Starting phenix.real_space_refine on Sun Jun 29 10:49:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kev_62295/06_2025/9kev_62295.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kev_62295/06_2025/9kev_62295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kev_62295/06_2025/9kev_62295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kev_62295/06_2025/9kev_62295.map" model { file = "/net/cci-nas-00/data/ceres_data/9kev_62295/06_2025/9kev_62295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kev_62295/06_2025/9kev_62295.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 197 5.49 5 Mg 1 5.21 5 S 95 5.16 5 C 20973 2.51 5 N 6107 2.21 5 O 6946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34321 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2143 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 266} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1748 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 219} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8554 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 9838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 9838 Classifications: {'peptide': 1263} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 59, 'TRANS': 1202} Chain breaks: 2 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "H" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2044 Classifications: {'DNA': 99} Link IDs: {'rna3p': 98} Chain: "G" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2007 Classifications: {'DNA': 98} Link IDs: {'rna3p': 97} Chain breaks: 1 Chain: "F" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2529 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 313} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "J" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 801 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 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 19488 SG CYS D 891 72.414 68.760 56.594 1.00 94.33 S ATOM 20055 SG CYS D 968 73.282 70.558 59.834 1.00121.84 S ATOM 20097 SG CYS D 975 76.085 69.741 57.309 1.00119.85 S ATOM 20115 SG CYS D 978 73.613 72.325 56.466 1.00110.71 S ATOM 12942 SG CYS D 60 92.213 48.669 118.882 1.00152.52 S ATOM 13069 SG CYS D 75 88.740 45.711 119.210 1.00159.46 S ATOM 13095 SG CYS D 78 88.192 48.171 118.622 1.00160.51 S Time building chain proxies: 23.75, per 1000 atoms: 0.69 Number of scatterers: 34321 At special positions: 0 Unit cell: (248.4, 155.4, 161.4, 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 95 16.00 P 197 15.00 Mg 1 11.99 O 6946 8.00 N 6107 7.00 C 20973 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: 9.43 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " Number of angles added : 6 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7178 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 52 sheets defined 44.2% alpha, 14.5% beta 82 base pairs and 140 stacking pairs defined. Time for finding SS restraints: 13.89 Creating SS restraints... Processing helix chain 'A' and resid 29 through 45 removed outlier: 4.212A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 3.520A 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 151 through 155 Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.649A pdb=" N LEU A 218 " --> pdb=" O THR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.734A pdb=" N LEU A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 632 removed outlier: 3.592A pdb=" N ASP A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 651 Processing helix chain 'B' and resid 29 through 46 removed outlier: 4.148A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 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 Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.078A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.741A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) 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 301 removed outlier: 3.553A pdb=" N ALA C 292 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.555A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 537 removed outlier: 3.801A pdb=" N ASP C 537 " --> pdb=" O ALA C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 533 through 537' Processing helix chain 'C' and resid 590 through 594 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 613 removed outlier: 4.057A pdb=" N ARG C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 4.323A pdb=" N ARG C 633 " --> pdb=" O GLY C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 778 through 782 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 856 through 858 No H-bonds generated for 'chain 'C' and resid 856 through 858' Processing helix chain 'C' and resid 920 through 926 removed outlier: 4.290A pdb=" N ARG C 924 " --> pdb=" O HIS C 920 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 943 removed outlier: 4.247A pdb=" N ILE C 931 " --> pdb=" O ASN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1040 Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1090 removed outlier: 4.082A pdb=" N LEU C1085 " --> pdb=" O ALA C1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 1095 through 1109 Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.655A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 140 through 186 removed outlier: 4.926A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.872A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.711A pdb=" N TYR D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.203A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 340 through 361 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 393 through 397 removed outlier: 3.895A pdb=" N ARG D 397 " --> pdb=" O PRO D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 482 No H-bonds generated for 'chain 'D' and resid 480 through 482' Processing helix chain 'D' and resid 483 through 492 removed outlier: 3.783A 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 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 578 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 652 Processing helix chain 'D' and resid 668 through 677 Processing helix chain 'D' and resid 689 through 703 Processing helix chain 'D' and resid 705 through 727 removed outlier: 4.104A pdb=" N THR D 725 " --> pdb=" O PHE D 721 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG D 726 " --> pdb=" O TYR D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 762 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 818 Processing helix chain 'D' and resid 845 through 882 removed outlier: 3.531A pdb=" N ALA D 864 " --> pdb=" O LEU D 860 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA D 868 " --> pdb=" O ALA D 864 " (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 Processing helix chain 'D' and resid 1006 through 1010 Processing helix chain 'D' and resid 1027 through 1037 Processing helix chain 'D' and resid 1117 through 1144 Proline residue: D1127 - end of helix removed outlier: 3.739A pdb=" N VAL D1130 " --> pdb=" O GLY D1126 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1162 removed outlier: 4.364A pdb=" N ILE D1154 " --> pdb=" O HIS D1150 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1195 removed outlier: 3.650A pdb=" N ALA D1195 " --> pdb=" O ARG D1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 1209 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 removed outlier: 3.648A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 49 through 71 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 212 through 221 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 removed outlier: 4.111A pdb=" N GLU F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.943A pdb=" N ASP F 280 " --> pdb=" O ALA F 276 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N MET F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.700A pdb=" N LYS F 339 " --> pdb=" O ASP F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.812A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 removed outlier: 3.819A pdb=" N VAL F 375 " --> pdb=" O HIS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 404 Processing helix chain 'F' and resid 406 through 417 Processing helix chain 'F' and resid 434 through 438 Processing helix chain 'F' and resid 448 through 467 removed outlier: 3.609A pdb=" N LEU F 467 " --> pdb=" O VAL