 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN C 153 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 151 " --> pdb=" O ASN C 171 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 634 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 641 through 643 removed outlier: 3.604A pdb=" N THR C 634 " --> pdb=" O ALA C 641 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 579 " --> pdb=" O SER C 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 594 through 595 Processing sheet with id=AA6, first strand: chain 'C' and resid 594 through 595 removed outlier: 3.665A pdb=" N SER C 588 " --> pdb=" O TYR C 563 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 563 " --> pdb=" O SER C 588 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 529 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 491 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 494 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 265 through 266 removed outlier: 4.040A pdb=" N GLY C 266 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 293 " --> pdb=" O GLY C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 277 removed outlier: 4.190A pdb=" N SER C 277 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP C 307 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 306 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 322 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 308 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE C 320 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS C 318 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 677 through 680 removed outlier: 3.710A pdb=" N GLY C 719 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 721 " --> pdb=" O LEU C 654 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.542A pdb=" N ASN C 689 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER C 711 " --> pdb=" O ASN C 689 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'C' and resid 730 through 732 Processing sheet with id=AB4, first strand: chain 'C' and resid 756 through 758 removed outlier: 3.642A pdb=" N GLY C 758 " --> pdb=" O VAL C 749 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 779 " --> pdb=" O GLN C 786 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN C 786 " --> pdb=" O VAL C 779 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP C 781 " --> pdb=" O LYS C 784 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 4 removed outlier: 3.568A pdb=" N SER D 3 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 8 through 12 removed outlier: 6.542A pdb=" N ALA D 9 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ARG D 116 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE D 11 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.624A pdb=" N GLN D 57 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 32 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR D 109 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU D 92 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 107 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL D 102 " --> pdb=" O ALA K 169 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ALA K 171 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN D 104 " --> pdb=" O ALA K 171 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE K 173 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA D 106 " --> pdb=" O PHE K 173 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU K 175 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN D 108 " --> pdb=" O LEU K 175 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR K 177 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS D 110 " --> pdb=" O TYR K 177 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR K 176 " --> pdb=" O THR K 85 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 50 through 52 removed outlier: 4.076A pdb=" N ILE D 51 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 177 through 181 removed outlier: 3.699A pdb=" N SER D 177 " --> pdb=" O ASN D 145 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 133 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 171 through 172 removed outlier: 3.850A pdb=" N VAL D 171 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 153 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR D 152 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 194 " --> pdb=" O THR D 152 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N SER D 192 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 66 through 70 removed outlier: 3.772A pdb=" N GLU K 66 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA K 148 " --> pdb=" O GLU K 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 110 through 112 Processing sheet with id=AC4, first strand: chain 'G' and resid 57 through 61 removed outlier: 6.914A pdb=" N PHE G 26 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN G 180 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 81 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS G 182 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU G 79 