Starting phenix.real_space_refine on Sat Aug 8 00:17:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e8m_27944/08_2026/8e8m_27944.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e8m_27944/08_2026/8e8m_27944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8e8m_27944/08_2026/8e8m_27944.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e8m_27944/08_2026/8e8m_27944.cif" model { file = "/net/cci-nas-00/data/ceres_data/8e8m_27944/08_2026/8e8m_27944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e8m_27944/08_2026/8e8m_27944.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e8m_27944/08_2026/8e8m_27944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e8m_27944/08_2026/8e8m_27944.map" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.124 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 93 5.49 5 Mg 1 5.21 5 S 87 5.16 5 C 15114 2.51 5 N 4347 2.21 5 O 4929 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24573 Number of models: 1 Model: "" Number of chains: 9 Chain: "O" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 543 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "P" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 685 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "R" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 698 Classifications: {'RNAv2': 33} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 16, 'rna3p_pyr': 15} Link IDs: {'rna2p': 2, 'rna3p': 30} Chain breaks: 1 Chain: "A" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1724 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1769 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 8600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8600 Classifications: {'peptide': 1110} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1047} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 9902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1268, 9902 Classifications: {'peptide': 1268} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 3, 'PTRANS': 57, 'TRANS': 1207} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14525 SG CYS D 60 86.147 104.708 107.050 1.00126.79 S ATOM 14543 SG CYS D 62 85.663 106.192 110.128 1.00128.57 S ATOM 14652 SG CYS D 75 88.641 105.157 110.876 1.00129.67 S ATOM 14678 SG CYS D 78 86.203 103.602 110.793 1.00119.66 S ATOM 21093 SG CYS D 891 101.031 40.025 87.562 1.00 63.22 S ATOM 21660 SG CYS D 968 97.814 42.182 89.257 1.00 59.07 S ATOM 21702 SG CYS D 975 98.965 41.970 85.600 1.00 58.50 S ATOM 21720 SG CYS D 978 97.966 39.607 86.221 1.00 51.59 S Time building chain proxies: 5.76, per 1000 atoms: 0.23 Number of scatterers: 24573 At special positions: 0 Unit cell: (123.405, 133.148, 198.097, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 87 16.00 P 93 15.00 Mg 1 11.99 O 4929 8.00 N 4347 7.00 C 15114 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 975 " Number of angles added : 12 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 41 sheets defined 39.6% alpha, 15.6% beta 41 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.633A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 34 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.253A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.940A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.766A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.862A pdb=" N LEU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.810A pdb=" N TRP C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 4.295A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASP C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.797A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.571A pdb=" N ARG C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.580A pdb=" N ILE C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.809A pdb=" N LEU C 417 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 420 through 431 removed outlier: 3.706A pdb=" N PHE C 431 " --> pdb=" O ILE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.571A pdb=" N ARG C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 590 through 594 removed outlier: 3.879A pdb=" N ILE C 594 " --> pdb=" O THR C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 removed outlier: 3.606A pdb=" N HIS C 599 " --> pdb=" O PHE C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 611 Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.778A pdb=" N GLY C 639 " --> pdb=" O ALA C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 removed outlier: 4.067A pdb=" N ALA C 782 " --> pdb=" O GLU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 824 Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.390A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1070 through 1080 removed outlier: 3.594A pdb=" N TRP C1074 " --> pdb=" O GLU C1070 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C1075 " --> pdb=" O MET C1071 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 3.829A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.354A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1130 removed outlier: 3.998A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.599A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 112 through 119 removed outlier: 3.507A pdb=" N LEU D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 187 removed outlier: 3.611A pdb=" N HIS D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.665A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.578A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.983A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 305 removed outlier: 3.606A pdb=" N LYS D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.679A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 4.118A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 417 Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.574A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 491 removed outlier: 4.223A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 579 through 589 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 675 removed outlier: 3.524A pdb=" N VAL D 671 " --> pdb=" O THR D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 727 removed outlier: 3.919A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.526A pdb=" N ILE D 745 " --> pdb=" O ARG D 741 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 819 removed outlier: 3.705A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 3.919A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 removed outlier: 3.511A pdb=" N VAL D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1027 through 1036 Processing helix chain 'D' and resid 1117 through 1126 removed outlier: 3.622A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1146 removed outlier: 3.712A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR D1142 " --> pdb=" O VAL D1138 