F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 525 removed outlier: 4.315A pdb=" N ASP F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 188 Processing helix chain 'J' and resid 194 through 202 Processing helix chain 'J' and resid 212 through 226 Processing helix chain 'K' and resid 175 through 188 Processing helix chain 'K' and resid 194 through 203 Processing helix chain 'K' and resid 211 through 226 removed outlier: 4.012A pdb=" N GLU K 215 " --> pdb=" O VAL K 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS K 224 " --> pdb=" O TYR K 220 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP K 226 " --> pdb=" O ARG K 222 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 188 Processing helix chain 'M' and resid 194 through 202 Processing helix chain 'M' and resid 212 through 226 removed outlier: 3.627A pdb=" N ASP M 226 " --> pdb=" O ARG M 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 188 removed outlier: 3.739A pdb=" N ASN L 188 " --> pdb=" O TYR L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 202 Processing helix chain 'L' and resid 211 through 226 removed outlier: 3.721A pdb=" N GLU L 215 " --> pdb=" O VAL L 211 " (cutoff:3.500A) Processing helix chain 'N' and resid 175 through 188 Processing helix chain 'N' and resid 194 through 202 Processing helix chain 'N' and resid 211 through 226 removed outlier: 3.799A pdb=" N GLU N 215 " --> pdb=" O VAL N 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 188 Processing helix chain 'O' and resid 194 through 202 Processing helix chain 'O' and resid 211 through 225 removed outlier: 3.700A pdb=" N GLU O 215 " --> pdb=" O VAL O 211 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.622A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.970A 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 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.741A pdb=" N ARG B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.549A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 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: 6.392A 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: 5.304A pdb=" N LEU C 105 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE C 140 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N PHE C 107 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU C 138 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASP C 109 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR C 136 " --> pdb=" O ASP C 109 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.548A 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: 6.808A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER C 499 " --> pdb=" O CYS C 484 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.597A pdb=" N HIS C 200 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AB8, first strand: chain 'C' and resid 505 through 506 removed outlier: 7.341A pdb=" N ILE C 512 " --> pdb=" O LEU C 531 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU C 531 " --> pdb=" O ILE C 512 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR C 514 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 529 " --> pdb=" O THR C 514 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR C 516 " --> pdb=" O GLU C 527 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU C 527 " --> pdb=" O TYR C 516 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS C 518 " --> pdb=" O SER C 525 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC1, first strand: chain 'C' and resid 558 through 562 Processing sheet with id=AC2, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.670A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 667 through 671 removed outlier: 3.713A pdb=" N GLU C 652 " --> pdb=" O THR C 659 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N MET C 661 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE C 650 " --> pdb=" O MET C 661 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.916A pdb=" N ILE C 735 " --> pdb=" O LYS C 897 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU C 899 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU C 737 " --> pdb=" O LEU C 899 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ILE C 915 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU C 720 " --> pdb=" O ILE C 915 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LEU C 917 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA C 722 " --> pdb=" O LEU C 917 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 765 through 766 removed outlier: 6.609A pdb=" N ASP C 761 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL C 865 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC8, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.844A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD1, first strand: chain 'C' and resid 1042 through 1044 removed outlier: 7.844A pdb=" N ILE D 522 " --> pdb=" O ARG D 427 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL D 429 " --> pdb=" O ILE D 522 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU D 524 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL D 431 " --> pdb=" O LEU D 524 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AD3, first strand: chain 'C' and resid 1136 through 1138 Processing sheet with id=AD4, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.635A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 233 through 235 removed outlier: 3.907A pdb=" N GLN D 233 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 328 through 329 Processing sheet with id=AD7, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD8, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AD9, first strand: chain 'D' and resid 897 through 899 removed outlier: 4.478A pdb=" N THR D 924 " --> pdb=" O ARG D 963 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1043 through 1044 Processing sheet with id=AE2, first strand: chain 'D' and resid 1051 through 1056 Processing sheet with id=AE3, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 4.491A pdb=" N ARG D1164 " --> pdb=" O VAL D1206 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL D1206 " --> pdb=" O ARG D1164 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE5, first strand: chain 'J' and resid 151 through 153 Processing sheet with id=AE6, first strand: chain 'J' and resid 233 through 236 Processing sheet with id=AE7, first strand: chain 'K' and resid 151 through 153 Processing sheet with id=AE8, first strand: chain 'K' and resid 233 through 236 Processing sheet with id=AE9, first strand: chain 'M' and resid 151 through 153 Processing sheet with id=AF1, first strand: chain 'M' and resid 235 through 236 Processing sheet with id=AF2, first strand: chain 'L' and resid 151 through 153 Processing sheet with id=AF3, first strand: chain 'L' and resid 193 through 194 Processing sheet with id=AF4, first strand: chain 'N' and resid 151 through 153 removed outlier: 3.803A pdb=" N GLU N 164 " --> pdb=" O ASP N 159 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 233 through 236 Processing sheet with id=AF6, first strand: chain 'O' and resid 151 through 153 Processing sheet with id=AF7, first strand: chain 'O' and resid 233 through 236 1454 hydrogen bonds defined for protein. 4053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 213 hydrogen bonds 422 hydrogen bond angles 0 basepair planarities 82 basepair parallelities 140 stacking parallelities Total time for adding SS restraints: 20.47 Time building geometry restraints manager: 11.