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA G 184 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR G 77 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG G 78 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP G 128 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS G 126 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA G 82 " --> pdb=" O GLY G 124 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLY G 124 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL G 84 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LEU G 122 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE G 120 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 57 through 61 removed outlier: 6.914A pdb=" N PHE G 26 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN G 180 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 81 " --> pdb=" O GLN G 180 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS G 182 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU G 79 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA G 184 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR G 77 " --> pdb=" O ALA G 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 33 through 40 removed outlier: 3.578A pdb=" N TYR G 35 " --> pdb=" O LEU G 208 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 210 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS G 212 " --> pdb=" O GLY G 37 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN G 39 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE G 211 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.600A pdb=" N GLU G 101 " --> pdb=" O LYS G 157 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AC9, first strand: chain 'G' and resid 240 through 241 Processing sheet with id=AD1, first strand: chain 'G' and resid 256 through 261 removed outlier: 3.523A pdb=" N ARG G 256 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR G 330 " --> pdb=" O LEU G 260 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3737 1.34 - 1.46: 2826 1.46 - 1.58: 5240 1.58 - 1.70: 2 1.70 - 1.83: 52 Bond restraints: 11857 Sorted by residual: bond pdb=" C THR D 71 " pdb=" N THR D 72 " ideal model delta sigma weight residual 1.327 1.480 -0.153 1.71e-02 3.42e+03 8.01e+01 bond pdb=" C LYS D 77 " pdb=" N LEU D 78 " ideal model delta sigma weight residual 1.328 1.398 -0.070 1.14e-02 7.69e+03 3.80e+01 bond pdb=" CA LEU C 86 " pdb=" CB LEU C 86 " ideal model delta sigma weight residual 1.527 1.599 -0.072 1.75e-02 3.27e+03 1.70e+01 bond pdb=" C VAL C 288 " pdb=" N PRO C 289 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.25e-02 6.40e+03 1.18e+01 bond pdb=" CA CYS K 75 " pdb=" C CYS K 75 " ideal model delta sigma weight residual 1.522 1.565 -0.042 1.37e-02 5.33e+03 9.62e+00 ... (remaining 11852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 15715 4.85 - 9.70: 354 9.70 - 14.55: 35 14.55 - 19.40: 2 19.40 - 24.25: 1 Bond angle restraints: 16107 Sorted by residual: angle pdb=" N ILE C 235 " pdb=" CA ILE C 235 " pdb=" C ILE C 235 " ideal model delta sigma weight residual 111.62 100.76 10.86 7.90e-01 1.60e+00 1.89e+02 angle pdb=" C THR D 71 " pdb=" N THR D 72 " pdb=" CA THR D 72 " ideal model delta sigma weight residual 123.15 147.40 -24.25 2.23e+00 2.01e-01 1.18e+02 angle pdb=" C TYR K 58 " pdb=" N PRO K 59 " pdb=" CA PRO K 59 " ideal model delta sigma weight residual 120.38 131.09 -10.71 1.03e+00 9.43e-01 1.08e+02 angle pdb=" N ASN C 368 " pdb=" CA ASN C 368 " pdb=" C ASN C 368 " ideal model delta sigma weight residual 110.44 99.09 11.35 1.20e+00 6.94e-01 8.94e+01 angle pdb=" CA TYR C 26 " pdb=" CB TYR C 26 " pdb=" CG TYR C 26 " ideal model delta sigma weight residual 113.90 130.59 -16.69 1.80e+00 3.09e-01 8.60e+01 ... (remaining 16102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 6140 17.08 - 34.16: 681 34.16 - 51.24: 145 51.24 - 68.32: 28 68.32 - 85.40: 14 Dihedral angle restraints: 7008 sinusoidal: 2749 harmonic: 4259 Sorted by residual: dihedral pdb=" C ASP C 481 " pdb=" N ASP C 481 " pdb=" CA ASP C 481 " pdb=" CB ASP C 481 " ideal model delta harmonic sigma weight residual -122.60 -133.64 11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" N ASP C 481 " pdb=" C ASP C 481 " pdb=" CA ASP C 481 " pdb=" CB ASP C 481 " ideal model delta harmonic sigma weight residual 122.80 132.58 -9.78 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" C VAL C 7 " pdb=" N VAL C 7 " pdb=" CA VAL C 7 " pdb=" CB VAL C 7 " ideal model delta harmonic sigma weight residual -122.00 -130.96 8.96 0 2.50e+00 1.60e-01 1.28e+01 ... (remaining 7005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1295 0.084 - 0.168: 362 0.168 - 0.252: 66 0.252 - 0.336: 19 0.336 - 0.419: 5 Chirality restraints: 1747 Sorted by residual: chirality pdb=" CA CYS D 207 " pdb=" N CYS D 207 " pdb=" C CYS D 207 " pdb=" CB CYS D 207 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CB ILE D 194 " pdb=" CA ILE D 194 " pdb=" CG1 ILE D 194 " pdb=" CG2 ILE D 194 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CA TRP C 92 " pdb=" N TRP C 92 " pdb=" C TRP C 92 " pdb=" CB TRP C 92 