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.339A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 4.062A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1216 Processing helix chain 'D' and resid 1219 through 1227 Processing helix chain 'D' and resid 1228 through 1240 Processing helix chain 'D' and resid 1247 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 Processing helix chain 'D' and resid 1275 through 1282 Processing helix chain 'E' and resid 33 through 37 Processing helix chain 'E' and resid 39 through 47 removed outlier: 3.671A pdb=" N ARG E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 71 removed outlier: 3.571A pdb=" N ILE E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 3.624A pdb=" N LEU A 14 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.005A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.556A pdb=" N GLY A 103 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 126 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 removed outlier: 3.611A pdb=" N GLY A 145 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 26 removed outlier: 5.937A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 173 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.630A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 141 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 removed outlier: 3.684A pdb=" N ALA B 126 " --> pdb=" O VAL B 105 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.602A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.682A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB5, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.392A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 Processing sheet with id=AB7, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AB8, first strand: chain 'C' and resid 354 through 355 Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 removed outlier: 7.069A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC2, first strand: chain 'C' and resid 558 through 562 Processing sheet with id=AC3, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.387A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.791A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 708 through 709 removed outlier: 3.617A pdb=" N GLU C 712 " --> pdb=" O ASP C 709 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.698A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 749 through 760 removed outlier: 6.291A pdb=" N SER C 749 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS C 876 " --> pdb=" O SER C 749 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS C 751 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA C 874 " --> pdb=" O HIS C 751 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU C 753 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR C 872 " --> pdb=" O GLU C 753 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS C 755 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG C 870 " --> pdb=" O HIS C 755 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 757 " --> pdb=" O LEU C 868 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU C 868 " --> pdb=" O ILE C 757 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA C 759 " --> pdb=" O ASN C 866 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC9, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.853A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD2, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.545A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1067 through 1068 Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.939A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.339A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.478A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 3.581A pdb=" N TYR D 134 " --> pdb=" O ILE D 235 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 328 through 330 Processing sheet with id=AD8, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'D' and resid 822 through 825 removed outlier: 9.548A pdb=" N GLY D 822 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ARG D 834 " --> pdb=" O GLY D 822 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL D 824 " --> pdb=" O ILE D 832 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.748A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1075 through 1077 removed outlier: 3.720A pdb=" N VAL D1075 " --> pdb=" O ILE D1066 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D1051 " --> pdb=" O VAL D1105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.673A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1271 through 1274 removed outlier: 3.533A pdb=" N THR E 107 " --> pdb=" O ALA D1271 " (cutoff:3.500A) 943 hydrogen bonds defined for protein. 2649 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7628 1.33 - 1.45: 3399 1.45 - 1.57: 13823 1.57 - 1.69: 181 1.69 - 1.81: 153 Bond restraints: 25184 Sorted by residual: bond pdb=" C3' DT O 19 " pdb=" C2' DT O 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.78e+00 bond pdb=" C3' DA P 118 " pdb=" C2' DA P 118 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.80e+00 bond pdb=" C3' DA O 30 " pdb=" C2' DA O 30 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.53e+00 bond pdb=" C1' DT O 27 " pdb=" N1 DT O 27 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.12e+00 bond pdb=" C3' DT P 120 " pdb=" C2' DT P 120 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.67e+00 ... (remaining 25179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 32987 1.29 - 2.58: 1188 2.58 - 3.86: 325 3.86 - 5.15: 27 5.15 - 6.44: 3 Bond angle restraints: 34530 Sorted by residual: angle pdb=" N3 DT P 130 " pdb=" C4 DT P 130 " pdb=" O4 DT P 130 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT P 125 " pdb=" C4 DT P 125 " pdb=" O4 DT P 125 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT P 115 " pdb=" C4 DT P 115 " pdb=" O4 DT P 115 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT O 37 " pdb=" C4 DT O 37 " pdb=" O4 DT O 37 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT O 41 " pdb=" C4 DT O 41 " pdb=" O4 DT O 41 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 34525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 14686 33.93 - 67.85: 481 67.85 - 101.78: 7 101.78 - 135.71: 0 135.71 - 169.63: 5 Dihedral angle restraints: 15179 sinusoidal: 6819 harmonic: 8360 Sorted by residual: dihedral pdb=" C4' C R 19 " pdb=" C3' C R 19 " pdb=" C2' C R 19 " pdb=" C1' C R 19 " ideal model delta sinusoidal sigma weight residual 36.34 -35.28 71.63 1 3.10e+00 1.04e-01 6.84e+02 dihedral pdb=" C4' U R 20 " pdb=" C3' U R 20 " pdb=" C2' U R 20 " pdb=" C1' U R 20 " ideal model delta sinusoidal sigma weight residual 36.34 -35.03 71.37 1 3.10e+00 1.04e-01 6.80e+02 dihedral pdb=" O4' C R 19 " pdb=" C4' C R 19 " pdb=" C3' C R 19 " pdb=" C2' C R 19 " ideal model delta sinusoidal sigma weight