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9719 1.33 - 1.46: 6710 1.46 - 1.58: 18349 1.58 - 1.70: 392 1.70 - 1.82: 167 Bond restraints: 35337 Sorted by residual: bond pdb=" CA GLU A 224 " pdb=" C GLU A 224 " ideal model delta sigma weight residual 1.522 1.585 -0.064 1.72e-02 3.38e+03 1.37e+01 bond pdb=" N LEU L 182 " pdb=" CA LEU L 182 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.72e+00 bond pdb=" N ASP A 90 " pdb=" CA ASP A 90 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.62e+00 bond pdb=" N ARG L 183 " pdb=" CA ARG L 183 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.06e+00 bond pdb=" C GLN K 170 " pdb=" N PRO K 171 " ideal model delta sigma weight residual 1.332 1.356 -0.024 1.30e-02 5.92e+03 3.40e+00 ... (remaining 35332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 47778 1.94 - 3.87: 848 3.87 - 5.81: 96 5.81 - 7.74: 21 7.74 - 9.68: 5 Bond angle restraints: 48748 Sorted by residual: angle pdb=" N VAL M 239 " pdb=" CA VAL M 239 " pdb=" C VAL M 239 " ideal model delta sigma weight residual 113.20 107.92 5.28 9.60e-01 1.09e+00 3.02e+01 angle pdb=" CA LYS B 213 " pdb=" CB LYS B 213 " pdb=" CG LYS B 213 " ideal model delta sigma weight residual 114.10 123.01 -8.91 2.00e+00 2.50e-01 1.99e+01 angle pdb=" CA TRP K 166 " pdb=" CB TRP K 166 " pdb=" CG TRP K 166 " ideal model delta sigma weight residual 113.60 121.79 -8.19 1.90e+00 2.77e-01 1.86e+01 angle pdb=" CB LYS K 167 " pdb=" CG LYS K 167 " pdb=" CD LYS K 167 " ideal model delta sigma weight residual 111.30 120.97 -9.67 2.30e+00 1.89e-01 1.77e+01 angle pdb=" CA LYS K 167 " pdb=" CB LYS K 167 " pdb=" CG LYS K 167 " ideal model delta sigma weight residual 114.10 121.61 -7.51 2.00e+00 2.50e-01 1.41e+01 ... (remaining 48743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 19343 35.54 - 71.07: 1478 71.07 - 106.61: 59 106.61 - 142.15: 10 142.15 - 177.69: 9 Dihedral angle restraints: 20899 sinusoidal: 9743 harmonic: 11156 Sorted by residual: dihedral pdb=" CA LYS K 230 " pdb=" C LYS K 230 " pdb=" N ARG K 231 " pdb=" CA ARG K 231 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL K 165 " pdb=" C VAL K 165 " pdb=" N TRP K 166 " pdb=" CA TRP K 166 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA VAL D 110 " pdb=" C VAL D 110 " pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 20896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4544 0.051 - 0.102: 851 0.102 - 0.153: 168 0.153 - 0.203: 6 0.203 - 0.254: 2 Chirality restraints: 5571 Sorted by residual: chirality pdb=" CB THR C 992 " pdb=" CA THR C 992 " pdb=" OG1 THR C 992 " pdb=" CG2 THR C 992 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU M 221 " pdb=" CB LEU M 221 " pdb=" CD1 LEU M 221 " pdb=" CD2 LEU M 221 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA GLN C 232 " pdb=" N GLN C 232 " pdb=" C GLN C 232 " pdb=" CB GLN C 232 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 5568 not shown) Planarity restraints: 5662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 195 " -0.062 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO K 196 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO K 196 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO K 196 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN J 170 " -0.060 5.00e-02 4.00e+02 9.04e-02 1.31e+01 pdb=" N PRO J 171 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO J 171 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO J 171 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 320 " -0.042 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO D 321 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 321 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 321 " -0.036 5.00e-02 4.00e+02 ... (remaining 5659 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 354 2.56 - 3.14: 26890 3.14 - 3.73: 58791 3.73 - 4.31: 74219 4.31 - 4.90: 121559 Nonbonded interactions: 281813 Sorted by model distance: nonbonded pdb=" OD1 ASP D 535 " pdb="MG MG D2002 " model vdw 1.969 2.170 nonbonded pdb=" N ASP D 537 " pdb="MG MG D2002 " model vdw 2.055 2.250 nonbonded pdb=" OD1 ASP J 210 " pdb=" N VAL J 211 " model vdw 2.153 3.120 nonbonded pdb=" C ASP D 535 " pdb="MG MG D2002 " model vdw 2.188 2.400 nonbonded pdb=" NH1 ARG D 77 " pdb="ZN ZN D2001 " model vdw 2.189 2.310 ... (remaining 281808 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 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 160.920 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: 0.040 Extract box with map and model: 2.180 Check model and map are aligned: 0.290 Set scattering table: 0.340 Process input model: 104.610 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.220 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: 0.020 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 272.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.003 0.075 35344 Z= 0.138 Angle : 0.605 9.679 48754 Z= 0.329 Chirality : 0.041 0.254 5571 Planarity : 0.004 0.092 5662 Dihedral : 21.680 177.686 13721 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.37 % Allowed : 33.93 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.28 (0.14), residues: 3859 helix: 1.46 (0.14), residues: 1565 sheet: 0.15 (0.27), residues: 390 loop : -0.89 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP N 166 HIS 0.012 0.001 HIS C 841 PHE 0.042 0.001 PHE M 185 TYR 0.044 0.001 TYR M 220 ARG 0.007 0.000 ARG D1054 Details of bonding type rmsd hydrogen bonds : bond 0.06619 ( 1665) hydrogen bonds : angle 4.66275 ( 4475) metal coordination : bond 0.00363 ( 7) metal coordination : angle 2.64727 ( 6) covalent geometry : bond 0.00295 (35337) covalent geometry : angle 0.60433 (48748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 353 time to evaluate : 5.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8482 (tt0) cc_final: 0.8243 (tt0) REVERT: A 90 ASP cc_start: 0.8521 (p0) cc_final: 0.8278 (p0) REVERT: D 515 MET cc_start: 0.8108 (mtt) cc_final: 0.7879 (mtt) REVERT: F 330 ARG cc_start: 0.8399 (tpt90) cc_final: 0.8161 (tpt90) outliers start: 12 outliers final: 8 residues processed: 359 average time/residue: 0.8514 time to fit residues: 497.7267 Evaluate side-chains 343 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 335 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain M residue 177 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 10.0000 chunk 303 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 204 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 313 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 363 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 79 ASN B 226 ASN C 387 ASN C 612 GLN ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 HIS ** D 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 HIS ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS N 163 HIS ** N 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.109338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.090477 restraints weight = 121455.773| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.21 r_work: 0.3234 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.118 35344 Z= 0.405 Angle : 0.754 12.433 48754 Z= 0.400 Chirality : 0.048 0.188 5571 Planarity : 0.006 0.065 5662 Dihedral : 22.066 179.328 6413 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 6.43 % Allowed : 29.74 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: -0.08 (0.14), residues: 3859 helix: 1.06 (0.13), residues: 1585 sheet: -0.02 (0.28), residues: 359 loop : -1.01 (0.14), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 166 HIS 0.008 0.002 HIS C 841 PHE 0.026 0.002 PHE M 185 TYR 0.033 0.002 TYR M 220 ARG 0.013 0.001 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.06587 ( 1665) hydrogen bonds : angle 4.85988 ( 4475) metal coordination : bond 0.01600 ( 7) metal coordination : angle 3.30117 ( 6) covalent geometry : bond 0.00935 (35337) covalent geometry : angle 0.75330 (48748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 325 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8213 (mm-30) REVERT: A 90 ASP cc_start: 0.8809 (p0) cc_final: 0.8561 (p0) REVERT: A 120 ASN cc_start: 0.8121 (p0) cc_final: 0.7920 (p0) REVERT: C 231 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7390 (mtm-85) REVERT: C 569 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: C 607 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8869 (mtm) REVERT: C 679 ASN cc_start: 0.9349 (OUTLIER) cc_final: 0.9092 (m-40) REVERT: D 155 MET cc_start: 0.8554 (tpp) cc_final: 0.8064 (tmm) REVERT: D 480 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8693 (mmt90) REVERT: D 515 MET cc_start: 0.8517 (mtt) cc_final: 0.8271 (mtt) REVERT: D 1097 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6934 (mtt90) REVERT: D 1104 HIS cc_start: 0.6784 (OUTLIER) cc_final: 0.6265 (t-90) REVERT: D 1208 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.9145 (ptm) REVERT: E 41 ASP cc_start: 0.8698 (p0) cc_final: 0.8413 (p0) REVERT: J 167 LYS cc_start: 0.8371 (ptmt) cc_final: 0.7989 (pptt) REVERT: J 170 GLN cc_start: 0.8421 (pm20) cc_final: 0.7578 (pm20) REVERT: J 210 ASP cc_start: 0.8446 (t0) cc_final: 0.8219 (t0) REVERT: J 241 TYR