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 1744 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 72 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO D 73 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO D 73 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 73 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 327 " 0.061 5.00e-02 4.00e+02 9.26e-02 1.37e+01 pdb=" N PRO C 328 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO C 328 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 328 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 698 " -0.055 5.00e-02 4.00e+02 8.33e-02 1.11e+01 pdb=" N PRO C 699 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 699 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 699 " -0.045 5.00e-02 4.00e+02 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3558 2.84 - 3.35: 9196 3.35 - 3.87: 19317 3.87 - 4.38: 19881 4.38 - 4.90: 35363 Nonbonded interactions: 87315 Sorted by model distance: nonbonded pdb=" O ASN G 196 " pdb=" OG1 THR G 200 " model vdw 2.325 3.040 nonbonded pdb=" OG1 THR C 72 " pdb=" OD1 ASP C 74 " model vdw 2.334 3.040 nonbonded pdb=" OG SER C 612 " pdb=" OG SER C 628 " model vdw 2.340 3.040 nonbonded pdb=" OG SER D 159 " pdb=" OE1 GLN D 162 " model vdw 2.345 3.040 nonbonded pdb=" O VAL C 1 " pdb=" OG SER C 22 " model vdw 2.353 3.040 ... (remaining 87310 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 32.480 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.008 0.153 11857 Z= 0.394 Angle : 1.665 24.249 16107 Z= 1.009 Chirality : 0.084 0.419 1747 Planarity : 0.009 0.104 2112 Dihedral : 14.921 85.404 4308 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.26 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 14.72 % Favored : 85.28 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.17), residues: 1482 helix: -4.64 (0.30), residues: 52 sheet: -2.41 (0.20), residues: 530 loop : -3.30 (0.15), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 781 HIS 0.026 0.004 HIS K 36 PHE 0.045 0.004 PHE G 209 TYR 0.038 0.004 TYR K 58 ARG 0.027 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.28354 ( 323) hydrogen bonds : angle 11.50063 ( 915) covalent geometry : bond 0.00789 (11857) covalent geometry : angle 1.66526 (16107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 470 MET cc_start: 0.8237 (ttp) cc_final: 0.7485 (tmm) REVERT: C 790 ASN cc_start: 0.8581 (t0) cc_final: 0.8338 (t0) REVERT: D 7 THR cc_start: 0.8834 (t) cc_final: 0.8633 (m) REVERT: D 87 TYR cc_start: 0.8365 (m-10) cc_final: 0.8145 (m-10) REVERT: D 193 TYR cc_start: 0.8469 (p90) cc_final: 0.8221 (p90) REVERT: D 212 CYS cc_start: 0.8349 (p) cc_final: 0.8006 (p) REVERT: K 30 LEU cc_start: 0.8478 (tp) cc_final: 0.7937 (mp) REVERT: K 66 GLU cc_start: 0.8658 (tp30) cc_final: 0.8400 (tp30) REVERT: K 101 LYS cc_start: 0.9054 (mttm) cc_final: 0.8849 (mmmm) REVERT: K 112 ILE cc_start: 0.9137 (mm) cc_final: 0.8620 (mp) REVERT: K 130 ASN cc_start: 0.8570 (m-40) cc_final: 0.8290 (p0) REVERT: K 174 GLU cc_start: 0.6869 (pm20) cc_final: 0.6303 (pm20) REVERT: G 84 VAL cc_start: 0.7642 (t) cc_final: 0.7418 (t) REVERT: G 269 HIS cc_start: 0.4733 (m-70) cc_final: 0.4445 (m90) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.3232 time to fit residues: 114.6789 Evaluate side-chains 166 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 124 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 115 optimal weight: 40.0000 chunk 44 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 HIS C 123 GLN C 177 ASN ** C 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN K 43 ASN G 94 ASN ** G 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.109419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.088583 restraints weight = 34552.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.091255 restraints weight = 18177.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.093014 restraints weight = 11724.748| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 11857 Z= 0.255 Angle : 0.785 10.333 16107 Z= 0.412 Chirality : 0.048 0.212 1747 Planarity : 0.006 0.101 2112 Dihedral : 5.383 64.529 1650 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.62 % Allowed : 18.42 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.19), residues: 1482 helix: -3.48 (0.54), residues: 42 sheet: -2.20 (0.19), residues: 603 loop : -2.62 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 92 HIS 0.011 0.002 HIS G 239 PHE 0.027 0.002 PHE G 209 TYR 0.023 0.002 TYR C 471 ARG 0.012 0.001 ARG K 27 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 323) hydrogen bonds : angle 7.73136 ( 915) covalent geometry : bond 0.00562 (11857) covalent geometry : angle 0.78503 (16107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 LEU cc_start: 0.8733 (mt) cc_final: 0.8504 (mp) REVERT: C 470 MET cc_start: 0.8141 (ttp) cc_final: 0.7490 (tmm) REVERT: C 790 ASN cc_start: 0.8664 (t0) cc_final: 0.8460 (t0) REVERT: D 87 TYR cc_start: 0.8925 (m-10) cc_final: 0.8692 (m-10) REVERT: D 121 LYS cc_start: 0.9250 (tttt) cc_final: 0.8890 (tptt) REVERT: D 132 LEU cc_start: 