residual -35.15 24.76 -59.90 1 4.00e+00 6.25e-02 2.99e+02 ... (remaining 15176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3294 0.056 - 0.112: 497 0.112 - 0.167: 137 0.167 - 0.223: 11 0.223 - 0.279: 28 Chirality restraints: 3967 Sorted by residual: chirality pdb=" C2' U R 20 " pdb=" C3' U R 20 " pdb=" O2' U R 20 " pdb=" C1' U R 20 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C2' C R 19 " pdb=" C3' C R 19 " pdb=" O2' C R 19 " pdb=" C1' C R 19 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" P C R 9 " pdb=" OP1 C R 9 " pdb=" OP2 C R 9 " pdb=" O5' C R 9 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3964 not shown) Planarity restraints: 4212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 433 " -0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO D 434 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 434 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 434 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 657 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO D 658 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 658 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 658 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 832 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO D 833 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 833 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 833 " 0.024 5.00e-02 4.00e+02 ... (remaining 4209 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 206 2.58 - 3.16: 20536 3.16 - 3.74: 36165 3.74 - 4.32: 51468 4.32 - 4.90: 87404 Nonbonded interactions: 195779 Sorted by model distance: nonbonded pdb=" O3' U R 42 " pdb="MG MG D2002 " model vdw 2.001 2.170 nonbonded pdb=" O ASP C 761 " pdb=" OG1 THR C 762 " model vdw 2.059 3.040 nonbonded pdb=" O THR C 195 " pdb=" NH2 ARG D1060 " model vdw 2.060 3.120 nonbonded pdb=" O PRO D 326 " pdb=" OG SER D 338 " model vdw 2.101 3.040 nonbonded pdb=" O GLY D1007 " pdb=" N GLN D1009 " model vdw 2.110 3.120 ... (remaining 195774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 226)) \ selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 29.880 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 : 0.004 0.063 25192 Z= 0.231 Angle : 0.792 56.579 34542 Z= 0.397 Chirality : 0.050 0.279 3967 Planarity : 0.004 0.048 4212 Dihedral : 14.517 169.632 9807 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.57 % Favored : 95.15 % Rotamer: Outliers : 2.37 % Allowed : 6.38 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 2910 helix: 0.94 (0.17), residues: 1023 sheet: -0.86 (0.25), residues: 411 loop : -1.33 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 834 TYR 0.011 0.001 TYR A 168 PHE 0.012 0.001 PHE C 431 TRP 0.007 0.001 TRP D 778 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.23 (25184) covalent geometry : angle 0.60522 / 0.39 (34530) hydrogen bonds : bond 0.16149 / 17.61 ( 1036) hydrogen bonds : angle 6.30002 / 6.48 ( 2839) metal coordination : bond 0.03892 / 3.80 ( 8) metal coordination : angle 27.41587 / 55.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 417 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.7577 (tt0) cc_final: 0.7366 (tm-30) REVERT: A 6 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7649 (mtp-110) REVERT: A 191 LYS cc_start: 0.9085 (tttm) cc_final: 0.8846 (tttm) REVERT: B 17 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8000 (p0) REVERT: B 70 LYS cc_start: 0.8660 (tttt) cc_final: 0.8331 (ttmm) REVERT: B 133 LYS cc_start: 0.7672 (ttmt) cc_final: 0.7224 (mmtt) REVERT: B 191 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8822 (ttpp) REVERT: B 233 GLU cc_start: 0.8187 (pt0) cc_final: 0.7930 (mp0) REVERT: C 114 ASP cc_start: 0.8015 (m-30) cc_final: 0.7794 (m-30) REVERT: C 393 MET cc_start: 0.8089 (mmt) cc_final: 0.7725 (mmt) REVERT: C 428 LYS cc_start: 0.8656 (ttpt) cc_final: 0.8182 (ttmm) REVERT: C 525 SER cc_start: 0.8564 (m) cc_final: 0.8083 (p) REVERT: C 607 MET cc_start: 0.8292 (mtp) cc_final: 0.7922 (mtt) REVERT: C 630 MET cc_start: 0.8533 (tpt) cc_final: 0.8164 (tpt) REVERT: C 657 TYR cc_start: 0.8348 (p90) cc_final: 0.8106 (p90) REVERT: C 763 LYS cc_start: 0.7649 (mttt) cc_final: 0.7312 (mmmt) REVERT: C 950 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8184 (pttm) REVERT: C 962 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: C 1029 TYR cc_start: 0.9092 (t80) cc_final: 0.8621 (t80) REVERT: C 1031 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8780 (mtm) REVERT: C 1063 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: D 70 PHE cc_start: 0.7346 (m-80) cc_final: 0.7144 (m-80) REVERT: D 143 MET cc_start: 0.6976 (ttt) cc_final: 0.6193 (tpt) REVERT: D 215 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6180 (pp20) REVERT: D 392 THR cc_start: 0.8977 (p) cc_final: 0.8723 (t) REVERT: D 443 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8856 (mp) REVERT: D 688 MET cc_start: 0.9062 (mmt) cc_final: 0.8625 (mmt) REVERT: D 706 MET cc_start: 0.7294 (mtm) cc_final: 0.7080 (mmp) REVERT: D 744 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: D 790 ARG cc_start: 0.7651 (tpt-90) cc_final: 0.7415 (ttp-170) REVERT: D 858 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7695 (ttpp) REVERT: D 942 GLN cc_start: 0.8447 (mm110) cc_final: 0.8239 (mm110) REVERT: D 1062 TYR cc_start: 0.7539 (m-10) cc_final: 0.7325 (m-10) REVERT: D 1085 ARG cc_start: 0.7151 (mtt180) cc_final: 0.6278 (mtm-85) REVERT: D 1087 ARG cc_start: 0.7132 (tpt-90) cc_final: 0.6807 (tpp80) REVERT: D 1097 ARG cc_start: 0.3523 (OUTLIER) cc_final: 0.2298 (ptp-170) REVERT: D 1112 MET cc_start: 0.8248 (mmm) cc_final: 0.7580 (mmm) REVERT: E 33 LEU cc_start: 0.7744 (tp) cc_final: 0.7416 (mt) REVERT: E 88 GLN cc_start: 0.7334 (pm20) cc_final: 0.6899 (pm20) outliers start: 58 outliers final: 14 residues processed: 457 average time/residue: 0.1983 time to fit residues: 134.5960 Evaluate side-chains 278 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 350 GLU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 858 LYS Chi-restraints excluded: chain D residue 1097 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN C 543 GLN D 239 ASN D 262 GLN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112032 restraints weight = 31318.354| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.19 r_work: 0.3162 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25192 Z= 0.149 Angle : 0.673 22.067 34542 Z= 0.339 Chirality : 0.052 1.038 3967 Planarity : 0.005 0.045 4212 Dihedral : 15.404 178.334 4317 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.54 % Favored : 95.19 % Rotamer: Outliers : 2.29 % Allowed : 9.49 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2910 helix: 1.23 (0.17), residues: 1041 sheet: -0.52 (0.26), residues: 396 loop : -1.15 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 620 TYR 0.013 0.001 TYR A 168 PHE 0.017 0.001 PHE D 226 TRP 0.010 0.001 TRP C 938 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (25184) covalent geometry : angle 0.66704 / 0.34 (34530) hydrogen bonds : bond 0.05538 / 6.17 ( 1036) hydrogen bonds : angle 4.86586 / 5.14 ( 2839) metal coordination : bond 0.00946 / 0.64 ( 8) metal coordination : angle 4.96379 / 9.