cc_start: 0.9300 (m-80) cc_final: 0.9041 (m-80) REVERT: K 167 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6801 (mmtp) REVERT: M 207 PHE cc_start: 0.7581 (t80) cc_final: 0.7298 (t80) REVERT: M 231 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7233 (ptp90) REVERT: L 229 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6856 (tp30) REVERT: N 174 LEU cc_start: 0.1440 (OUTLIER) cc_final: 0.1180 (mt) REVERT: N 204 ARG cc_start: 0.8221 (mpp-170) cc_final: 0.7846 (mpp-170) outliers start: 209 outliers final: 132 residues processed: 493 average time/residue: 0.4645 time to fit residues: 376.7200 Evaluate side-chains 457 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 313 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 679 ASN Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 480 ARG Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 583 THR Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 785 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 832 ILE Chi-restraints excluded: chain D residue 845 THR Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 881 SER Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1097 ARG Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1193 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 212 ASN Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 201 HIS Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 229 GLU Chi-restraints excluded: chain N residue 166 TRP Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 197 LYS Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain N residue 236 LEU Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 212 ASN Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 231 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 275 optimal weight: 0.8980 chunk 344 optimal weight: 0.8980 chunk 317 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 325 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN C 442 GLN C 679 ASN ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 GLN D 854 HIS D1251 ASN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS L 163 HIS N 163 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.114509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.095859 restraints weight = 118825.744| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.25 r_work: 0.3321 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35344 Z= 0.136 Angle : 0.590 10.404 48754 Z= 0.316 Chirality : 0.041 0.167 5571 Planarity : 0.004 0.064 5662 Dihedral : 22.005 178.360 6406 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.93 % Allowed : 30.02 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.20 (0.14), residues: 3859 helix: 1.35 (0.13), residues: 1572 sheet: 0.10 (0.28), residues: 364 loop : -0.90 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 166 HIS 0.010 0.001 HIS C 841 PHE 0.039 0.001 PHE M 185 TYR 0.045 0.001 TYR M 220 ARG 0.006 0.000 ARG M 150 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 1665) hydrogen bonds : angle 4.46370 ( 4475) metal coordination : bond 0.00331 ( 7) metal coordination : angle 2.04124 ( 6) covalent geometry : bond 0.00305 (35337) covalent geometry : angle 0.58912 (48748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 348 time to evaluate : 9.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8719 (tttt) REVERT: A 71 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8159 (mm-30) REVERT: A 90 ASP cc_start: 0.8762 (p0) cc_final: 0.8493 (p0) REVERT: A 120 ASN cc_start: 0.7960 (p0) cc_final: 0.7498 (p0) REVERT: B 179 ASP cc_start: 0.8285 (t70) cc_final: 0.7972 (t70) REVERT: C 232 GLN cc_start: 0.8189 (mp10) cc_final: 0.7556 (mp10) REVERT: C 569 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: C 607 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8718 (mtm) REVERT: C 667 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8993 (ptp-110) REVERT: C 926 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8115 (mpp) REVERT: C 999 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: D 155 MET cc_start: 0.8499 (tpp) cc_final: 0.7986 (tmm) REVERT: D 297 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8607 (mtmt) REVERT: D 414 ARG cc_start: 0.9520 (OUTLIER) cc_final: 0.8718 (mtp180) REVERT: D 497 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8754 (pp) REVERT: D 1208 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.9111 (ptm) REVERT: E 45 ASP cc_start: 0.8751 (p0) cc_final: 0.8508 (p0) REVERT: E 46 ARG cc_start: 0.8827 (mtt90) cc_final: 0.8599 (mtt90) REVERT: F 377 ASN cc_start: 0.8842 (m-40) cc_final: 0.8632 (m110) REVERT: J 210 ASP cc_start: 0.8487 (t0) cc_final: 0.8266 (t0) REVERT: K 167 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.6889 (mmtp) REVERT: K 183 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7788 (tpt170) REVERT: M 153 PHE cc_start: 0.7707 (t80) cc_final: 0.7097 (t80) REVERT: M 207 PHE cc_start: 0.7426 (t80) cc_final: 0.7184 (t80) REVERT: M 222 ARG cc_start: 0.8726 (tpt90) cc_final: 0.8520 (tpt90) REVERT: M 229 GLU cc_start: 0.8918 (mp0) cc_final: 0.8642 (mp0) REVERT: M 231 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7184 (ptp90) REVERT: L 229 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6762 (tp30) REVERT: N 174 LEU cc_start: 0.1404 (OUTLIER) cc_final: 0.0848 (mt) outliers start: 160 outliers final: 90 residues processed: 477 average time/residue: 0.7889 time to fit residues: 618.5942 Evaluate side-chains 431 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 326 time to evaluate : 6.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 667 THR Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 416 TYR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 212 ASN Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain L residue 229 GLU Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 197 LYS Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 231 ARG Chi-restraints excluded: chain O residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 163 optimal weight: 9.9990 chunk 343 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 350 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 chunk 282 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 HIS N 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.114772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095935 restraints weight = 119199.177| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.37 r_work: 0.3323 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35344 Z= 0.141 Angle : 0.572 11.242 48754 Z= 0.306 Chirality : 0.041 0.209 5571 Planarity : 0.004 0.063 5662 Dihedral : 21.899 177.348 6403 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.11 % Allowed : 29.83 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.27 (0.14), residues: 3859 helix: 1.43 (0.14), residues: 1566 sheet: 0.09 (0.27), residues: 374 loop : -0.86 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 166 HIS 0.010 0.001 HIS C 841 PHE 0.037 0.001 PHE M 185 TYR 0.042 0.001 TYR M 220 ARG 0.015 0.000 ARG O 244 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 1665) hydrogen bonds : angle 4.35489 ( 4475) metal coordination : bond 0.00334 ( 7) metal coordination : angle 1.69217 ( 6) covalent geometry : bond 0.00321 (35337) covalent geometry : angle 0.57216 (48748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 352 time to evaluate : 3.