Starting phenix.real_space_refine on Sun Jan 26 12:33:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e8m_27944/01_2025/8e8m_27944.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e8m_27944/01_2025/8e8m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8e8m_27944/01_2025/8e8m_27944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e8m_27944/01_2025/8e8m_27944.map" model { file = "/net/cci-nas-00/data/ceres_data/8e8m_27944/01_2025/8e8m_27944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e8m_27944/01_2025/8e8m_27944.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 1.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'RNA': 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, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} 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: {'GLU:plan': 2, 'ASN:plan1': 1, '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: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} 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: 14.59, per 1000 atoms: 0.59 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: 7.34 Conformation dependent library (CDL) restraints added in 3.3 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: 9.49 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: 12.95 Time building geometry restraints manager: 7.37 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=" N GLY D -1 " pdb=" CA GLY D -1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.05e+00 bond pdb=" CA PRO D 321 " pdb=" C PRO D 321 " ideal model delta sigma weight residual 1.514 1.501 0.013 5.50e-03 3.31e+04 5.52e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.72e+00 bond pdb=" C3' DA O 28 " pdb=" O3' DA O 28 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.77e+00 ... (remaining 25179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 33267 1.29 - 2.58: 1019 2.58 - 3.86: 219 3.86 - 5.15: 22 5.15 - 6.44: 3 Bond angle restraints: 34530 Sorted by residual: angle pdb=" C VAL C 204 " pdb=" N ILE C 205 " pdb=" CA ILE C 205 " ideal model delta sigma weight residual 122.60 120.21 2.39 6.80e-01 2.16e+00 1.23e+01 angle pdb=" CA GLY C 943 " pdb=" C GLY C 943 " pdb=" O GLY C 943 " ideal model delta sigma weight residual 122.29 119.66 2.63 8.10e-01 1.52e+00 1.05e+01 angle pdb=" N GLY C 374 " pdb=" CA GLY C 374 " pdb=" C GLY C 374 " ideal model delta sigma weight residual 115.62 110.47 5.15 1.71e+00 3.42e-01 9.08e+00 angle pdb=" N SER C 582 " pdb=" CA SER C 582 " pdb=" C SER C 582 " ideal model delta sigma weight residual 108.13 110.74 -2.61 9.00e-01 1.23e+00 8.42e+00 angle pdb=" C PHE C 431 " pdb=" CA PHE C 431 " pdb=" CB PHE C 431 " ideal model delta sigma weight residual 111.22 107.82 3.40 1.23e+00 6.61e-01 7.64e+00 ... (remaining 34525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.93: 14767 33.93 - 67.85: 498 67.85 - 101.78: 13 101.78 - 135.71: 0 135.71 - 169.63: 5 Dihedral angle restraints: 15283 sinusoidal: 6923 harmonic: 8360 Sorted by residual: dihedral pdb=" CA PHE D 6 " pdb=" C PHE D 6 " pdb=" N PHE D 7 " pdb=" CA PHE D 7 " ideal model delta harmonic sigma weight residual -180.00 -147.29 -32.71 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA ASN D 5 " pdb=" C ASN D 5 " pdb=" N PHE D 6 " pdb=" CA PHE D 6 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA SER C 582 " pdb=" C SER C 582 " pdb=" N PRO C 583 " pdb=" CA PRO C 583 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 15280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2440 0.031 - 0.061: 1025 0.061 - 0.092: 276 0.092 - 0.123: 188 0.123 - 0.153: 38 Chirality restraints: 3967 Sorted by residual: chirality pdb=" CA ILE D 509 " pdb=" N ILE D 509 " pdb=" C ILE D 509 " pdb=" CB ILE D 509 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA ILE D 832 " pdb=" N ILE D 832 " pdb=" C ILE D 832 " pdb=" CB ILE D 832 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE C 594 " pdb=" N ILE C 594 " pdb=" C ILE C 594 " pdb=" CB ILE C 594 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.900 Check model and map are aligned: 0.190 Set scattering table: 0.210 Process input model: 68.950 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 0.040 25184 Z= 0.239 Angle : 0.562 6.439 34530 Z= 0.326 Chirality : 0.042 0.153 3967 Planarity : 0.004 0.048 4212 Dihedral : 14.851 169.632 9911 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP D 778 HIS 0.005 0.001 HIS D 94 PHE 0.012 0.001 PHE C 431 TYR 0.011 0.001 TYR A 168 ARG 0.004 0.000 ARG D 834 *********************** 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 : 2.497 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: 0.7912 (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: 0.4450 time to fit residues: 298.9393 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 : 2.539 ------------------------------------------------------------------------------- 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 251 optimal weight: 0.9990 chunk 225 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 90 optimal weight: 0.2980 chunk 142 