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 265 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7662 (mtp-110) REVERT: B 70 LYS cc_start: 0.8776 (tttt) cc_final: 0.8491 (ttmm) REVERT: B 123 MET cc_start: 0.8372 (ttt) cc_final: 0.8145 (ttp) REVERT: B 133 LYS cc_start: 0.7561 (ttmt) cc_final: 0.7294 (mmtt) REVERT: B 230 GLU cc_start: 0.8431 (tt0) cc_final: 0.8154 (tp30) REVERT: B 233 GLU cc_start: 0.8729 (pt0) cc_final: 0.8348 (mp0) REVERT: C 114 ASP cc_start: 0.8304 (m-30) cc_final: 0.8066 (m-30) REVERT: C 139 PHE cc_start: 0.7710 (t80) cc_final: 0.7366 (t80) REVERT: C 310 ARG cc_start: 0.8638 (ttm110) cc_final: 0.8070 (mtm-85) REVERT: C 355 MET cc_start: 0.8801 (ttp) cc_final: 0.8494 (tmm) REVERT: C 393 MET cc_start: 0.8694 (mmt) cc_final: 0.8442 (mmt) REVERT: C 402 GLU cc_start: 0.8005 (tp30) cc_final: 0.7646 (tp30) REVERT: C 428 LYS cc_start: 0.8855 (ttpt) cc_final: 0.8497 (ttmm) REVERT: C 525 SER cc_start: 0.8874 (m) cc_final: 0.8443 (p) REVERT: C 584 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7480 (ptp90) REVERT: C 607 MET cc_start: 0.8440 (mtp) cc_final: 0.8154 (mtt) REVERT: C 645 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7925 (mt-10) REVERT: C 950 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8191 (pttm) REVERT: C 962 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: C 1029 TYR cc_start: 0.8973 (t80) cc_final: 0.8692 (t80) REVERT: C 1063 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: D 129 ILE cc_start: 0.8697 (pt) cc_final: 0.8483 (mt) REVERT: D 143 MET cc_start: 0.6939 (ttt) cc_final: 0.6197 (tpt) REVERT: D 392 THR cc_start: 0.9080 (p) cc_final: 0.8781 (t) REVERT: D 485 ASP cc_start: 0.8357 (t0) cc_final: 0.8149 (m-30) REVERT: D 663 MET cc_start: 0.8907 (tpp) cc_final: 0.8644 (tpp) REVERT: D 706 MET cc_start: 0.7659 (mtm) cc_final: 0.7394 (mmt) REVERT: D 790 ARG cc_start: 0.7900 (tpt-90) cc_final: 0.7694 (ttp-170) REVERT: D 1087 ARG cc_start: 0.7453 (tpt-90) cc_final: 0.7152 (tpp80) REVERT: D 1088 VAL cc_start: 0.7797 (OUTLIER) cc_final: 0.7334 (m) REVERT: D 1097 ARG cc_start: 0.3419 (OUTLIER) cc_final: 0.2264 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8422 (mp) cc_final: 0.8123 (tp) REVERT: E 33 LEU cc_start: 0.7808 (tp) cc_final: 0.7590 (mp) outliers start: 56 outliers final: 26 residues processed: 305 average time/residue: 0.1651 time to fit residues: 78.3594 Evaluate side-chains 265 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 645 GLU Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 265 optimal weight: 4.9990 chunk 2 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 chunk 142 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 91 optimal weight: 1.9990 chunk 291 optimal weight: 0.1980 chunk 140 optimal weight: 3.9990 chunk 6 optimal weight: 30.0000 overall best weight: 1.2564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 ASN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1153 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.160033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110756 restraints weight = 31204.407| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.00 r_work: 0.3206 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25192 Z= 0.153 Angle : 0.618 13.990 34542 Z= 0.314 Chirality : 0.047 0.551 3967 Planarity : 0.004 0.044 4212 Dihedral : 15.282 178.048 4292 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.64 % Favored : 95.15 % Rotamer: Outliers : 2.91 % Allowed : 10.84 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 2910 helix: 1.29 (0.17), residues: 1037 sheet: -0.56 (0.25), residues: 406 loop : -1.08 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 620 TYR 0.019 0.001 TYR C 657 PHE 0.017 0.001 PHE C 252 TRP 0.009 0.001 TRP C 70 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (25184) covalent geometry : angle 0.61393 / 0.31 (34530) hydrogen bonds : bond 0.05223 / 5.85 ( 1036) hydrogen bonds : angle 4.56920 / 4.86 ( 2839) metal coordination : bond 0.00766 / 0.64 ( 8) metal coordination : angle 3.79000 / 7.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 261 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8228 (p0) REVERT: B 70 LYS cc_start: 0.8790 (tttt) cc_final: 0.8580 (ttmm) REVERT: B 133 LYS cc_start: 0.7554 (ttmt) cc_final: 0.7232 (mmtt) REVERT: B 233 GLU cc_start: 0.8668 (pt0) cc_final: 0.8258 (mp0) REVERT: C 205 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8663 (mp) REVERT: C 310 ARG cc_start: 0.8525 (ttm110) cc_final: 0.7992 (mtm-85) REVERT: C 402 GLU cc_start: 0.7930 (tp30) cc_final: 0.7549 (mm-30) REVERT: C 428 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8426 (ttmm) REVERT: C 525 SER cc_start: 0.8823 (m) cc_final: 0.8389 (p) REVERT: C 584 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7414 (ptp90) REVERT: C 713 MET cc_start: 0.8946 (mmt) cc_final: 0.8443 (mmt) REVERT: C 835 THR cc_start: 0.8803 (p) cc_final: 0.8583 (p) REVERT: C 950 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8148 (pttm) REVERT: C 962 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: C 1031 MET cc_start: 0.8829 (mtm) cc_final: 0.8449 (mtm) REVERT: C 1063 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: D 143 MET cc_start: 0.6925 (ttt) cc_final: 0.6211 (tpt) REVERT: D 392 THR cc_start: 0.9058 (p) cc_final: 0.8793 (t) REVERT: D 663 MET cc_start: 0.8853 (tpp) cc_final: 0.8538 (tpp) REVERT: D 688 MET cc_start: 0.8755 (mmt) cc_final: 0.8315 (mmt) REVERT: D 858 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7785 (mtmt) REVERT: D 866 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7621 (mtm-85) REVERT: D 1087 ARG cc_start: 0.7402 (tpt-90) cc_final: 0.7134 (tpp80) REVERT: D 1088 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7366 (m) REVERT: D 1097 ARG cc_start: 0.3334 (OUTLIER) cc_final: 0.2149 (ptp-170) REVERT: D 1112 MET cc_start: 0.8550 (mmm) cc_final: 0.8057 (mmm) REVERT: D 1176 LEU cc_start: 0.8420 (mp) cc_final: 0.8109 (tp) REVERT: E 33 LEU cc_start: 0.7816 (tp) cc_final: 0.7547 (mp) REVERT: E 87 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6983 (tm) outliers start: 71 outliers final: 34 residues processed: 310 average time/residue: 0.1711 time to fit residues: 81.8543 Evaluate side-chains 272 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 858 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain E residue 87 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 282 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 295 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.158267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109588 