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8119 (mm-30) REVERT: A 78 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9301 (mp) REVERT: A 90 ASP cc_start: 0.8800 (p0) cc_final: 0.8507 (p0) REVERT: A 120 ASN cc_start: 0.7760 (p0) cc_final: 0.7178 (p0) REVERT: B 179 ASP cc_start: 0.8365 (t70) cc_final: 0.8003 (t70) REVERT: B 189 PHE cc_start: 0.8254 (m-80) cc_final: 0.7988 (m-80) REVERT: C 231 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6888 (mtm-85) REVERT: C 232 GLN cc_start: 0.8144 (mp10) cc_final: 0.7698 (mp10) REVERT: C 569 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: C 607 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8695 (mtm) REVERT: C 667 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.9012 (ptp-110) REVERT: C 999 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8680 (m-30) REVERT: D 155 MET cc_start: 0.8526 (tpp) cc_final: 0.8021 (tmm) REVERT: D 297 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8579 (mttt) REVERT: D 383 ASP cc_start: 0.8998 (OUTLIER) cc_final: 0.8719 (m-30) REVERT: D 414 ARG cc_start: 0.9514 (OUTLIER) cc_final: 0.8718 (mtp180) REVERT: D 497 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8696 (pp) REVERT: D 576 MET cc_start: 0.8676 (tpp) cc_final: 0.8324 (tpp) REVERT: D 944 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9030 (tt) REVERT: F 477 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8960 (mm) REVERT: J 210 ASP cc_start: 0.8447 (t0) cc_final: 0.8240 (t0) REVERT: K 183 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7720 (tpt170) REVERT: M 153 PHE cc_start: 0.7773 (t80) cc_final: 0.7330 (t80) REVERT: M 207 PHE cc_start: 0.7475 (t80) cc_final: 0.7153 (t80) REVERT: M 229 GLU cc_start: 0.8917 (mp0) cc_final: 0.8695 (mp0) REVERT: M 231 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7177 (ptp90) REVERT: N 174 LEU cc_start: 0.1371 (OUTLIER) cc_final: 0.0813 (mt) REVERT: N 235 THR cc_start: 0.6829 (OUTLIER) cc_final: 0.6605 (m) outliers start: 166 outliers final: 103 residues processed: 492 average time/residue: 0.4980 time to fit residues: 395.2734 Evaluate side-chains 439 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 320 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 416 TYR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain N residue 235 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 231 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 78 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 363 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 318 optimal weight: 0.9980 chunk 256 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 169 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 GLN ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 201 HIS M 163 HIS N 163 HIS ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.110155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.091110 restraints weight = 120749.152| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.30 r_work: 0.3248 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 35344 Z= 0.324 Angle : 0.701 11.689 48754 Z= 0.370 Chirality : 0.045 0.206 5571 Planarity : 0.005 0.063 5662 Dihedral : 22.079 176.961 6403 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.40 % Allowed : 29.71 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.00 (0.14), residues: 3859 helix: 1.13 (0.13), residues: 1582 sheet: -0.08 (0.28), residues: 354 loop : -0.94 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 166 HIS 0.010 0.001 HIS C 841 PHE 0.036 0.002 PHE M 185 TYR 0.040 0.002 TYR M 220 ARG 0.012 0.001 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.05750 ( 1665) hydrogen bonds : angle 4.68495 ( 4475) metal coordination : bond 0.01234 ( 7) metal coordination : angle 1.83280 ( 6) covalent geometry : bond 0.00750 (35337) covalent geometry : angle 0.70040 (48748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 319 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8301 (mm-30) REVERT: A 90 ASP cc_start: 0.8820 (p0) cc_final: 0.8586 (p0) REVERT: A 120 ASN cc_start: 0.8125 (p0) cc_final: 0.7782 (p0) REVERT: B 189 PHE cc_start: 0.8313 (m-80) cc_final: 0.8020 (m-80) REVERT: B 213 LYS cc_start: 0.8528 (pptt) cc_final: 0.8297 (pptt) REVERT: C 231 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.7097 (mtm-85) REVERT: C 232 GLN cc_start: 0.8232 (mp10) cc_final: 0.7543 (mp10) REVERT: C 569 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: C 607 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8795 (mtm) REVERT: C 667 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.9037 (ptp-110) REVERT: C 724 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8961 (ptt) REVERT: C 926 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8088 (mpp) REVERT: C 999 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8698 (m-30) REVERT: D 84 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8413 (mtp180) REVERT: D 155 MET cc_start: 0.8615 (tpp) cc_final: 0.8107 (tmm) REVERT: D 205 MET cc_start: 0.8320 (ptp) cc_final: 0.7691 (mmt) REVERT: D 297 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8542 (mttt) REVERT: D 383 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8837 (m-30) REVERT: D 497 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8890 (pp) REVERT: D 690 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.8500 (tptm) REVERT: D 944 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9093 (tt) REVERT: D 1104 HIS cc_start: 0.6754 (OUTLIER) cc_final: 0.6207 (t-90) REVERT: D 1208 MET cc_start: 0.9350 (OUTLIER) cc_final: 0.9117 (ptm) REVERT: F 281 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8147 (mmp) REVERT: F 390 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8158 (tt) REVERT: F 477 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8976 (mm) REVERT: J 241 TYR cc_start: 0.9240 (m-80) cc_final: 0.8914 (m-80) REVERT: M 150 ARG cc_start: 0.8858 (ttp-170) cc_final: 0.8347 (ttp-170) REVERT: M 153 PHE cc_start: 0.7853 (t80) cc_final: 0.7421 (t80) REVERT: M 229 GLU cc_start: 0.9019 (mp0) cc_final: 0.8720 (mp0) REVERT: M 231 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7177 (ptp90) REVERT: N 174 LEU cc_start: 0.1525 (OUTLIER) cc_final: 0.1260 (mt) REVERT: N 235 THR cc_start: 0.6822 (OUTLIER) cc_final: 0.6567 (m) outliers start: 208 outliers final: 148 residues processed: 491 average time/residue: 0.4849 time to fit residues: 388.5630 Evaluate side-chains 476 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 307 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 770 THR Chi-restraints excluded: chain C residue 807 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 738 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 825 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 879 ASP Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1252 VAL Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 410 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 201 HIS Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 223 ARG Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain N residue 166 TRP Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain N residue 231 ARG Chi-restraints excluded: chain N residue 235 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 309 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 371 optimal weight: 0.9990 chunk 341 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS L 163 HIS N 163 HIS ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.113948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095099 restraints weight = 118951.511| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.28 r_work: 0.3307 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35344 Z= 0.139 Angle : 0.593 12.778 48754 Z= 0.316 Chirality : 0.042 0.180 5571 Planarity : 0.004 0.063 5662 Dihedral : 22.038 178.089 6403 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.02 % Allowed : 31.07 % Favored : 63.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.20 (0.14), residues: 3859 helix: 1.34 (0.13), residues: 1565 sheet: 0.01 (0.28), residues: 360 loop : -0.85 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 166 HIS 0.019 0.001 HIS J 201 PHE 0.041 0.001 PHE M 185 TYR 0.042 0.001 TYR M 220 ARG 0.007 0.000 ARG D 214 Details of bonding type rmsd hydrogen bonds : bond 0.04196 ( 1665) hydrogen bonds : angle 4.40825 ( 4475) metal coordination : bond 0.00273 ( 7) metal coordination : angle 1.52521 ( 6) covalent geometry : bond 0.00314 (35337) covalent geometry : angle 0.59246 (48748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 336 time to evaluate : 3.