0.9301 (mt) cc_final: 0.9063 (mt) REVERT: K 26 PHE cc_start: 0.7856 (p90) cc_final: 0.7500 (p90) REVERT: K 30 LEU cc_start: 0.8929 (tp) cc_final: 0.8276 (mt) REVERT: K 66 GLU cc_start: 0.8910 (tp30) cc_final: 0.8638 (tp30) REVERT: K 112 ILE cc_start: 0.9176 (mm) cc_final: 0.8794 (mp) REVERT: K 130 ASN cc_start: 0.8544 (m-40) cc_final: 0.8281 (p0) REVERT: K 149 TYR cc_start: 0.8677 (p90) cc_final: 0.7734 (p90) REVERT: G 24 ILE cc_start: 0.7613 (mt) cc_final: 0.7309 (mm) REVERT: G 230 ASP cc_start: 0.6840 (t0) cc_final: 0.6523 (t0) outliers start: 45 outliers final: 26 residues processed: 205 average time/residue: 0.2409 time to fit residues: 70.4975 Evaluate side-chains 170 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 209 PHE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 3 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 193 GLN C 232 ASN ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.107949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.084414 restraints weight = 35649.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.087278 restraints weight = 18351.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.089163 restraints weight = 11711.798| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.180 11857 Z= 0.257 Angle : 0.780 13.543 16107 Z= 0.400 Chirality : 0.048 0.210 1747 Planarity : 0.006 0.089 2112 Dihedral : 5.286 51.860 1650 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.75 % Allowed : 22.61 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.20), residues: 1482 helix: -3.17 (0.64), residues: 37 sheet: -2.14 (0.19), residues: 628 loop : -2.38 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 133 HIS 0.016 0.003 HIS G 279 PHE 0.029 0.002 PHE G 209 TYR 0.032 0.003 TYR C 720 ARG 0.011 0.001 ARG K 158 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 323) hydrogen bonds : angle 7.17357 ( 915) covalent geometry : bond 0.00577 (11857) covalent geometry : angle 0.78050 (16107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 150 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 470 MET cc_start: 0.8203 (ttp) cc_final: 0.7734 (tmm) REVERT: C 790 ASN cc_start: 0.8793 (t0) cc_final: 0.8589 (t0) REVERT: D 121 LYS cc_start: 0.9306 (tttt) cc_final: 0.8943 (tptt) REVERT: K 30 LEU cc_start: 0.9023 (tp) cc_final: 0.8642 (mm) REVERT: K 66 GLU cc_start: 0.9163 (tp30) cc_final: 0.8787 (tp30) REVERT: K 92 GLU cc_start: 0.8995 (tt0) cc_final: 0.8694 (tp30) REVERT: K 112 ILE cc_start: 0.9206 (mm) cc_final: 0.8809 (mp) REVERT: K 130 ASN cc_start: 0.8636 (m-40) cc_final: 0.8279 (p0) REVERT: G 24 ILE cc_start: 0.8183 (mt) cc_final: 0.7924 (mm) REVERT: G 56 ILE cc_start: 0.8605 (tt) cc_final: 0.8373 (pt) REVERT: G 180 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8044 (pm20) REVERT: G 196 ASN cc_start: 0.7954 (p0) cc_final: 0.7736 (p0) REVERT: G 230 ASP cc_start: 0.7004 (t0) cc_final: 0.6669 (t0) REVERT: G 279 HIS cc_start: 0.7941 (t70) cc_final: 0.7709 (t70) outliers start: 59 outliers final: 33 residues processed: 199 average time/residue: 0.2459 time to fit residues: 70.8728 Evaluate side-chains 170 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 209 PHE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 72 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.109871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.086493 restraints weight = 35248.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.089425 restraints weight = 18110.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.091339 restraints weight = 11575.620| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 11857 Z= 0.151 Angle : 0.685 9.505 16107 Z= 0.349 Chirality : 0.046 0.183 1747 Planarity : 0.005 0.080 2112 Dihedral : 5.086 51.329 1650 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.42 % Allowed : 24.30 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.20), residues: 1482 helix: -2.54 (0.75), residues: 37 sheet: -1.94 (0.20), residues: 603 loop : -2.31 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 133 HIS 0.007 0.002 HIS G 279 PHE 0.036 0.002 PHE K 26 TYR 0.030 0.002 TYR C 720 ARG 0.009 0.001 ARG K 158 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 323) hydrogen bonds : angle 6.84598 ( 915) covalent geometry : bond 0.00341 (11857) covalent geometry : angle 0.68460 (16107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 154 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ARG cc_start: 0.9154 (tmm160) cc_final: 0.8829 (tmm-80) REVERT: C 246 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8945 (tt) REVERT: C 470 MET cc_start: 0.8218 (ttp) cc_final: 0.7731 (tmm) REVERT: C 586 LEU cc_start: 0.8857 (mm) cc_final: 0.8556 (mt) REVERT: D 15 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: D 121 LYS cc_start: 0.9286 (tttt) cc_final: 0.8932 (tptt) REVERT: D 172 MET cc_start: 0.7995 (tpp) cc_final: 0.7792 (tpt) REVERT: K 30 LEU cc_start: 0.9002 (tp) cc_final: 0.8675 (mm) REVERT: K 51 ARG cc_start: 0.7996 (mmp-170) cc_final: 0.7672 (mmp80) REVERT: K 66 GLU cc_start: 0.9087 (tp30) cc_final: 0.8577 (tp30) REVERT: K 