restraints weight = 31250.458| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.08 r_work: 0.3168 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25192 Z= 0.199 Angle : 0.630 10.118 34542 Z= 0.322 Chirality : 0.047 0.404 3967 Planarity : 0.005 0.048 4212 Dihedral : 15.308 178.751 4292 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.29 % Favored : 94.50 % Rotamer: Outliers : 3.15 % Allowed : 12.27 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 2910 helix: 1.17 (0.16), residues: 1036 sheet: -0.40 (0.26), residues: 389 loop : -1.14 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 620 TYR 0.016 0.001 TYR A 168 PHE 0.018 0.001 PHE C 252 TRP 0.009 0.001 TRP C 70 HIS 0.006 0.001 HIS D 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (25184) covalent geometry : angle 0.62679 / 0.32 (34530) hydrogen bonds : bond 0.05451 / 6.07 ( 1036) hydrogen bonds : angle 4.54599 / 4.88 ( 2839) metal coordination : bond 0.00807 / 0.68 ( 8) metal coordination : angle 3.29167 / 6.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 236 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8653 (ttm110) cc_final: 0.7984 (mmm160) REVERT: A 117 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8500 (p) REVERT: B 70 LYS cc_start: 0.8836 (tttt) cc_final: 0.8629 (ttmm) REVERT: B 133 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7246 (mmtt) REVERT: B 233 GLU cc_start: 0.8675 (pt0) cc_final: 0.8152 (mp0) REVERT: C 232 GLN cc_start: 0.7304 (mt0) cc_final: 0.7088 (mt0) REVERT: C 310 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8041 (mtm-85) REVERT: C 428 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8391 (ttmm) REVERT: C 525 SER cc_start: 0.8855 (m) cc_final: 0.8452 (p) REVERT: C 584 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7497 (ptp90) REVERT: C 661 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8330 (tpt) REVERT: C 713 MET cc_start: 0.8990 (mmt) cc_final: 0.8493 (mmt) REVERT: C 950 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8256 (pttm) REVERT: C 962 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: C 1063 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: D 143 MET cc_start: 0.6983 (ttt) cc_final: 0.6272 (tpt) REVERT: D 215 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6651 (pp20) REVERT: D 392 THR cc_start: 0.9114 (p) cc_final: 0.8855 (t) REVERT: D 663 MET cc_start: 0.8902 (tpp) cc_final: 0.8590 (tpp) REVERT: D 688 MET cc_start: 0.8853 (mmt) cc_final: 0.8387 (mmt) REVERT: D 858 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7842 (mtmt) REVERT: D 866 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7650 (mtm-85) REVERT: D 1087 ARG cc_start: 0.7415 (tpt-90) cc_final: 0.7118 (tpp80) REVERT: D 1088 VAL cc_start: 0.7828 (OUTLIER) cc_final: 0.7385 (m) REVERT: D 1097 ARG cc_start: 0.3320 (OUTLIER) cc_final: 0.2025 (ptp-170) REVERT: D 1112 MET cc_start: 0.8621 (mmm) cc_final: 0.8159 (mmm) REVERT: D 1176 LEU cc_start: 0.8413 (mp) cc_final: 0.8119 (tp) REVERT: E 33 LEU cc_start: 0.7832 (tp) cc_final: 0.7474 (mp) REVERT: E 36 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9014 (p) REVERT: E 87 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6998 (tm) outliers start: 77 outliers final: 41 residues processed: 292 average time/residue: 0.1751 time to fit residues: 78.2423 Evaluate side-chains 276 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 223 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 858 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 75 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 250 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN C 543 GLN C1035 HIS ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.158600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109641 restraints weight = 31130.798| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.03 r_work: 0.3178 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25192 Z= 0.172 Angle : 0.601 9.079 34542 Z= 0.309 Chirality : 0.046 0.377 3967 Planarity : 0.004 0.046 4212 Dihedral : 15.240 179.067 4289 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.81 % Favored : 95.02 % Rotamer: Outliers : 2.99 % Allowed : 12.77 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 2910 helix: 1.26 (0.17), residues: 1032 sheet: -0.42 (0.27), residues: 379 loop : -1.09 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 620 TYR 0.015 0.001 TYR A 168 PHE 0.020 0.001 PHE C 252 TRP 0.010 0.001 TRP C 70 HIS 0.006 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (25184) covalent geometry : angle 0.59798 / 0.31 (34530) hydrogen bonds : bond 0.05117 / 5.71 ( 1036) hydrogen bonds : angle 4.43271 / 4.76 ( 2839) metal coordination : bond 0.00652 / 0.57 ( 8) metal coordination : angle 3.09682 / 5.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 242 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8856 (tttt) cc_final: 0.8643 (ttmm) REVERT: B 133 LYS cc_start: 0.7651 (ttmt) cc_final: 0.7268 (mmtt) REVERT: B 233 GLU cc_start: 0.8649 (pt0) cc_final: 0.8061 (pm20) REVERT: C 310 ARG cc_start: 0.8499 (ttm110) cc_final: 0.8095 (mtm110) REVERT: C 428 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8343 (ttmm) REVERT: C 525 SER cc_start: 0.8794 (m) cc_final: 0.8426 (p) REVERT: C 584 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7445 (ptp90) REVERT: C 713 MET cc_start: 0.8915 (mmt) cc_final: 0.8558 (mmt) REVERT: C 950 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8130 (pttm) REVERT: C 962 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: C 1031 MET cc_start: 0.8985 (mtm) cc_final: 0.8536 (mtm) REVERT: C 1063 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7742 (m-80) REVERT: D 140 ASP cc_start: 0.7818 (t0) cc_final: 0.7507 (t70) REVERT: D 143 MET cc_start: 0.7021 (ttt) cc_final: 0.6380 (tpt) REVERT: D 215 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6672 (pp20) REVERT: D 288 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7686 (mtpp) REVERT: D 392 THR cc_start: 0.9090 (p) cc_final: 0.8848 (t) REVERT: D 663 MET cc_start: 0.8943 (tpp) cc_final: 0.8514 (tpp) REVERT: D 688 MET cc_start: 0.8814 (mmt) cc_final: 0.8330 (mmt) REVERT: D 858 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7856 (mtmt) REVERT: D 866 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7636 (mtm-85) REVERT: D 1087 ARG cc_start: 0.7483 (tpt-90) cc_final: 0.7151 (tpp80) REVERT: D 1088 VAL cc_start: 0.7839 (OUTLIER) cc_final: 0.7403 (m) REVERT: D 1097 ARG cc_start: 0.3359 (OUTLIER) cc_final: 0.2004 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8383 (mp) cc_final: 0.8080 (tp) REVERT: E 33 LEU cc_start: 0.7835 (tp) cc_final: 0.7479 (mp) REVERT: E 36 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.9042 (p) REVERT: E 87 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7032 (tm) outliers