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8279 (mm-30) REVERT: A 78 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9271 (mp) REVERT: A 90 ASP cc_start: 0.8735 (p0) cc_final: 0.8441 (p0) REVERT: A 120 ASN cc_start: 0.7863 (p0) cc_final: 0.7234 (p0) REVERT: B 189 PHE cc_start: 0.8345 (m-80) cc_final: 0.7893 (m-80) REVERT: C 211 TRP cc_start: 0.7583 (m-10) cc_final: 0.7296 (m-10) REVERT: C 231 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7028 (mtm-85) REVERT: C 232 GLN cc_start: 0.8154 (mp10) cc_final: 0.7433 (mp10) REVERT: C 467 ARG cc_start: 0.8197 (tpp80) cc_final: 0.7809 (tpp80) REVERT: C 569 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: C 607 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8707 (mtm) REVERT: C 667 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.9027 (ptp-110) REVERT: C 724 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8616 (ptt) REVERT: C 926 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8098 (mpp) REVERT: C 999 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8633 (m-30) REVERT: D 155 MET cc_start: 0.8623 (tpp) cc_final: 0.8099 (tmm) REVERT: D 297 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8606 (mtmt) REVERT: D 383 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8714 (m-30) REVERT: D 414 ARG cc_start: 0.9524 (OUTLIER) cc_final: 0.8772 (mtp180) REVERT: D 497 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8741 (pp) REVERT: D 944 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9018 (tt) REVERT: D 983 MET cc_start: 0.9020 (mmm) cc_final: 0.8705 (tmm) REVERT: D 1104 HIS cc_start: 0.6709 (OUTLIER) cc_final: 0.6213 (t-90) REVERT: D 1208 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.9057 (ptm) REVERT: F 281 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8047 (mmp) REVERT: F 390 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8085 (tt) REVERT: F 477 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8973 (mm) REVERT: J 201 HIS cc_start: 0.8901 (OUTLIER) cc_final: 0.8487 (t-90) REVERT: K 183 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7734 (tpt170) REVERT: M 150 ARG cc_start: 0.8851 (ttp-170) cc_final: 0.8535 (ttp-170) REVERT: M 153 PHE cc_start: 0.7723 (t80) cc_final: 0.7260 (t80) REVERT: M 231 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7063 (ptp90) REVERT: N 174 LEU cc_start: 0.1472 (OUTLIER) cc_final: 0.0961 (mt) REVERT: N 235 THR cc_start: 0.6808 (OUTLIER) cc_final: 0.6573 (m) outliers start: 163 outliers final: 116 residues processed: 469 average time/residue: 0.4953 time to fit residues: 375.2815 Evaluate side-chains 457 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 318 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1130 SER Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 201 HIS Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 212 ASN Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain N residue 166 TRP Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain N residue 235 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 239 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 332 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 300 optimal weight: 10.0000 chunk 377 optimal weight: 5.9990 chunk 251 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 ASN ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 HIS N 163 HIS ** N 170 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 = 0.3866 r_free = 0.3866 target = 0.112968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.094193 restraints weight = 120052.390| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 3.32 r_work: 0.3299 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35344 Z= 0.170 Angle : 0.600 11.935 48754 Z= 0.320 Chirality : 0.042 0.222 5571 Planarity : 0.004 0.063 5662 Dihedral : 21.999 177.903 6403 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.20 % Allowed : 31.37 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.20 (0.14), residues: 3859 helix: 1.33 (0.13), residues: 1571 sheet: -0.04 (0.27), residues: 380 loop : -0.85 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 166 HIS 0.011 0.001 HIS C 841 PHE 0.043 0.001 PHE M 185 TYR 0.044 0.001 TYR M 220 ARG 0.008 0.000 ARG D 211 Details of bonding type rmsd hydrogen bonds : bond 0.04379 ( 1665) hydrogen bonds : angle 4.42285 ( 4475) metal coordination : bond 0.00490 ( 7) metal coordination : angle 1.29991 ( 6) covalent geometry : bond 0.00392 (35337) covalent geometry : angle 0.60016 (48748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 332 time to evaluate : 4.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8308 (mm-30) REVERT: A 78 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9280 (mp) REVERT: A 90 ASP cc_start: 0.8746 (p0) cc_final: 0.8462 (p0) REVERT: A 109 ASP cc_start: 0.8279 (m-30) cc_final: 0.7823 (t0) REVERT: A 120 ASN cc_start: 0.7848 (p0) cc_final: 0.7212 (p0) REVERT: B 1 MET cc_start: 0.4708 (OUTLIER) cc_final: 0.4507 (mtp) REVERT: C 211 TRP cc_start: 0.7565 (m-10) cc_final: 0.7285 (m-10) REVERT: C 231 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7033 (mtm-85) REVERT: C 232 GLN cc_start: 0.8149 (mp10) cc_final: 0.7415 (mp10) REVERT: C 263 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8431 (mm-30) REVERT: C 569 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: C 607 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8671 (mtm) REVERT: C 667 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.9057 (ptp-110) REVERT: C 724 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8725 (ptt) REVERT: C 926 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8082 (mpp) REVERT: C 999 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8670 (m-30) REVERT: D 155 MET cc_start: 0.8628 (tpp) cc_final: 0.8109 (tmm) REVERT: D 297 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8582 (mtmt) REVERT: D 383 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8779 (m-30) REVERT: D 414 ARG cc_start: 0.9523 (OUTLIER) cc_final: 0.8758 (mtp180) REVERT: D 497 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8781 (pp) REVERT: D 576 MET cc_start: 0.8703 (tpp) cc_final: 0.8395 (tpp) REVERT: D 690 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8495 (tptm) REVERT: D 944 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9026 (tt) REVERT: D 1104 HIS cc_start: 0.6690 (OUTLIER) cc_final: 0.6203 (t-90) REVERT: D 1208 MET cc_start: 0.9332 (OUTLIER) cc_final: 0.9094 (ptm) REVERT: D 1212 LYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8903 (mtmm) REVERT: E 41 ASP cc_start: 0.8691 (p0) cc_final: 0.8489 (p0) REVERT: F 281 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8101 (mmp) REVERT: F 390 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8033 (tt) REVERT: F 477 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8946 (mm) REVERT: K 183 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7769 (tpt170) REVERT: M 153 PHE cc_start: 0.7775 (t80) cc_final: 0.7326 (t80) REVERT: M 229 GLU cc_start: 0.9023 (mp0) cc_final: 0.8735 (mp0) REVERT: M 231 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7213 (ptp90) REVERT: N 174 LEU cc_start: 0.1488 (OUTLIER) cc_final: 0.0957 (mt) REVERT: N 235 THR cc_start: 0.6806 (OUTLIER) cc_final: 0.6562 (m) outliers start: 169 outliers final: 121 residues processed: 470 average time/residue: 0.5211 time to fit residues: 397.2345 Evaluate side-chains 461 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 315 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 414 ARG Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1212 LYS Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 416 TYR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain K residue 183 ARG Chi-restraints excluded: chain K residue 211 VAL Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain N residue 166 TRP Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 200 ASP Chi-restraints excluded: chain N residue 235 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 239 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 265 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 292 optimal weight: 0.0060 chunk 213 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 211 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 375 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 HIS N 163 HIS ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.116553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097673 restraints weight = 119756.429| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.31 r_work: 0.3352 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35344 Z= 0.123 Angle : 0.590 13.161 48754 Z= 0.313 Chirality : 0.041 0.232 5571 Planarity : 0.004 0.063 5662 Dihedral : 21.899 178.737 6403 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.22 % Allowed : 32.24 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.29 (0.14), residues: 3859 helix: 1.41 (0.14), residues: 1562 sheet: 0.13 (0.28), residues: 367 loop : -0.81 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 166 HIS 0.012 0.001 HIS C 841 PHE 0.045 0.001 PHE M 185 TYR 0.048 0.001 TYR M 220 ARG 0.008 0.000 ARG B 186 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 1665) hydrogen bonds : angle 4.32202 ( 4475) metal coordination : bond 0.00197 ( 7) metal coordination : angle 1.44510 ( 6) covalent geometry : bond 0.00274 (35337) covalent geometry : angle 0.58985 (48748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 357 time to evaluate : 4.