92 GLU cc_start: 0.8974 (tt0) cc_final: 0.8653 (tp30) REVERT: K 112 ILE cc_start: 0.9211 (mm) cc_final: 0.8811 (mp) REVERT: K 130 ASN cc_start: 0.8622 (m-40) cc_final: 0.8250 (p0) REVERT: K 149 TYR cc_start: 0.8662 (p90) cc_final: 0.8095 (p90) REVERT: G 24 ILE cc_start: 0.8133 (mt) cc_final: 0.7810 (mm) REVERT: G 56 ILE cc_start: 0.8606 (tt) cc_final: 0.8383 (pt) REVERT: G 180 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: G 196 ASN cc_start: 0.7983 (p0) cc_final: 0.7737 (p0) REVERT: G 230 ASP cc_start: 0.6944 (t0) cc_final: 0.6573 (t0) outliers start: 55 outliers final: 32 residues processed: 205 average time/residue: 0.2616 time to fit residues: 76.3050 Evaluate side-chains 179 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 138 CYS Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 25 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 chunk 113 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 chunk 39 optimal weight: 0.0000 chunk 144 optimal weight: 1.9990 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN C 669 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.106628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.083231 restraints weight = 35423.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.086421 restraints weight = 18797.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.088306 restraints weight = 10553.981| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 11857 Z= 0.237 Angle : 0.730 10.214 16107 Z= 0.376 Chirality : 0.048 0.176 1747 Planarity : 0.005 0.092 2112 Dihedral : 5.233 46.320 1650 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 5.71 % Allowed : 24.38 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.21), residues: 1482 helix: -2.85 (0.66), residues: 39 sheet: -1.85 (0.20), residues: 615 loop : -2.24 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 133 HIS 0.010 0.002 HIS G 279 PHE 0.033 0.002 PHE G 209 TYR 0.025 0.002 TYR C 720 ARG 0.012 0.001 ARG K 62 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 323) hydrogen bonds : angle 6.74676 ( 915) covalent geometry : bond 0.00527 (11857) covalent geometry : angle 0.72980 (16107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 142 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 246 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8913 (tt) REVERT: C 470 MET cc_start: 0.8275 (ttp) cc_final: 0.7828 (tmm) REVERT: D 15 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: D 121 LYS cc_start: 0.9303 (tttt) cc_final: 0.8977 (tptt) REVERT: K 49 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8470 (mtmm) REVERT: K 51 ARG cc_start: 0.8092 (mmp-170) cc_final: 0.7796 (mmp80) REVERT: K 66 GLU cc_start: 0.9148 (tp30) cc_final: 0.8763 (tp30) REVERT: K 92 GLU cc_start: 0.8952 (tt0) cc_final: 0.8582 (tp30) REVERT: K 112 ILE cc_start: 0.9202 (mm) cc_final: 0.8786 (mp) REVERT: K 130 ASN cc_start: 0.8773 (m-40) cc_final: 0.8241 (p0) REVERT: G 24 ILE cc_start: 0.8439 (mt) cc_final: 0.8172 (mm) REVERT: G 56 ILE cc_start: 0.8922 (tt) cc_final: 0.8609 (pt) REVERT: G 74 TRP cc_start: 0.6221 (p90) cc_final: 0.5945 (p90) REVERT: G 180 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.7920 (pm20) REVERT: G 196 ASN cc_start: 0.7984 (p0) cc_final: 0.7619 (p0) REVERT: G 230 ASP cc_start: 0.7017 (t0) cc_final: 0.6688 (t0) outliers start: 71 outliers final: 39 residues processed: 201 average time/residue: 0.3428 time to fit residues: 102.8845 Evaluate side-chains 173 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 295 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 120 optimal weight: 0.0060 chunk 114 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.104648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.081549 restraints weight = 36084.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.084287 restraints weight = 18272.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.086103 restraints weight = 11630.777| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11857 Z= 0.222 Angle : 0.718 11.127 16107 Z= 0.370 Chirality : 0.047 0.182 1747 Planarity : 0.005 0.090 2112 Dihedral : 5.219 44.310 1650 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.23 % Allowed : 24.70 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.20), residues: 1482 helix: -2.66 (0.68), residues: 39 sheet: -1.86 (0.20), residues: 621 loop : -2.24 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 133 HIS 0.007 0.002 HIS K 36 PHE 0.043 0.002 PHE K 26 TYR 0.026 0.002 TYR C 720 ARG 0.012 0.001 ARG K 158 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 323) hydrogen bonds : angle 6.75220 ( 915) covalent geometry : bond 0.00484 (11857) covalent geometry : angle 0.71849 (16107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 142 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 246 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8917 (tt) REVERT: C 393 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8227 (mm) REVERT: C 451 MET cc_start: 0.8979 (tpp) cc_final: 0.8691 (tpp) REVERT: C 470 MET cc_start: 0.8296 (ttp) cc_final: 0.7867 (tmm) REVERT: C 586 LEU cc_start: 0.8896 (mm) cc_final: 0.8593 (mt) REVERT: D 15 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: D 74 ASP cc_start: 0.7623 (t0) cc_final: 0.7074 (t0) REVERT: D 121 LYS cc_start: 0.9324 (tttt) cc_final: 0.9014 (tptt) REVERT: D 172 MET cc_start: 0.8253 (tpp) cc_final: 0.7929 (tpt) REVERT: K 30 LEU cc_start: 0.9036 (tp) cc_final: 0.8495 (mp) REVERT: K 49 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8368 (mtmm) REVERT: K 51 ARG cc_start: 0.7980 (mmp-170) cc_final: 0.7670 (mmp80) REVERT: K 66 GLU cc_start: 0.9087 (tp30) cc_final: 0.8694 (tp30) REVERT: K 92 GLU cc_start: 0.8938 (tt0) cc_final: 0.8697 (tp30) REVERT: K 101 LYS cc_start: 0.9156 (mmtp) cc_final: 0.8711 (mmmt) REVERT: K 112 ILE cc_start: 0.9223 (mm) cc_final: 0.8804 (mp) REVERT: K 130 ASN cc_start: 0.8702 (m-40) cc_final: 0.8124 (p0) REVERT: G 180 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: G 196 ASN cc_start: 0.7976 (p0) cc_final: 0.7672 (p0) REVERT: G 277 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8636 (mp) outliers start: 65 outliers final: 43 residues processed: 198 average time/residue: 0.2141 time to fit residues: 62.1718 Evaluate side-chains 179 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 726 LEU Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 49 LYS Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 55 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 75 optimal weight: 0.4980 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.105217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.082405 restraints weight = 36009.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.085207 restraints weight = 18305.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.087172 restraints weight = 10460.453| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11857 Z= 0.218 Angle : 0.719 11.473 16107 Z= 0.372 Chirality : 0.047 0.202 1747 Planarity : 0.005 0.088 2112 Dihedral : 5.214 42.408 1650 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 4.91 % Allowed : 25.82 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.21), residues: 1482 helix: -2.34 (0.69), residues: 39 sheet: -1.84 (0.20), residues: 608 loop : -2.14 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP C 133 HIS 0.013 0.002 HIS G 279 PHE 0.030 0.002 PHE G 209 TYR 0.030 0.002 TYR C 720 ARG 0.012 0.001 ARG K 158 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 323) hydrogen bonds : angle 6.76055 ( 915) covalent geometry : bond 0.00479 (11857) covalent geometry : angle 0.71929 (16107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 142 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ARG cc_start: 0.9187 (tmm160) cc_final: 0.8773 (tmm-80) REVERT: C 246 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8898 (tt) REVERT: C 252 MET cc_start: 0.8572 (mmm) cc_final: 0.8326 (mmt) REVERT: C 470 MET cc_start: 0.8318 (ttp) cc_final: 0.7670 (tmm) REVERT: C 586 LEU cc_start: 0.8937 (mm) cc_final: 0.8667 (mt) REVERT: D 15 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: D 74 ASP cc_start: 0.7704 (t0) cc_final: 0.7191 (t0) REVERT: D 121 LYS cc_start: 0.9331 (tttt) cc_final: 0.9023 (tptt) REVERT: D 172 MET cc_start: 0.8493 (tpp) cc_final: 0.8159 (tpt) REVERT: D 207 CYS cc_start: 0.8315 (p) cc_final: 0.7767 (t) REVERT: K 66 GLU cc_start: 0.9168 (tp30) cc_final: 0.8769 (tp30) REVERT: K 92 GLU cc_start: 0.8899 (tt0) cc_final: 0.8670 (tp30) REVERT: K 101 LYS cc_start: 0.9159 (mmtp) cc_final: 0.8637 (mmmt) REVERT: K 112 ILE cc_start: 0.9209 (mm) cc_final: 0.8780 (mp) REVERT: K 130 ASN cc_start: 0.8688 (m-40) cc_final: 0.8140 (p0) REVERT: G 74 TRP cc_start: 0.6286 (p90) cc_final: 0.5943 (p90) REVERT: G 180 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7833 (pm20) REVERT: G 196 ASN cc_start: 0.7878 (p0) cc_final: 0.7555 (p0) outliers start: 61 outliers final: 45 residues processed: 192 average time/residue: 0.2352 time to fit residues: 65.4615 Evaluate side-chains 182 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 490 TYR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 28 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 115 optimal weight: 30.0000 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 167 GLN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 129 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.106068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.082173 restraints weight = 35785.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.085017 restraints weight = 17988.