start: 73 outliers final: 45 residues processed: 298 average time/residue: 0.1745 time to fit residues: 80.1247 Evaluate side-chains 284 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 775 ASN Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 327 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 858 LYS Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 36 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 214 optimal weight: 0.0470 chunk 48 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 271 optimal weight: 0.0570 chunk 186 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 ASN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.174485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122824 restraints weight = 33537.461| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.82 r_work: 0.3247 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25192 Z= 0.112 Angle : 0.561 8.555 34542 Z= 0.289 Chirality : 0.044 0.350 3967 Planarity : 0.004 0.046 4212 Dihedral : 15.113 179.476 4285 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.71 % Favored : 95.12 % Rotamer: Outliers : 2.41 % Allowed : 13.83 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2910 helix: 1.47 (0.17), residues: 1043 sheet: -0.37 (0.26), residues: 384 loop : -0.96 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 620 TYR 0.010 0.001 TYR C 278 PHE 0.018 0.001 PHE C 252 TRP 0.012 0.001 TRP C 70 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (25184) covalent geometry : angle 0.55881 / 0.29 (34530) hydrogen bonds : bond 0.04328 / 4.83 ( 1036) hydrogen bonds : angle 4.26388 / 4.59 ( 2839) metal coordination : bond 0.00392 / 0.34 ( 8) metal coordination : angle 2.77899 / 5.29 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 254 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 117 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8520 (p) REVERT: B 133 LYS cc_start: 0.7628 (ttmt) cc_final: 0.7299 (mmtt) REVERT: B 233 GLU cc_start: 0.8632 (pt0) cc_final: 0.8110 (pm20) REVERT: C 296 LEU cc_start: 0.7409 (tm) cc_final: 0.7057 (tp) REVERT: C 310 ARG cc_start: 0.8476 (ttm110) cc_final: 0.8108 (mtm110) REVERT: C 428 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8343 (ttmm) REVERT: C 525 SER cc_start: 0.8773 (m) cc_final: 0.8441 (p) REVERT: C 584 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7361 (ptp90) REVERT: C 661 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8160 (tpt) REVERT: C 713 MET cc_start: 0.8834 (mmt) cc_final: 0.8524 (mmt) REVERT: C 950 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8024 (pttm) REVERT: C 962 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: C 1031 MET cc_start: 0.8777 (mtm) cc_final: 0.8368 (mtm) REVERT: C 1063 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: D 140 ASP cc_start: 0.7872 (t0) cc_final: 0.7503 (t70) REVERT: D 143 MET cc_start: 0.6827 (ttt) cc_final: 0.6245 (tpt) REVERT: D 215 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6741 (pp20) REVERT: D 288 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7759 (mtpp) REVERT: D 392 THR cc_start: 0.9063 (p) cc_final: 0.8848 (t) REVERT: D 858 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7916 (mtmt) REVERT: D 866 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7590 (mtm-85) REVERT: D 985 THR cc_start: 0.9156 (t) cc_final: 0.8930 (p) REVERT: D 1087 ARG cc_start: 0.7471 (tpt-90) cc_final: 0.7166 (tpp80) REVERT: D 1088 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7471 (m) REVERT: D 1097 ARG cc_start: 0.3341 (OUTLIER) cc_final: 0.1972 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8347 (mp) cc_final: 0.8080 (tp) REVERT: E 33 LEU cc_start: 0.7805 (tp) cc_final: 0.7498 (mp) REVERT: E 36 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.9033 (p) REVERT: E 87 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6988 (tm) outliers start: 59 outliers final: 37 residues processed: 299 average time/residue: 0.1908 time to fit residues: 87.7671 Evaluate side-chains 280 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 858 LYS Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 87 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 57 optimal weight: 0.9980 chunk 290 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 219 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1125 GLN ** 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 = 0.4062 r_free = 0.4062 target = 0.174355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.122715 restraints weight = 33563.960| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.81 r_work: 0.3240 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25192 Z= 0.120 Angle : 0.561 8.135 34542 Z= 0.289 Chirality : 0.044 0.297 3967 Planarity : 0.004 0.064 4212 Dihedral : 15.020 178.846 4285 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.71 % Favored : 95.15 % Rotamer: Outliers : 2.45 % Allowed : 14.16 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2910 helix: 1.54 (0.17), residues: 1046 sheet: -0.27 (0.27), residues: 384 loop : -0.91 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 465 TYR 0.015 0.001 TYR C 278 PHE 0.019 0.001 PHE C 252 TRP 0.010 0.001 TRP C 70 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (25184) covalent geometry : angle 0.55873 / 0.29 (34530) hydrogen bonds : bond 0.04304 / 4.80 ( 1036) hydrogen bonds : angle 4.19645 / 4.52 ( 2839) metal coordination : bond 0.00406 / 0.35 ( 8) metal coordination : angle 2.67800 / 5.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 238 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7304 (mmtt) REVERT: B 233 GLU cc_start: 0.8657 (pt0) cc_final: 0.8117 (pm20) REVERT: C 232 GLN cc_start: 0.7417 (mt0) cc_final: 0.7169 (mt0) REVERT: C 280 LYS cc_start: 0.8030 (tppt) cc_final: 0.7244 (ttmm) REVERT: C 296 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7051 (tp) REVERT: C 310 ARG cc_start: 0.8463 (ttm110) cc_final: 0.8115 (mtm110) REVERT: C 428 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8334 (ttmm) REVERT: C 525 SER cc_start: 0.8775 (m) cc_final: 0.8436 (p) REVERT: C 584 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7367 (ptp90) REVERT: C 661 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8070 (tpt) REVERT: C 713 MET cc_start: 0.8857 (mmt) cc_final: 0.8551 (mmt) REVERT: C 950 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8063 (pttm) REVERT: C 962 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: C 1031 MET cc_start: 0.8800 (mtm) cc_final: 0.8438 (mtm) REVERT: C 1063 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: D 140 ASP cc_start: 0.7914 (t0) cc_final: 0.7595 (t70) REVERT: D 143 MET cc_start: 0.6845 (ttt) cc_final: 0.6371 (tpt) REVERT: D 215 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6788 (pp20) REVERT: D 288 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7726 (mtpp) REVERT: D 663 