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8310 (mm-30) REVERT: A 78 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9278 (mp) REVERT: A 90 ASP cc_start: 0.8795 (p0) cc_final: 0.8487 (p0) REVERT: A 109 ASP cc_start: 0.8197 (m-30) cc_final: 0.7744 (t0) REVERT: A 120 ASN cc_start: 0.7521 (p0) cc_final: 0.6786 (p0) REVERT: B 1 MET cc_start: 0.4847 (OUTLIER) cc_final: 0.4624 (mtp) REVERT: C 211 TRP cc_start: 0.7555 (m-10) cc_final: 0.7287 (m-10) REVERT: C 231 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6945 (mtm-85) REVERT: C 232 GLN cc_start: 0.8077 (mp10) cc_final: 0.7349 (mp10) REVERT: C 263 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8352 (mm-30) REVERT: C 569 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: C 607 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8627 (mtm) REVERT: C 657 TYR cc_start: 0.8919 (p90) cc_final: 0.8674 (p90) REVERT: C 724 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8476 (ptt) REVERT: C 999 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8686 (m-30) REVERT: D 27 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: D 84 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8327 (mtp180) REVERT: D 151 LEU cc_start: 0.9322 (mm) cc_final: 0.9064 (mm) REVERT: D 155 MET cc_start: 0.8563 (tpp) cc_final: 0.8026 (tmm) REVERT: D 205 MET cc_start: 0.8238 (ptp) cc_final: 0.7615 (mmt) REVERT: D 297 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8560 (mttt) REVERT: D 497 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8513 (pp) REVERT: D 944 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8968 (tt) REVERT: D 1104 HIS cc_start: 0.6600 (OUTLIER) cc_final: 0.6185 (t-90) REVERT: D 1208 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.9080 (ptm) REVERT: F 390 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7859 (tt) REVERT: F 477 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8941 (mm) REVERT: K 183 ARG cc_start: 0.8105 (tpt170) cc_final: 0.7668 (tpt170) REVERT: M 150 ARG cc_start: 0.8920 (ttp-170) cc_final: 0.8639 (ttp-170) REVERT: M 153 PHE cc_start: 0.7783 (t80) cc_final: 0.7331 (t80) REVERT: M 229 GLU cc_start: 0.9041 (mp0) cc_final: 0.8665 (tp30) REVERT: M 231 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7173 (ptp90) REVERT: N 235 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6639 (m) outliers start: 137 outliers final: 99 residues processed: 465 average time/residue: 0.6026 time to fit residues: 452.7604 Evaluate side-chains 450 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 333 time to evaluate : 3.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1134 LEU Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 56 TYR Chi-restraints excluded: chain F residue 315 MET Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 416 TYR Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain N residue 235 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 239 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 40 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 334 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 372 optimal weight: 7.9990 chunk 119 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 chunk 364 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS N 163 HIS ** N 170 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 = 0.3830 r_free = 0.3830 target = 0.110328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.091446 restraints weight = 120231.208| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.13 r_work: 0.3260 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 35344 Z= 0.312 Angle : 0.704 13.081 48754 Z= 0.372 Chirality : 0.045 0.274 5571 Planarity : 0.005 0.065 5662 Dihedral : 22.068 177.920 6403 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.59 % Allowed : 31.99 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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: 0.09 (0.14), residues: 3859 helix: 1.20 (0.13), residues: 1575 sheet: 0.14 (0.28), residues: 360 loop : -0.92 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 166 HIS 0.011 0.001 HIS C 841 PHE 0.050 0.002 PHE M 185 TYR 0.048 0.002 TYR M 220 ARG 0.008 0.001 ARG N 204 Details of bonding type rmsd hydrogen bonds : bond 0.05524 ( 1665) hydrogen bonds : angle 4.64973 ( 4475) metal coordination : bond 0.01189 ( 7) metal coordination : angle 1.56571 ( 6) covalent geometry : bond 0.00721 (35337) covalent geometry : angle 0.70380 (48748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 324 time to evaluate : 4.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8338 (mm-30) REVERT: A 90 ASP cc_start: 0.8783 (p0) cc_final: 0.8544 (p0) REVERT: A 109 ASP cc_start: 0.8361 (m-30) cc_final: 0.7984 (t0) REVERT: A 120 ASN cc_start: 0.8075 (p0) cc_final: 0.7513 (p0) REVERT: B 189 PHE cc_start: 0.8402 (m-80) cc_final: 0.8108 (m-80) REVERT: C 211 TRP cc_start: 0.7646 (m-10) cc_final: 0.7348 (m-10) REVERT: C 231 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7111 (mtt90) REVERT: C 232 GLN cc_start: 0.8192 (mp10) cc_final: 0.7664 (mp10) REVERT: C 263 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8407 (mm-30) REVERT: C 569 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: C 607 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8767 (mtm) REVERT: C 667 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.9043 (ptp-110) REVERT: C 926 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8200 (mpp) REVERT: C 999 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8723 (m-30) REVERT: D 84 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8335 (mtp180) REVERT: D 155 MET cc_start: 0.8682 (tpp) cc_final: 0.8189 (tmm) REVERT: D 205 MET cc_start: 0.8322 (ptp) cc_final: 0.7686 (mmt) REVERT: D 497 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8886 (pp) REVERT: D 690 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8495 (tptm) REVERT: D 944 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9091 (tt) REVERT: D 1104 HIS cc_start: 0.6763 (OUTLIER) cc_final: 0.6225 (t-90) REVERT: D 1208 MET cc_start: 0.9316 (OUTLIER) cc_final: 0.9083 (ptm) REVERT: D 1212 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8922 (mtmm) REVERT: F 390 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8117 (tt) REVERT: F 477 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8964 (mm) REVERT: J 244 ARG cc_start: 0.7908 (ptp-110) cc_final: 0.7690 (ptp-170) REVERT: M 150 ARG cc_start: 0.8840 (ttp-170) cc_final: 0.8391 (ttp-170) REVERT: M 231 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7139 (ptp90) REVERT: N 235 THR cc_start: 0.6770 (OUTLIER) cc_final: 0.6515 (m) outliers start: 149 outliers final: 114 residues processed: 442 average time/residue: 0.7066 time to fit residues: 517.1046 Evaluate side-chains 440 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 309 time to evaluate : 4.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1102 VAL Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 210 ASP Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1212 LYS Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain E residue 69 ASN Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 422 SER Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain M residue 172 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 201 HIS Chi-restraints excluded: chain M residue 216 SER Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 193 LEU Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain N residue 166 TRP Chi-restraints excluded: chain N residue 231 ARG Chi-restraints excluded: chain N residue 235 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 172 optimal weight: 2.9990 chunk 391 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 334 optimal weight: 20.0000 chunk 195 optimal weight: 0.0670 chunk 210 optimal weight: 0.9980 chunk 302 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 293 optimal weight: 3.