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.086882 restraints weight = 11453.565| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11857 Z= 0.197 Angle : 0.704 11.199 16107 Z= 0.363 Chirality : 0.046 0.184 1747 Planarity : 0.005 0.085 2112 Dihedral : 5.136 40.841 1650 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.91 % Allowed : 26.23 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.21), residues: 1482 helix: -2.32 (0.67), residues: 39 sheet: -1.74 (0.21), residues: 595 loop : -2.11 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 133 HIS 0.007 0.002 HIS K 36 PHE 0.041 0.002 PHE K 26 TYR 0.024 0.002 TYR C 720 ARG 0.013 0.001 ARG K 158 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 323) hydrogen bonds : angle 6.69050 ( 915) covalent geometry : bond 0.00433 (11857) covalent geometry : angle 0.70368 (16107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 142 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8637 (pmm) cc_final: 0.8374 (pmm) REVERT: C 77 ARG cc_start: 0.9168 (tmm160) cc_final: 0.8794 (tmm-80) REVERT: C 246 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8884 (tt) REVERT: C 393 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8137 (mm) REVERT: C 451 MET cc_start: 0.9028 (mmm) cc_final: 0.8629 (tpp) REVERT: C 470 MET cc_start: 0.8304 (ttp) cc_final: 0.7694 (tmm) REVERT: C 586 LEU cc_start: 0.8928 (mm) cc_final: 0.8626 (mt) REVERT: D 15 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: D 74 ASP cc_start: 0.7839 (t0) cc_final: 0.7370 (t0) REVERT: D 121 LYS cc_start: 0.9317 (tttt) cc_final: 0.9010 (tptt) REVERT: D 172 MET cc_start: 0.8552 (tpp) cc_final: 0.8203 (tpt) REVERT: D 193 TYR cc_start: 0.8779 (p90) cc_final: 0.8315 (p90) REVERT: D 207 CYS cc_start: 0.8278 (p) cc_final: 0.7761 (t) REVERT: K 30 LEU cc_start: 0.8918 (tp) cc_final: 0.8444 (mp) REVERT: K 66 GLU cc_start: 0.9224 (tp30) cc_final: 0.8709 (tp30) REVERT: K 92 GLU cc_start: 0.8937 (tt0) cc_final: 0.8669 (tp30) REVERT: K 101 LYS cc_start: 0.9087 (mmtp) cc_final: 0.8614 (mmmt) REVERT: K 112 ILE cc_start: 0.9185 (mm) cc_final: 0.8758 (mp) REVERT: K 130 ASN cc_start: 0.8796 (m-40) cc_final: 0.8119 (p0) REVERT: K 131 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7662 (mmtm) REVERT: G 180 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: G 196 ASN cc_start: 0.7963 (p0) cc_final: 0.7623 (p0) outliers start: 61 outliers final: 48 residues processed: 192 average time/residue: 0.2309 time to fit residues: 65.2669 Evaluate side-chains 190 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 490 TYR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 97 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 110 optimal weight: 40.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 232 ASN ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.106578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.082779 restraints weight = 35599.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.085644 restraints weight = 17831.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.087535 restraints weight = 11326.329| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11857 Z= 0.173 Angle : 0.690 10.816 16107 Z= 0.356 Chirality : 0.046 0.182 1747 Planarity : 0.005 0.079 2112 Dihedral : 5.046 41.582 1650 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.67 % Allowed : 26.87 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.21), residues: 1482 helix: -2.16 (0.70), residues: 39 sheet: -1.74 (0.20), residues: 594 loop : -2.03 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 133 HIS 0.015 0.002 HIS G 279 PHE 0.029 0.002 PHE G 209 TYR 0.022 0.002 TYR C 720 ARG 0.014 0.001 ARG K 158 Details of bonding type rmsd hydrogen bonds : bond 0.03111 ( 323) hydrogen bonds : angle 6.59706 ( 915) covalent geometry : bond 0.00380 (11857) covalent geometry : angle 0.68968 (16107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 144 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ARG cc_start: 0.9140 (tmm160) cc_final: 0.8783 (tmm-80) REVERT: C 192 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7526 (mm-30) REVERT: C 246 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8873 (tt) REVERT: C 287 MET cc_start: 0.8626 (mmm) cc_final: 0.8362 (mmm) REVERT: C 393 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8199 (mm) REVERT: C 470 MET cc_start: 0.8310 (ttp) cc_final: 0.7718 (tmm) REVERT: C 586 LEU cc_start: 0.8880 (mm) cc_final: 0.8568 (mt) REVERT: D 15 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: D 74 ASP cc_start: 0.7790 (t0) cc_final: 0.7350 (t0) REVERT: D 121 LYS cc_start: 0.9311 (tttt) cc_final: 0.9009 (tptt) REVERT: D 172 MET cc_start: 0.8564 (tpp) cc_final: 0.8169 (tpt) REVERT: D 207 CYS cc_start: 0.8230 (p) cc_final: 0.7684 (t) REVERT: K 30 LEU cc_start: 0.9020 (tp) cc_final: 0.8661 (mm) REVERT: K 51 ARG cc_start: 0.8043 (mmp-170) cc_final: 0.7580 (mmp-170) REVERT: K 66 GLU cc_start: 0.9192 (tp30) cc_final: 0.8687 (tp30) REVERT: K 101 LYS cc_start: 0.9099 (mmtp) cc_final: 0.8614 (mmmt) REVERT: K 112 ILE cc_start: 0.9194 (mm) cc_final: 0.8777 (mp) REVERT: K 130 ASN cc_start: 0.8684 (m-40) cc_final: 0.8025 (p0) REVERT: G 74 TRP cc_start: 0.6138 (p90) cc_final: 0.5877 (p90) REVERT: G 180 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: G 196 ASN cc_start: 0.7986 (p0) cc_final: 0.7645 (p0) outliers start: 58 outliers final: 50 residues processed: 191 average time/residue: 0.2497 time to fit residues: 70.5534 Evaluate side-chains 190 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 135 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 490 TYR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 146 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 74 optimal weight: 0.3980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.106427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.082598 restraints weight = 35260.