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3919 r_free = 0.3919 target = 0.154330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.100669 restraints weight = 31361.715| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.33 r_work: 0.2998 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25184 Z= 0.186 Angle : 0.583 10.574 34530 Z= 0.307 Chirality : 0.042 0.177 3967 Planarity : 0.004 0.044 4212 Dihedral : 16.085 177.577 4421 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.64 % Favored : 95.09 % Rotamer: Outliers : 2.17 % Allowed : 9.94 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2910 helix: 1.34 (0.17), residues: 1037 sheet: -0.53 (0.26), residues: 399 loop : -1.12 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 70 HIS 0.005 0.001 HIS D 94 PHE 0.015 0.001 PHE D 226 TYR 0.011 0.001 TYR A 168 ARG 0.017 0.001 ARG D1087 *********************** 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 324 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 2.559 Fit side-chains revert: symmetry clash REVERT: A 6 ARG cc_start: 0.8414 (mtp85) cc_final: 0.7657 (mtp-110) REVERT: A 191 LYS cc_start: 0.9024 (tttm) cc_final: 0.8794 (tttm) REVERT: B 70 LYS cc_start: 0.8756 (tttt) cc_final: 0.8464 (ttmm) REVERT: B 123 MET cc_start: 0.8186 (ttt) cc_final: 0.7919 (ttp) REVERT: B 133 LYS cc_start: 0.7664 (ttmt) cc_final: 0.7240 (mmtt) REVERT: B 233 GLU cc_start: 0.8535 (pt0) cc_final: 0.8089 (mp0) REVERT: C 114 ASP cc_start: 0.8185 (m-30) cc_final: 0.7966 (m-30) REVERT: C 139 PHE cc_start: 0.7693 (t80) cc_final: 0.7328 (t80) REVERT: C 310 ARG cc_start: 0.8426 (ttm110) cc_final: 0.7835 (mtm-85) REVERT: C 355 MET cc_start: 0.8763 (ttp) cc_final: 0.8463 (tmm) REVERT: C 393 MET cc_start: 0.8461 (mmt) cc_final: 0.8193 (mmt) REVERT: C 402 GLU cc_start: 0.7880 (tp30) cc_final: 0.7463 (mm-30) REVERT: C 428 LYS cc_start: 0.8669 (ttpt) cc_final: 0.8244 (ttmm) REVERT: C 525 SER cc_start: 0.8723 (m) cc_final: 0.8237 (p) REVERT: C 584 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7284 (ptp90) REVERT: C 607 MET cc_start: 0.8222 (mtp) cc_final: 0.7989 (mtt) REVERT: C 645 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: C 657 TYR cc_start: 0.8526 (p90) cc_final: 0.8257 (p90) REVERT: C 763 LYS cc_start: 0.7703 (mttt) cc_final: 0.7385 (mmmt) REVERT: C 835 THR cc_start: 0.8855 (p) cc_final: 0.8654 (p) REVERT: C 950 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8285 (pttm) REVERT: C 962 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: C 1028 MET cc_start: 0.8973 (mtp) cc_final: 0.8695 (ttp) REVERT: C 1063 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: D 143 MET cc_start: 0.6859 (ttt) cc_final: 0.6152 (tpt) REVERT: D 392 THR cc_start: 0.9065 (p) cc_final: 0.8748 (t) REVERT: D 663 MET cc_start: 0.8800 (tpp) cc_final: 0.8490 (tpp) REVERT: D 1087 ARG cc_start: 0.7190 (tpt-90) cc_final: 0.6588 (tpp80) REVERT: D 1088 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7317 (m) REVERT: D 1097 ARG cc_start: 0.3396 (OUTLIER) cc_final: 0.2241 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8322 (mp) cc_final: 0.7993 (tp) REVERT: E 33 LEU cc_start: 0.7610 (tp) cc_final: 0.7301 (mp) outliers start: 53 outliers final: 27 residues processed: 307 average time/residue: 0.4053 time to fit residues: 192.4493 Evaluate side-chains 268 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 2.514 ------------------------------------------------------------------------------- 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 54 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 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 789 ILE 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 1063 PHE Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 338 SER 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 227 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 293 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1035 HIS D 239 ASN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1153 HIS E 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.159029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.115058 restraints weight = 32308.033| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.40 r_work: 0.3063 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 25184 Z= 0.559 Angle : 0.713 9.360 34530 Z= 0.371 Chirality : 0.049 0.222 3967 Planarity : 0.005 0.049 4212 Dihedral : 16.085 177.203 4396 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.43 % Favored : 94.33 % Rotamer: Outliers : 3.40 % Allowed : 11.46 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 2910 helix: 0.93 (0.16), residues: 1018 sheet: -0.55 (0.26), residues: 380 loop : -1.36 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D1220 HIS 0.007 0.001 HIS D 689 PHE 0.021 0.002 PHE D 7 TYR 0.023 0.002 TYR A 168 ARG 0.007 0.001 ARG C 620 *********************** 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 335 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 252 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8450 (tmm) cc_final: 0.8232 (tmm) REVERT: B 17 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8417 (p0) REVERT: B 70 LYS cc_start: 0.8894 (tttt) cc_final: 0.8667 (ttmm) REVERT: B 133 LYS cc_start: 0.7743 (ttmt) cc_final: 0.7350 (mmtt) REVERT: C 114 ASP cc_start: 0.8333 (m-30) cc_final: 0.8105 (m-30) REVERT: C 302 LYS cc_start: 0.7259 (ttmt) cc_final: 0.6596 (mttp) REVERT: C 428 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8442 (ttmm) REVERT: C 525 SER cc_start: 0.8935 (m) cc_final: 0.8536 (p) REVERT: C 584 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7676 (ptp90) REVERT: C 607 MET cc_start: 0.8549 (mtp) cc_final: 0.8261 (mtt) REVERT: C 645 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: C 657 TYR cc_start: 0.8666 (p90) cc_final: 0.8416 (p90) REVERT: C 763 LYS cc_start: 0.7735 (mttt) cc_final: 0.7532 (mmmt) REVERT: C 835 THR cc_start: 0.8941 (p) cc_final: 0.8721 (p) REVERT: C 950 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8192 (pttm) REVERT: C 962 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7975 (pt0) REVERT: C 1063 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: D 143 MET cc_start: 0.7079 (ttt) cc_final: 0.6484 (tpt) REVERT: D 215 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6434 (pp20) REVERT: D 392 THR cc_start: 0.9139 (p) cc_final: 0.8871 (t) REVERT: D 663 MET cc_start: 0.9110 (tpp) cc_final: 0.8817 (tpp) REVERT: D 688 MET cc_start: 0.8980 (mmt) cc_final: 0.8565 (mmt) REVERT: D 866 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7848 (mtm-85) REVERT: D 1085 ARG cc_start: 0.7459 (mtt180) cc_final: 0.6896 (mtm-85) REVERT: D 1087 ARG cc_start: 0.7520 (tpt-90) cc_final: 0.7225 (tpp80) REVERT: D 1088 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7388 (m) REVERT: D 1097 ARG cc_start: 0.3691 (OUTLIER) cc_final: 0.2414 (ptp-170) REVERT: D 1112 MET cc_start: 0.8764 (mmm) cc_final: 0.8331 (mmm) REVERT: D 1176 LEU cc_start: 0.8510 (mp) cc_final: 0.8200 (tp) REVERT: E 33 LEU cc_start: 0.7917 (tp) cc_final: 0.7653 (mp) REVERT: E 87 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7107 (tm) outliers start: 83 outliers final: 42 residues processed: 315 average time/residue: 0.4139 time to fit residues: 198.5957 Evaluate side-chains 285 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 233 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL 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 136 VAL Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 54 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 373 PHE Chi-restraints excluded: chain C residue 400 VAL 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 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 645 GLU 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 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 1063 PHE Chi-restraints excluded: chain D residue 181 LEU 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 327 MET 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 733 MET Chi-restraints excluded: chain D residue 835 PRO Chi-restraints excluded: chain D residue 846 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 161 optimal weight: 8.9990 chunk 258 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 45 optimal weight: 6.9990 chunk 215 optimal weight: 0.6980 chunk 220 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 293 GLN C 435 GLN ** D1125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.153067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099600 restraints weight = 31442.380| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.29 r_work: 0.2979 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25184 Z= 0.172 Angle : 0.545 9.426 34530 Z= 0.288 Chirality : 0.041 0.219 3967 Planarity : 0.004 0.046 4212 Dihedral : 15.893 178.568 4396 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.26 % Favored : 95.53 % Rotamer: Outliers : 2.82 % Allowed : 12.89 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2910 helix: 1.24 (0.17), residues: 1041 sheet: -0.46 (0.26), residues: 386 loop : -1.11 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 70 HIS 0.005 0.001 HIS D 94 PHE 0.016 0.001 PHE C 252 TYR 0.012 0.001 TYR A 168 ARG 0.010 0.000 ARG C 620 *********************** 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 319 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 250 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 MET cc_start: 0.8167 (tmm) cc_final: 0.7957 (tmm) REVERT: B 70 LYS cc_start: 0.8806 (tttt) cc_final: 0.8605 (ttmm) REVERT: B 133 LYS cc_start: 0.7708 (ttmt) cc_final: 0.7274 (mmtt) REVERT: C 114 ASP cc_start: 0.8149 (m-30) cc_final: 0.7889 (m-30) REVERT: C 310 ARG cc_start: 0.8500 (ttm110) cc_final: 0.8076 (mtm110) REVERT: C 402 GLU cc_start: 0.7780 (tp30) cc_final: 0.7576 (tp30) REVERT: C 428 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8135 (ttmm) REVERT: C 525 SER cc_start: 0.8701 (m) cc_final: 0.8312 (p) REVERT: C 584 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7355 (ptp90) REVERT: C 645 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: C 657 TYR cc_start: 