MET cc_start: 0.8684 (tpp) cc_final: 0.8279 (tpp) REVERT: D 688 MET cc_start: 0.8660 (mmt) cc_final: 0.8263 (mmt) REVERT: D 858 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7868 (ttmt) REVERT: D 866 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7594 (mtm-85) REVERT: D 985 THR cc_start: 0.9153 (t) cc_final: 0.8946 (p) REVERT: D 1087 ARG cc_start: 0.7495 (tpt-90) cc_final: 0.7180 (tpp80) REVERT: D 1088 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7566 (m) REVERT: D 1097 ARG cc_start: 0.3316 (OUTLIER) cc_final: 0.1936 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8327 (mp) cc_final: 0.8065 (tp) REVERT: E 33 LEU cc_start: 0.7824 (tp) cc_final: 0.7516 (mp) REVERT: E 87 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6969 (tm) outliers start: 60 outliers final: 41 residues processed: 284 average time/residue: 0.1966 time to fit residues: 85.2606 Evaluate side-chains 280 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 858 LYS Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain E residue 87 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 203 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 GLN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.111082 restraints weight = 30984.774| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.13 r_work: 0.3177 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25192 Z= 0.169 Angle : 0.593 8.471 34542 Z= 0.305 Chirality : 0.045 0.267 3967 Planarity : 0.004 0.054 4212 Dihedral : 14.999 179.150 4285 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 2.58 % Allowed : 14.57 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2910 helix: 1.44 (0.16), residues: 1040 sheet: -0.48 (0.26), residues: 413 loop : -1.00 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 421 TYR 0.014 0.001 TYR A 168 PHE 0.023 0.001 PHE C 153 TRP 0.009 0.001 TRP D 223 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (25184) covalent geometry : angle 0.59094 / 0.30 (34530) hydrogen bonds : bond 0.04839 / 5.39 ( 1036) hydrogen bonds : angle 4.25068 / 4.58 ( 2839) metal coordination : bond 0.00565 / 0.48 ( 8) metal coordination : angle 2.85433 / 5.42 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 238 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7341 (mmtt) REVERT: C 280 LYS cc_start: 0.8136 (tppt) cc_final: 0.7677 (ttmm) REVERT: C 296 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6934 (tp) REVERT: C 310 ARG cc_start: 0.8464 (ttm110) cc_final: 0.8078 (mtm110) REVERT: C 428 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8328 (ttmm) REVERT: C 525 SER cc_start: 0.8779 (m) cc_final: 0.8428 (p) REVERT: C 584 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7434 (ptp90) REVERT: C 661 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8159 (tpt) REVERT: C 713 MET cc_start: 0.8958 (mmt) cc_final: 0.8603 (mmt) REVERT: C 950 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7920 (pttm) REVERT: C 962 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: C 1031 MET cc_start: 0.8944 (mtm) cc_final: 0.8606 (mtm) REVERT: C 1063 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: D 71 LYS cc_start: 0.7667 (mtpp) cc_final: 0.7329 (tttt) REVERT: D 140 ASP cc_start: 0.7876 (t0) cc_final: 0.7552 (t70) REVERT: D 143 MET cc_start: 0.6854 (ttt) cc_final: 0.6373 (tpt) REVERT: D 215 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6723 (pp20) REVERT: D 663 MET cc_start: 0.8832 (tpp) cc_final: 0.8442 (tpp) REVERT: D 688 MET cc_start: 0.8805 (mmt) cc_final: 0.8391 (mmt) REVERT: D 741 ARG cc_start: 0.7407 (mtp-110) cc_final: 0.7008 (ptt-90) REVERT: D 858 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7927 (ttmt) REVERT: D 866 ARG cc_start: 0.7905 (ttp80) cc_final: 0.7625 (mtm-85) REVERT: D 1087 ARG cc_start: 0.7498 (tpt-90) cc_final: 0.7146 (tpp80) REVERT: D 1088 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7579 (m) REVERT: D 1097 ARG cc_start: 0.3404 (OUTLIER) cc_final: 0.2066 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8311 (mp) cc_final: 0.8036 (tp) REVERT: E 33 LEU cc_start: 0.7728 (tp) cc_final: 0.7447 (mp) REVERT: E 87 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6975 (tm) outliers start: 63 outliers final: 44 residues processed: 286 average time/residue: 0.1927 time to fit residues: 85.1084 Evaluate side-chains 286 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 858 LYS Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain E residue 87 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 69 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 232 optimal weight: 0.5980 chunk 139 optimal weight: 0.0980 chunk 3 optimal weight: 10.0000 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.122788 restraints weight = 33518.754| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.84 r_work: 0.3292 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 25192 Z= 0.114 Angle : 0.562 11.127 34542 Z= 0.289 Chirality : 0.044 0.268 3967 Planarity : 0.004 0.048 4212 Dihedral : 14.908 178.267 4285 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.67 % Favored : 95.15 % Rotamer: Outliers : 2.37 % Allowed : 14.61 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2910 helix: 1.55 (0.17), residues: 1047 sheet: -0.21 (0.27), residues: 382 loop : -0.88 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 620 TYR 0.011 0.001 TYR C 278 PHE 0.021 0.001 PHE C 153 TRP 0.012 0.001 TRP C 70 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (25184) covalent geometry : angle 0.55955 / 0.29 (34530) hydrogen bonds : bond 0.04181 / 4.67 ( 1036) hydrogen bonds : angle 4.13910 / 4.46 ( 2839) metal coordination : bond 0.00364 / 0.31 ( 8) metal coordination : angle 2.62709 / 4.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 236 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 LEU cc_start: 0.8454 (pp) cc_final: 0.8127 (mt) REVERT: B 133 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7401 (mmtt) REVERT: C 296 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6879 (tp) REVERT: C 310 ARG cc_start: 0.8462 (ttm110) cc_final: 0.8153 (mtm110) REVERT: C 373 PHE cc_start: 0.9310 (OUTLIER) cc_final: 0.8345 (t80) REVERT: C 428 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8336 (ttmm) REVERT: C 525 SER cc_start: 0.8746 (m) cc_final: 0.8422 (p) REVERT: C 584 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7318 (ptp90) REVERT: C 661 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8072 (tpt) REVERT: C 713 MET cc_start: 0.8821 (mmt) cc_final: 0.8522 (mmt) REVERT: C 950 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7987 (pttm) REVERT: C 962 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: C 1031 MET cc_start: 0.8787 (mtm) cc_final: 0.8513 (mtm) REVERT: C 1063 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: D 71 LYS cc_start: 0.7555 (mtpp) cc_final: 0.7275 (tttt) REVERT: D 140 ASP cc_start: 0.7844 (t0) cc_final: 0.7531 (t70) REVERT: D 143 MET cc_start: 0.6886 (ttt) cc_final: 0.6400 (tpt) REVERT: D 215 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6740 (pp20) REVERT: D 288 LYS cc_start: 0.8014 (mmmt) cc_final: 0.7699 (mtpp) REVERT: D 663 MET cc_start: 0.8678 (tpp) cc_final: 0.8263 (tpp) REVERT: D 688 MET cc_start: 0.8552 (mmt) cc_final: 0.8167 (mmt) REVERT: D 858 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7881 (ttmm) REVERT: D 866 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7590 (mtm-85) REVERT: D 1087 ARG cc_start: 0.7440 (tpt-90) cc_final: 0.7128 (tpp80) REVERT: D 1088 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7649 (m) REVERT: D 1097 ARG cc_start: 0.3362 (OUTLIER) cc_final: 0.2108 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8297 (mp) cc_final: 0.8056 (tp) REVERT: E 33 LEU cc_start: 0.7715 (tp) cc_final: 0.7481 (mp) REVERT: E 87 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6830 (tm) outliers start: 58 outliers final: 40 residues processed: 280 average time/residue: 0.1958 time to fit residues: 84.3811 Evaluate side-chains 283 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 231 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 858 LYS Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain E residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 237 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 249 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 86 optimal weight: 0.0470 chunk 243 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.174967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121729 restraints weight = 33528.849| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.80 r_work: 0.3266 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 25192 Z= 0.114 Angle : 0.554 8.420 34542 Z= 0.285 Chirality : 0.043 0.269 3967 Planarity : 0.004 0.063 4212 Dihedral : 14.844 177.040 4285 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 2.29 % Allowed : 14.77 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2910 helix: 1.64 (0.17), residues: 1047 sheet: -0.19 (0.27), residues: 382 loop : -0.84 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 465 TYR 0.010 0.001 TYR A 168 PHE 0.024 0.001 PHE C 153 TRP 0.013 0.001 TRP D 223 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (25184) covalent geometry : angle 0.55159 / 0.28 (34530) hydrogen bonds : bond 0.04054 / 4.52 ( 1036) hydrogen bonds : angle 4.07545 / 4.40 ( 2839) metal coordination : bond 0.00356 / 0.31 ( 8) metal coordination : angle 2.56974 / 4.80 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5820 Ramachandran restraints generated. 2910 Oldfield, 0 Emsley, 2910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 233 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7383 (mmtt) REVERT: C 296 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6690 (tp) REVERT: C 373 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8287 (t80) REVERT: C 428 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8239 (ttmm) REVERT: C 525 SER cc_start: 0.8642 (m) cc_final: 0.8291 (p) REVERT: C 584 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7149 (ptp90) REVERT: C 620 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7308 (mtt90) REVERT: C 661 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7979 (tpt) REVERT: C 713 MET cc_start: 0.8882 (mmt) cc_final: 0.8587 (mmt) REVERT: C 950 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7997 (pttm) REVERT: C 962 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 1031 MET cc_start: 0.8826 (mtm) cc_final: 0.8495 (mtm) REVERT: C 1063 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: D 71 LYS cc_start: 0.7584 (mtpp) cc_final: 0.7307 (tttt) REVERT: D 140 ASP cc_start: 0.7931 (t0) cc_final: 0.7571 (t70) REVERT: D 215 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6800 (pp20) REVERT: D 288 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7637 (mtpp) REVERT: D 741 ARG cc_start: 0.7287 (mtp-110) cc_final: 0.7011 (ptt-90) REVERT: D 858 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7818 (ttmt) REVERT: D 1087 ARG cc_start: 0.7377 (tpt-90) cc_final: 0.7034 (tpp80) REVERT: D 1088 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7645 (m) REVERT: D 1097 ARG cc_start: 0.3327 (OUTLIER) cc_final: 0.2252 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8234 (mp) cc_final: 0.7979 (tp) REVERT: E 33 LEU cc_start: 0.7640 (tp) cc_final: 0.7393 (mp) REVERT: E 87 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6779 (tm) outliers start: 56 outliers final: 40 residues processed: 276 average time/residue: 0.1943 time to fit residues: 82.6097 Evaluate side-chains 276 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 224 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 537 ASP Chi-restraints excluded: chain C residue 570 TYR Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 789 ILE Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 950 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 248 TYR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 649 GLU Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 858 LYS Chi-restraints excluded: chain D residue 1053 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain E residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 113 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 193 optimal weight: 0.9980 chunk 276 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 185 optimal weight: 20.0000 chunk 258 optimal weight: 0.0170 chunk 286 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 132 optimal weight: 0.0770 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.162152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114095 restraints weight = 31277.800| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.02 r_work: 0.3245 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 25192 Z= 0.108 Angle : 0.548 8.325 34542 Z= 0.283 Chirality : 0.043 0.272 3967 Planarity : 0.004 0.072 4212 Dihedral : 14.817 176.789 4284 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.57 % Favored : 95.29 % Rotamer: Outliers : 2.25 % Allowed : 14.89 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2910 helix: 1.69 (0.17), residues: 1048 sheet: -0.14 (0.27), residues: 382 loop : -0.79 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 465 TYR 0.013 0.001 TYR C 278 PHE 0.023 0.001 PHE C 153 TRP 0.014 0.001 TRP D 223 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (25184) covalent geometry : angle 0.54562 / 0.28 (34530) hydrogen bonds : bond 0.03869 / 4.32 ( 1036) hydrogen bonds : angle 4.03680 / 4.36 ( 2839) metal coordination : bond 0.00333 / 0.28 ( 8) metal coordination : angle 2.50893 / 4.67 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7250.55 seconds wall clock time: 124 minutes 24.26 seconds (7464.26 seconds total)