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.085445 restraints weight = 17788.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.087317 restraints weight = 11321.308| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.156 11857 Z= 0.219 Angle : 0.910 59.198 16107 Z= 0.510 Chirality : 0.048 0.427 1747 Planarity : 0.005 0.077 2112 Dihedral : 5.070 41.597 1650 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.30 % Favored : 91.63 % Rotamer: Outliers : 4.91 % Allowed : 27.03 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.21), residues: 1482 helix: -2.14 (0.70), residues: 39 sheet: -1.73 (0.21), residues: 594 loop : -2.04 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 133 HIS 0.016 0.002 HIS G 279 PHE 0.028 0.002 PHE G 209 TYR 0.031 0.002 TYR C 720 ARG 0.013 0.001 ARG K 158 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 323) hydrogen bonds : angle 6.59590 ( 915) covalent geometry : bond 0.00473 (11857) covalent geometry : angle 0.91021 (16107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2964 Ramachandran restraints generated. 1482 Oldfield, 0 Emsley, 1482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 135 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 77 ARG cc_start: 0.9144 (tmm160) cc_final: 0.8789 (tmm-80) REVERT: C 192 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: C 246 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8873 (tt) REVERT: C 287 MET cc_start: 0.8656 (mmm) cc_final: 0.8388 (mmm) REVERT: C 393 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8199 (mm) REVERT: C 470 MET cc_start: 0.8317 (ttp) cc_final: 0.7715 (tmm) REVERT: C 586 LEU cc_start: 0.8871 (mm) cc_final: 0.8565 (mt) REVERT: D 15 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: D 74 ASP cc_start: 0.7775 (t0) cc_final: 0.7339 (t0) REVERT: D 121 LYS cc_start: 0.9313 (tttt) cc_final: 0.9010 (tptt) REVERT: D 172 MET cc_start: 0.8558 (tpp) cc_final: 0.8156 (tpt) REVERT: D 207 CYS cc_start: 0.8236 (p) cc_final: 0.7679 (t) REVERT: K 30 LEU cc_start: 0.9016 (tp) cc_final: 0.8656 (mm) REVERT: K 51 ARG cc_start: 0.8048 (mmp-170) cc_final: 0.7589 (mmp-170) REVERT: K 66 GLU cc_start: 0.9196 (tp30) cc_final: 0.8696 (tp30) REVERT: K 101 LYS cc_start: 0.9095 (mmtp) cc_final: 0.8611 (mmmt) REVERT: K 112 ILE cc_start: 0.9193 (mm) cc_final: 0.8769 (mp) REVERT: K 130 ASN cc_start: 0.8684 (m-40) cc_final: 0.8033 (p0) REVERT: G 74 TRP cc_start: 0.6157 (p90) cc_final: 0.5890 (p90) REVERT: G 180 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7937 (pm20) REVERT: G 196 ASN cc_start: 0.7986 (p0) cc_final: 0.7645 (p0) outliers start: 61 outliers final: 52 residues processed: 184 average time/residue: 0.2206 time to fit residues: 59.5606 Evaluate side-chains 192 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 135 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 206 PHE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 299 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 490 TYR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 627 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 GLU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 36 HIS Chi-restraints excluded: chain K residue 58 TYR Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 THR Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 128 ASP Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 251 VAL Chi-restraints excluded: chain G residue 263 THR Chi-restraints excluded: chain G residue 291 ASP Chi-restraints excluded: chain G residue 295 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 126 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.106564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.082826 restraints weight = 35260.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.085692 restraints weight = 17746.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.087611 restraints weight = 11298.544| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 11857 Z= 0.208 Angle : 1.012 59.198 16107 Z= 0.578 Chirality : 0.047 0.210 1747 Planarity : 0.006 0.126 2112 Dihedral : 5.126 41.733 1650 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.23 % Favored : 91.63 % Rotamer: Outliers : 4.59 % Allowed : 27.19 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.21), residues: 1482 helix: -2.15 (0.70), residues: 39 sheet: -1.72 (0.21), residues: 595 loop : -2.03 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 133 HIS 0.022 0.003 HIS G 279 PHE 0.050 0.002 PHE G 86 TYR 0.033 0.002 TYR C 720 ARG 0.016 0.001 ARG K 158 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 323) hydrogen bonds : angle 6.61109 ( 915) covalent geometry : bond 0.00442 (11857) covalent geometry : angle 1.01238 (16107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3990.23 seconds wall clock time: 70 minutes 48.92 seconds (4248.92 seconds total)