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS L 163 HIS N 163 HIS ** N 170 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 = 0.3888 r_free = 0.3888 target = 0.114529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095881 restraints weight = 118122.431| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.26 r_work: 0.3325 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35344 Z= 0.136 Angle : 0.624 12.739 48754 Z= 0.330 Chirality : 0.042 0.262 5571 Planarity : 0.004 0.062 5662 Dihedral : 22.028 178.849 6403 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.73 % Allowed : 32.70 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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 (0.14), residues: 3859 helix: 1.36 (0.14), residues: 1558 sheet: 0.20 (0.28), residues: 363 loop : -0.83 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP N 166 HIS 0.012 0.001 HIS C 841 PHE 0.045 0.001 PHE M 185 TYR 0.053 0.001 TYR M 220 ARG 0.007 0.000 ARG B 182 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 1665) hydrogen bonds : angle 4.43320 ( 4475) metal coordination : bond 0.00231 ( 7) metal coordination : angle 1.28509 ( 6) covalent geometry : bond 0.00305 (35337) covalent geometry : angle 0.62436 (48748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7718 Ramachandran restraints generated. 3859 Oldfield, 0 Emsley, 3859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 328 time to evaluate : 3.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8296 (mm-30) REVERT: A 90 ASP cc_start: 0.8757 (p0) cc_final: 0.8457 (p0) REVERT: A 109 ASP cc_start: 0.8264 (m-30) cc_final: 0.7850 (t0) REVERT: A 120 ASN cc_start: 0.7665 (p0) cc_final: 0.6950 (p0) REVERT: B 189 PHE cc_start: 0.8338 (m-80) cc_final: 0.8086 (m-80) REVERT: C 211 TRP cc_start: 0.7588 (m-10) cc_final: 0.7323 (m-10) REVERT: C 231 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6999 (mtm-85) REVERT: C 232 GLN cc_start: 0.8141 (mp10) cc_final: 0.7392 (mp10) REVERT: C 263 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8390 (mm-30) REVERT: C 362 GLU cc_start: 0.8889 (tt0) cc_final: 0.8647 (tm-30) REVERT: C 569 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: C 607 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8675 (mtm) REVERT: C 667 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.9093 (ptp-110) REVERT: C 724 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8574 (ptt) REVERT: C 999 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8641 (m-30) REVERT: D 84 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8278 (mtp180) REVERT: D 155 MET cc_start: 0.8654 (tpp) cc_final: 0.8112 (tmm) REVERT: D 205 MET cc_start: 0.8316 (ptp) cc_final: 0.7670 (mmt) REVERT: D 297 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8567 (mtmt) REVERT: D 497 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8705 (pp) REVERT: D 944 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8973 (tt) REVERT: D 1104 HIS cc_start: 0.6679 (OUTLIER) cc_final: 0.6191 (t-90) REVERT: D 1208 MET cc_start: 0.9278 (OUTLIER) cc_final: 0.9025 (ptm) REVERT: F 390 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7895 (tt) REVERT: F 477 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8939 (mm) REVERT: J 244 ARG cc_start: 0.7826 (ptp-110) cc_final: 0.7559 (ptp-170) REVERT: K 183 ARG cc_start: 0.8074 (tpt170) cc_final: 0.7678 (tpt170) REVERT: M 150 ARG cc_start: 0.8869 (ttp-170) cc_final: 0.8626 (ttp-170) REVERT: M 153 PHE cc_start: 0.8309 (t80) cc_final: 0.8084 (t80) REVERT: M 229 GLU cc_start: 0.9050 (mp0) cc_final: 0.8654 (tp30) REVERT: M 231 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7140 (ptp90) REVERT: N 235 THR cc_start: 0.6834 (OUTLIER) cc_final: 0.6597 (m) outliers start: 121 outliers final: 99 residues processed: 426 average time/residue: 0.4930 time to fit residues: 340.8229 Evaluate side-chains 441 residues out of total 3322 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 326 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 185 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 617 HIS Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 305 ARG Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 439 PHE Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 569 GLU Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 707 CYS Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 904 MET Chi-restraints excluded: chain C residue 999 ASP Chi-restraints excluded: chain C residue 1024 THR Chi-restraints excluded: chain C residue 1089 LEU Chi-restraints excluded: chain C residue 1135 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 84 ARG Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 ASP Chi-restraints excluded: chain D residue 297 LYS Chi-restraints excluded: chain D residue 317 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 457 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 535 ASP Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 579 LEU Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 708 VAL Chi-restraints excluded: chain D residue 793 TYR Chi-restraints excluded: chain D residue 800 ILE Chi-restraints excluded: chain D residue 812 THR Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 962 VAL Chi-restraints excluded: chain D residue 1039 VAL Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1104 HIS Chi-restraints excluded: chain D residue 1111 LEU Chi-restraints excluded: chain D residue 1112 MET Chi-restraints excluded: chain D residue 1165 VAL Chi-restraints excluded: chain D residue 1173 THR Chi-restraints excluded: chain D residue 1176 LEU Chi-restraints excluded: chain D residue 1180 LEU Chi-restraints excluded: chain D residue 1207 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1270 ILE Chi-restraints excluded: chain D residue 1275 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 477 LEU Chi-restraints excluded: chain J residue 149 VAL Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 172 VAL Chi-restraints excluded: chain J residue 192 VAL Chi-restraints excluded: chain J residue 215 GLU Chi-restraints excluded: chain J residue 229 GLU Chi-restraints excluded: chain J residue 234 HIS Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 192 VAL Chi-restraints excluded: chain M residue 227 THR Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain M residue 239 VAL Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain L residue 214 VAL Chi-restraints excluded: chain N residue 166 TRP Chi-restraints excluded: chain N residue 235 THR Chi-restraints excluded: chain O residue 162 THR Chi-restraints excluded: chain O residue 214 VAL Chi-restraints excluded: chain O residue 239 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 285 optimal weight: 4.9990 chunk 241 optimal weight: 6.9990 chunk 398 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 302 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 HIS L 163 HIS N 163 HIS ** N 170 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 = 0.3872 r_free = 0.3872 target = 0.113258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.094733 restraints weight = 119031.317| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.21 r_work: 0.3305 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35344 Z= 0.166 Angle : 0.625 14.603 48754 Z= 0.330 Chirality : 0.042 0.244 5571 Planarity : 0.004 0.063 5662 Dihedral : 22.002 179.048 6403 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.82 % Allowed : 32.85 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.12 % 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 (0.14), residues: 3859 helix: 1.37 (0.14), residues: 1557 sheet: 0.15 (0.27), residues: 377 loop : -0.84 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP N 166 HIS 0.012 0.001 HIS C 841 PHE 0.049 0.001 PHE M 185 TYR 0.050 0.001 TYR M 220 ARG 0.013 0.000 ARG D1054 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 1665) hydrogen bonds : angle 4.45471 ( 4475) metal coordination : bond 0.00444 ( 7) metal coordination : angle 1.28638 ( 6) covalent geometry : bond 0.00385 (35337) covalent geometry : angle 0.62467 (48748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25163.60 seconds wall clock time: 446 minutes 58.64 seconds (26818.64 seconds total)