0.8557 (p90) cc_final: 0.8324 (p90) REVERT: C 763 LYS cc_start: 0.7666 (mttt) cc_final: 0.7340 (mmmt) REVERT: C 950 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7991 (pttm) REVERT: C 962 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: C 1063 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: D 143 MET cc_start: 0.6802 (ttt) cc_final: 0.6127 (tpt) REVERT: D 215 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6522 (pp20) REVERT: D 288 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7668 (mtpp) REVERT: D 392 THR cc_start: 0.9086 (p) cc_final: 0.8802 (t) REVERT: D 663 MET cc_start: 0.8956 (tpp) cc_final: 0.8479 (tpp) REVERT: D 866 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7603 (mtm-85) REVERT: D 1087 ARG cc_start: 0.7295 (tpt-90) cc_final: 0.6954 (tpp80) REVERT: D 1088 VAL cc_start: 0.7835 (OUTLIER) cc_final: 0.7403 (m) REVERT: D 1097 ARG cc_start: 0.3535 (OUTLIER) cc_final: 0.2247 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8297 (mp) cc_final: 0.7975 (tp) REVERT: E 33 LEU cc_start: 0.7619 (tp) cc_final: 0.7323 (mp) REVERT: E 87 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6959 (tm) outliers start: 69 outliers final: 37 residues processed: 303 average time/residue: 0.4363 time to fit residues: 201.3581 Evaluate side-chains 276 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 3.309 ------------------------------------------------------------------------------- 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 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 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 200 ASN 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 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 645 GLU Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 839 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 1037 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 181 LEU 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 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 1010 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 193 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 194 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 297 optimal weight: 0.4980 chunk 227 optimal weight: 0.5980 chunk 15 optimal weight: 0.3980 chunk 236 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 435 GLN C 493 ASN D 239 ASN ** 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 = 0.4065 r_free = 0.4065 target = 0.174579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121337 restraints weight = 33708.300| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.80 r_work: 0.3256 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25184 Z= 0.163 Angle : 0.523 10.133 34530 Z= 0.276 Chirality : 0.041 0.159 3967 Planarity : 0.004 0.046 4212 Dihedral : 15.696 179.421 4389 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.05 % Favored : 94.74 % Rotamer: Outliers : 2.54 % Allowed : 13.13 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2910 helix: 1.48 (0.17), residues: 1048 sheet: -0.30 (0.27), residues: 381 loop : -0.99 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 70 HIS 0.005 0.001 HIS D 94 PHE 0.017 0.001 PHE C 252 TYR 0.010 0.001 TYR A 168 ARG 0.011 0.000 ARG C 620 *********************** 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 314 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 252 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.7697 (mm) cc_final: 0.7451 (mp) REVERT: A 123 MET cc_start: 0.8266 (tmm) cc_final: 0.8061 (tmm) REVERT: B 133 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7342 (mmtt) REVERT: C 114 ASP cc_start: 0.8085 (m-30) cc_final: 0.7852 (m-30) REVERT: C 310 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8222 (mtm110) REVERT: C 428 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8243 (ttmm) REVERT: C 525 SER cc_start: 0.8708 (m) cc_final: 0.8331 (p) REVERT: C 584 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7273 (ptp90) REVERT: C 645 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: C 657 TYR cc_start: 0.8579 (p90) cc_final: 0.8372 (p90) REVERT: C 661 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7968 (tpt) REVERT: C 950 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7983 (pttm) REVERT: C 962 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: C 1063 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: D 140 ASP cc_start: 0.7802 (t0) cc_final: 0.7457 (t70) REVERT: D 143 MET cc_start: 0.6815 (ttt) cc_final: 0.6253 (tpt) REVERT: D 215 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6809 (pp20) REVERT: D 288 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7755 (mtpp) REVERT: D 392 THR cc_start: 0.9007 (p) cc_final: 0.8790 (t) REVERT: D 866 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7456 (mtm-85) REVERT: D 985 THR cc_start: 0.9333 (p) cc_final: 0.9077 (p) REVERT: D 1087 ARG cc_start: 0.7392 (tpt-90) cc_final: 0.7101 (tpp80) REVERT: D 1088 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7509 (m) REVERT: D 1097 ARG cc_start: 0.3511 (OUTLIER) cc_final: 0.2135 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8303 (mp) cc_final: 0.8014 (tp) REVERT: E 33 LEU cc_start: 0.7750 (tp) cc_final: 0.7530 (mp) REVERT: E 87 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6953 (tm) outliers start: 62 outliers final: 38 residues processed: 298 average time/residue: 0.4237 time to fit residues: 192.5214 Evaluate side-chains 279 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 2.831 ------------------------------------------------------------------------------- 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 89 GLU Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 127 THR 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 150 VAL Chi-restraints excluded: chain B residue 200 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 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 645 GLU Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 789 ILE 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 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 443 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 156 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3993 r_free = 0.3993 target = 0.158644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110420 restraints weight = 31066.993| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.15 r_work: 0.3149 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 25184 Z= 0.259 Angle : 0.551 7.352 34530 Z= 0.291 Chirality : 0.042 0.167 3967 Planarity : 0.004 0.050 4212 Dihedral : 15.708 179.795 4389 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 2.82 % Allowed : 14.03 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2910 helix: 1.37 (0.16), residues: 1047 sheet: -0.36 (0.26), residues: 398 loop : -1.05 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 70 HIS 0.005 0.001 HIS D 94 PHE 0.024 0.001 PHE C 153 TYR 0.014 0.001 TYR A 168 ARG 0.014 0.000 ARG C 797 *********************** 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 310 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 241 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ILE cc_start: 0.7830 (mm) cc_final: 0.7569 (mp) REVERT: B 133 LYS cc_start: 0.7820 (ttmt) cc_final: 0.7417 (mmtt) REVERT: C 114 ASP cc_start: 0.8185 (m-30) cc_final: 0.7960 (m-30) REVERT: C 296 LEU cc_start: 0.7207 (tm) cc_final: 0.6872 (tp) REVERT: C 310 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8269 (mtm110) REVERT: C 428 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8319 (ttmm) REVERT: C 525 SER cc_start: 0.8801 (m) cc_final: 0.8469 (p) REVERT: C 584 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7487 (ptp90) REVERT: C 645 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: C 661 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8203 (tpt) REVERT: C 950 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7870 (pttm) REVERT: C 962 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: C 1063 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7765 (m-80) REVERT: D 140 ASP cc_start: 0.7909 (t0) cc_final: 0.7575 (t70) REVERT: D 143 MET cc_start: 0.6813 (ttt) cc_final: 0.6433 (tpt) REVERT: D 215 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6724 (pp20) REVERT: D 392 THR cc_start: 0.9032 (p) cc_final: 0.8818 (t) REVERT: D 688 MET cc_start: 0.8868 (mmt) cc_final: 0.8379 (mmt) REVERT: D 741 ARG cc_start: 0.7464 (mtp-110) cc_final: 0.7098 (ptt-90) REVERT: D 866 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7702 (mtm-85) REVERT: D 985 THR cc_start: 0.9403 (p) cc_final: 0.9165 (p) REVERT: D 1087 ARG cc_start: 0.7486 (tpt-90) cc_final: 0.7185 (tpp80) REVERT: D 1088 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7579 (m) REVERT: D 1097 ARG cc_start: 0.3444 (OUTLIER) cc_final: 0.2087 (ptp-170) REVERT: D 1176 LEU cc_start: 0.8388 (mp) cc_final: 0.8115 (tp) REVERT: E 33 LEU cc_start: 0.7894 (tp) cc_final: 0.7663 (mp) REVERT: E 87 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6863 (tm) outliers start: 69 outliers final: 47 residues processed: 294 average time/residue: 0.3805 time to fit residues: 170.0530 Evaluate side-chains 285 residues out of total 2467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 89 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 54 ILE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 103 MET 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 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 645 GLU Chi-restraints excluded: chain C residue 661 MET 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 1037 VAL Chi-restraints excluded: chain C residue 1038 ASP Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 222 ILE 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 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 977 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 109 optimal weight: 1.9990 chunk 251 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 285 optimal weight: 0.9980 chunk 126 optimal weight: 0.0970 chunk 163 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: