Starting phenix.real_space_refine on Fri Mar 6 03:38:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f4g_31450/03_2026/7f4g_31450.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f4g_31450/03_2026/7f4g_31450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f4g_31450/03_2026/7f4g_31450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f4g_31450/03_2026/7f4g_31450.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f4g_31450/03_2026/7f4g_31450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f4g_31450/03_2026/7f4g_31450.map" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 162 5.16 5 C 17703 2.51 5 N 4833 2.21 5 O 5254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27957 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 8179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8179 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 982} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 7820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7820 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 45, 'TRANS': 932} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2038 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 15, 'TRANS': 238} Chain breaks: 1 Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 11, 'TRANS': 196} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 609 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "R" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1335 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "D" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1334 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21582 SG CYS I 17 37.971 100.229 138.807 1.00 88.60 S ATOM 21606 SG CYS I 20 41.791 100.886 137.557 1.00 90.53 S ATOM 21767 SG CYS I 39 41.159 97.743 138.696 1.00 96.96 S ATOM 21792 SG CYS I 42 41.465 100.917 140.979 1.00101.32 S ATOM 22144 SG CYS I 86 10.786 98.574 103.888 1.00 86.89 S ATOM 22168 SG CYS I 89 9.770 101.931 103.105 1.00 88.50 S ATOM 22372 SG CYS I 114 12.931 100.997 101.748 1.00 73.84 S ATOM 22407 SG CYS I 119 12.341 101.481 105.283 1.00 84.48 S ATOM 22517 SG CYS J 7 51.508 98.144 40.982 1.00 32.48 S ATOM 22541 SG CYS J 10 50.924 97.140 37.600 1.00 36.95 S ATOM 22805 SG CYS J 44 48.463 96.157 40.502 1.00 40.01 S ATOM 22811 SG CYS J 45 48.849 99.419 38.764 1.00 40.13 S ATOM 24769 SG CYS R 100 63.096 54.764 141.450 1.00173.07 S ATOM 24806 SG CYS R 105 62.977 53.749 145.282 1.00177.93 S ATOM 25063 SG CYS R 136 59.838 54.641 144.515 1.00172.29 S ATOM 25094 SG CYS R 140 62.843 57.228 144.642 1.00175.77 S Time building chain proxies: 5.95, per 1000 atoms: 0.21 Number of scatterers: 27957 At special positions: 0 Unit cell: (170.172, 146.16, 161.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 5 29.99 S 162 16.00 O 5254 8.00 N 4833 7.00 C 17703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN R 800 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 140 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 105 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 100 " pdb="ZN ZN R 800 " - pdb=" SG CYS R 136 " Number of angles added : 24 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6604 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 40 sheets defined 36.7% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.642A pdb=" N ARG A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.947A pdb=" N ALA A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 removed outlier: 3.593A pdb=" N ILE A 655 " --> pdb=" O SER A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.652A pdb=" N ARG A 666 " --> pdb=" O HIS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 733 through 758 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.961A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 816 through 821 removed outlier: 3.529A pdb=" N ARG A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 868 removed outlier: 3.708A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 914 through 921 Processing helix chain 'A' and resid 935 through 944 removed outlier: 3.567A pdb=" N LEU A 943 " --> pdb=" O VAL A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 970 Processing helix chain 'A' and resid 982 through 994 removed outlier: 3.712A pdb=" N TRP A 988 " --> pdb=" O LEU A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1017 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 removed outlier: 3.561A pdb=" N ASN A1042 " --> pdb=" O THR A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1057 Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.541A pdb=" N ASP A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.997A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1189 through 1198 removed outlier: 3.574A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1224 removed outlier: 3.508A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 Processing helix chain 'A' and resid 1280 through 1292 Processing helix chain 'A' and resid 1342 through 1347 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.615A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.791A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.129A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 60 removed outlier: 5.295A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 294 through 302 removed outlier: 3.578A pdb=" N GLU B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 360 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 426 removed outlier: 3.926A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.720A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 658 Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.643A pdb=" N GLU B 671 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.593A pdb=" N GLN B 683 " --> pdb=" O PRO B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.789A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.614A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.523A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.535A pdb=" N MET B 954 " --> pdb=" O GLN B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 976 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 977 through 994 removed outlier: 4.257A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1016 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.512A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 240 through 268 removed outlier: 3.540A pdb=" N ILE C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 24 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 96 removed outlier: 3.949A pdb=" N GLU E 96 " --> pdb=" O GLN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 99 No H-bonds generated for 'chain 'E' and resid 97 through 99' Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 removed outlier: 3.513A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.056A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.815A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.930A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'R' and resid 43 through 66 Processing helix chain 'R' and resid 71 through 80 Processing helix chain 'R' and resid 83 through 97 Processing helix chain 'R' and resid 131 through 135 Processing helix chain 'R' and resid 137 through 150 Processing helix chain 'R' and resid 155 through 159 Processing helix chain 'R' and resid 162 through 183 removed outlier: 3.548A pdb=" N ASP R 166 " --> pdb=" O GLU R 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.515A pdb=" N VAL D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.744A pdb=" N CYS D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 removed outlier: 3.722A pdb=" N GLU D 119 " --> pdb=" O PRO D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.694A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing sheet with id=AA1, first strand: chain 'A' and resid 367 through 369 Processing sheet with id=AA2, first strand: chain 'A' and resid 389 through 393 removed outlier: 6.638A pdb=" N LYS A 445 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE A 419 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU A 447 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.207A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE H 9 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.207A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AA6, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.765A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 902 through 904 Processing sheet with id=AA8, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id=AA9, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.895A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB2, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 93 removed outlier: 5.935A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AB5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.609A pdb=" N LYS B 524 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.823A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU B 220 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE B 235 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ARG B 222 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER B 233 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB9, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC1, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.671A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 748 through 751 removed outlier: 4.201A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 748 through 751 removed outlier: 4.201A pdb=" N LYS B 917 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AC5, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.178A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AC7, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.469A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AC9, first strand: chain 'C' and resid 8 through 15 removed outlier: 6.258A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.309A pdb=" N GLU C 158 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA C 54 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG C 160 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE C 52 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG C 162 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL C 50 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR C 164 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 113 through 116 Processing sheet with id=AD3, first strand: chain 'E' and resid 60 through 63 Processing sheet with id=AD4, first strand: chain 'E' and resid 104 through 106 removed outlier: 6.236A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 147 through 151 removed outlier: 4.913A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AD7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AD8, first strand: chain 'K' and resid 20 through 24 removed outlier: 4.606A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 117 through 120 removed outlier: 3.606A pdb=" N LYS R 125 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 3 through 13 removed outlier: 3.584A pdb=" N THR G 39 " --> pdb=" O GLY G 43 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 3 through 13 Processing sheet with id=AE3, first strand: chain 'G' and resid 169 through 170 removed outlier: 3.685A pdb=" N GLY G 169 " --> pdb=" O ARG G 144 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY G 161 " --> pdb=" O PHE G 107 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 118 through 120 removed outlier: 3.992A pdb=" N TYR G 128 " --> pdb=" O ILE G 137 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.65 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4766 1.29 - 1.42: 7014 1.42 - 1.55: 16449 1.55 - 1.68: 1 1.68 - 1.81: 254 Bond restraints: 28484 Sorted by residual: bond pdb=" C LEU J 24 " pdb=" O LEU J 24 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.34e-02 5.57e+03 2.87e+01 bond pdb=" CA SER B 304 " pdb=" CB SER B 304 " ideal model delta sigma weight residual 1.537 1.466 0.071 1.41e-02 5.03e+03 2.55e+01 bond pdb=" N HIS B 842 " pdb=" CA HIS B 842 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.50e+01 bond pdb=" C LEU B 348 " pdb=" O LEU B 348 " ideal model delta sigma weight residual 1.235 1.212 0.023 4.70e-03 4.53e+04 2.34e+01 bond pdb=" C LYS B 302 " pdb=" O LYS B 302 " ideal model delta sigma weight residual 1.241 1.194 0.047 9.80e-03 1.04e+04 2.33e+01 ... (remaining 28479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 37143 2.69 - 5.39: 1200 5.39 - 8.08: 119 8.08 - 10.78: 12 10.78 - 13.47: 3 Bond angle restraints: 38477 Sorted by residual: angle pdb=" C ILE B 556 " pdb=" N SER B 557 " pdb=" CA SER B 557 " ideal model delta sigma weight residual 121.83 135.30 -13.47 1.56e+00 4.11e-01 7.46e+01 angle pdb=" N LEU B 305 " pdb=" CA LEU B 305 " pdb=" C LEU B 305 " ideal model delta sigma weight residual 113.02 104.49 8.53 1.20e+00 6.94e-01 5.05e+01 angle pdb=" C PRO B 303 " pdb=" CA PRO B 303 " pdb=" CB PRO B 303 " ideal model delta sigma weight residual 111.56 100.76 10.80 1.65e+00 3.67e-01 4.29e+01 angle pdb=" N VAL B 742 " pdb=" CA VAL B 742 " pdb=" C VAL B 742 " ideal model delta sigma weight residual 113.71 107.61 6.10 9.50e-01 1.11e+00 4.12e+01 angle pdb=" CA THR B 898 " pdb=" C THR B 898 " pdb=" O THR B 898 " ideal model delta sigma weight residual 122.27 115.25 7.02 1.16e+00 7.43e-01 3.66e+01 ... (remaining 38472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15585 17.99 - 35.97: 1534 35.97 - 53.96: 265 53.96 - 71.94: 45 71.94 - 89.93: 23 Dihedral angle restraints: 17452 sinusoidal: 7260 harmonic: 10192 Sorted by residual: dihedral pdb=" CA GLY B 940 " pdb=" C GLY B 940 " pdb=" N GLN B 941 " pdb=" CA GLN B 941 " ideal model delta harmonic sigma weight residual 180.00 150.06 29.94 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ASP A1295 " pdb=" C ASP A1295 " pdb=" N MET A1296 " pdb=" CA MET A1296 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ARG C 240 " pdb=" C ARG C 240 " pdb=" N PRO C 241 " pdb=" CA PRO C 241 " ideal model delta harmonic sigma weight residual -180.00 -153.11 -26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 17449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3916 0.110 - 0.221: 369 0.221 - 0.331: 12 0.331 - 0.442: 6 0.442 - 0.552: 1 Chirality restraints: 4304 Sorted by residual: chirality pdb=" CB ILE A 811 " pdb=" CA ILE A 811 " pdb=" CG1 ILE A 811 " pdb=" CG2 ILE A 811 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA TYR J 29 " pdb=" N TYR J 29 " pdb=" C TYR J 29 " pdb=" CB TYR J 29 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ASN B 164 " pdb=" N ASN B 164 " pdb=" C ASN B 164 " pdb=" CB ASN B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 ... (remaining 4301 not shown) Planarity restraints: 4983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 388 " 0.035 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR B 388 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR B 388 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 388 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 388 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 388 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 388 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 388 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 752 " 0.014 2.00e-02 2.50e+03 2.26e-02 1.03e+01 pdb=" CG TYR B 752 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR B 752 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 752 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 752 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 752 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 752 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 752 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 668 " -0.018 2.00e-02 2.50e+03 2.29e-02 9.14e+00 pdb=" CG PHE A 668 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE A 668 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 668 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 668 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 668 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 668 " 0.002 2.00e-02 2.50e+03 ... (remaining 4980 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 193 2.50 - 3.10: 20892 3.10 - 3.70: 42043 3.70 - 4.30: 64924 4.30 - 4.90: 109894 Nonbonded interactions: 237946 Sorted by model distance: nonbonded pdb=" O GLU L 38 " pdb="ZN ZN L 101 " model vdw 1.898 2.230 nonbonded pdb=" NE2 HIS B 387 " pdb=" OE2 GLU B 671 " model vdw 2.047 3.120 nonbonded pdb=" OD1 ASP B 953 " pdb=" NH2 ARG C 36 " model vdw 2.069 3.120 nonbonded pdb=" O ASN C 190 " pdb=" NH1 ARG C 193 " model vdw 2.089 3.120 nonbonded pdb=" OG SER R 95 " pdb=" OG SER R 134 " model vdw 2.090 3.040 ... (remaining 237941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.080 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.017 0.428 28501 Z= 0.732 Angle : 1.147 26.419 38503 Z= 0.633 Chirality : 0.067 0.552 4304 Planarity : 0.006 0.071 4983 Dihedral : 14.672 89.931 10845 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.69 % Favored : 90.96 % Rotamer: Outliers : 1.43 % Allowed : 6.48 % Favored : 92.10 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.12), residues: 3441 helix: -2.63 (0.11), residues: 1201 sheet: -2.51 (0.20), residues: 487 loop : -2.66 (0.13), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1258 TYR 0.067 0.004 TYR B 388 PHE 0.051 0.004 PHE A 668 TRP 0.029 0.004 TRP C 49 HIS 0.011 0.002 HIS B 749 Details of bonding type rmsd covalent geometry : bond 0.01690 (28484) covalent geometry : angle 1.10903 (38477) SS BOND : bond 0.00178 ( 1) SS BOND : angle 1.34288 ( 2) hydrogen bonds : bond 0.16189 ( 1133) hydrogen bonds : angle 7.41711 ( 3237) metal coordination : bond 0.16425 ( 16) metal coordination : angle 11.80025 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 523 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 HIS cc_start: 0.7388 (t70) cc_final: 0.6140 (m90) REVERT: A 540 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6531 (m-30) REVERT: A 660 MET cc_start: 0.8092 (mmm) cc_final: 0.7850 (mmp) REVERT: A 701 ASP cc_start: 0.7730 (t70) cc_final: 0.7476 (t0) REVERT: A 711 GLN cc_start: 0.7114 (mt0) cc_final: 0.6791 (tm-30) REVERT: A 811 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8006 (pt) REVERT: A 859 TYR cc_start: 0.7869 (t80) cc_final: 0.7604 (t80) REVERT: A 947 HIS cc_start: 0.7305 (t70) cc_final: 0.6812 (t70) REVERT: A 951 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6740 (mt-10) REVERT: A 955 GLU cc_start: 0.7656 (tt0) cc_final: 0.7242 (tt0) REVERT: A 959 MET cc_start: 0.8457 (ttm) cc_final: 0.8188 (mtp) REVERT: A 1031 ARG cc_start: 0.7426 (mtt180) cc_final: 0.7171 (mtt90) REVERT: A 1146 GLN cc_start: 0.8389 (mp10) cc_final: 0.7784 (tp-100) REVERT: A 1230 GLN cc_start: 0.9030 (mt0) cc_final: 0.8800 (mt0) REVERT: A 1233 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7946 (mm-30) REVERT: A 1280 ASP cc_start: 0.7948 (m-30) cc_final: 0.7746 (m-30) REVERT: A 1289 GLU cc_start: 0.6723 (tm-30) cc_final: 0.6491 (tp30) REVERT: A 1293 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7136 (tt) REVERT: A 1376 LYS cc_start: 0.8223 (tptt) cc_final: 0.8022 (tppp) REVERT: B 61 ASP cc_start: 0.7093 (m-30) cc_final: 0.6728 (m-30) REVERT: B 92 TYR cc_start: 0.7594 (m-80) cc_final: 0.7015 (m-80) REVERT: B 281 ASP cc_start: 0.8615 (t0) cc_final: 0.8186 (t0) REVERT: B 606 ASP cc_start: 0.7165 (m-30) cc_final: 0.6814 (m-30) REVERT: B 632 LYS cc_start: 0.8260 (mttt) cc_final: 0.8055 (mttp) REVERT: C 3 TYR cc_start: 0.8390 (m-80) cc_final: 0.8185 (m-10) REVERT: C 260 GLN cc_start: 0.8372 (tp40) cc_final: 0.8010 (tt0) REVERT: E 79 GLU cc_start: 0.8506 (mp0) cc_final: 0.7989 (mp0) REVERT: E 117 SER cc_start: 0.8751 (t) cc_final: 0.8434 (t) REVERT: E 168 ASN cc_start: 0.8436 (p0) cc_final: 0.8066 (p0) REVERT: F 101 LYS cc_start: 0.8572 (mttp) cc_final: 0.8354 (mttm) REVERT: H 51 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7638 (p0) REVERT: H 54 ASP cc_start: 0.7953 (m-30) cc_final: 0.7698 (m-30) REVERT: H 57 ARG cc_start: 0.8064 (ttt-90) cc_final: 0.7838 (ttt180) REVERT: H 89 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8158 (mt-10) REVERT: H 146 LYS cc_start: 0.8442 (tttp) cc_final: 0.8214 (ttpt) REVERT: I 67 GLN cc_start: 0.8742 (mm110) cc_final: 0.8461 (mp10) REVERT: I 93 GLU cc_start: 0.8313 (tt0) cc_final: 0.7932 (tt0) REVERT: K 38 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7352 (mm-30) REVERT: K 70 LYS cc_start: 0.8738 (ptpt) cc_final: 0.8505 (ptpp) REVERT: L 42 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7900 (mtp85) REVERT: L 51 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8062 (ttm170) REVERT: D 62 MET cc_start: 0.3194 (mmp) cc_final: 0.2733 (mmp) REVERT: G 164 MET cc_start: 0.0910 (mmt) cc_final: 0.0239 (pp-130) outliers start: 44 outliers final: 13 residues processed: 560 average time/residue: 0.7870 time to fit residues: 500.3944 Evaluate side-chains 420 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 403 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 841 ARG Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 43 ASP Chi-restraints excluded: chain J residue 5 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN A 432 HIS A 504 HIS A 606 HIS A 678 ASN A 711 GLN A 721 HIS A 735 GLN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A 839 HIS A 885 GLN A 949 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 GLN A1230 GLN A1291 ASN A1332 GLN A1397 HIS B 56 GLN B 117 ASN B 265 GLN B 552 ASN B 582 GLN B 639 HIS B 649 ASN B 650 ASN B 654 GLN B 699 HIS ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1021 HIS ** B1040 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN C 18 ASN C 108 ASN C 260 GLN C 265 HIS E 19 GLN E 64 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 108 GLN I 41 ASN I 67 GLN I 84 HIS J 52 HIS K 22 ASN K 29 ASN K 69 HIS R 64 GLN R 86 HIS R 138 ASN R 199 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.181230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114460 restraints weight = 32557.444| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.37 r_work: 0.3407 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28501 Z= 0.162 Angle : 0.710 19.288 38503 Z= 0.357 Chirality : 0.047 0.253 4304 Planarity : 0.005 0.050 4983 Dihedral : 6.205 56.330 3832 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 3.34 % Allowed : 13.09 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.13), residues: 3441 helix: -1.01 (0.14), residues: 1208 sheet: -1.98 (0.21), residues: 492 loop : -1.99 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 169 TYR 0.025 0.002 TYR B 388 PHE 0.024 0.002 PHE G 77 TRP 0.016 0.002 TRP A 679 HIS 0.010 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00365 (28484) covalent geometry : angle 0.68894 (38477) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.78093 ( 2) hydrogen bonds : bond 0.04322 ( 1133) hydrogen bonds : angle 5.50879 ( 3237) metal coordination : bond 0.01311 ( 16) metal coordination : angle 6.87644 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 436 time to evaluate : 1.090 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 504 HIS cc_start: 0.7058 (t-90) cc_final: 0.5713 (m90) REVERT: A 508 SER cc_start: 0.7915 (OUTLIER) cc_final: 0.7521 (p) REVERT: A 540 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6615 (m-30) REVERT: A 637 MET cc_start: 0.8945 (ptm) cc_final: 0.8570 (ptp) REVERT: A 711 GLN cc_start: 0.6786 (mt0) cc_final: 0.6396 (tm-30) REVERT: A 803 LYS cc_start: 0.7829 (tppp) cc_final: 0.7232 (ttpp) REVERT: A 859 TYR cc_start: 0.7705 (t80) cc_final: 0.7235 (t80) REVERT: A 868 MET cc_start: 0.6938 (mtm) cc_final: 0.6601 (mtm) REVERT: A 927 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8085 (tm-30) REVERT: A 947 HIS cc_start: 0.6604 (t70) cc_final: 0.6279 (t70) REVERT: A 951 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6975 (mt-10) REVERT: A 955 GLU cc_start: 0.7131 (tt0) cc_final: 0.6776 (tt0) REVERT: A 1015 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7269 (mp0) REVERT: A 1152 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7667 (pt0) REVERT: A 1180 ASN cc_start: 0.8340 (m110) cc_final: 0.7983 (t0) REVERT: A 1230 GLN cc_start: 0.8966 (mt0) cc_final: 0.8689 (mt0) REVERT: A 1233 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 1279 MET cc_start: 0.7641 (mtp) cc_final: 0.7391 (mtm) REVERT: A 1280 ASP cc_start: 0.7889 (m-30) cc_final: 0.7657 (m-30) REVERT: A 1337 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7670 (mm-30) REVERT: A 1355 VAL cc_start: 0.8079 (m) cc_final: 0.7736 (p) REVERT: B 35 ASP cc_start: 0.8076 (m-30) cc_final: 0.7818 (m-30) REVERT: B 61 ASP cc_start: 0.7024 (m-30) cc_final: 0.6709 (m-30) REVERT: B 92 TYR cc_start: 0.7531 (m-80) cc_final: 0.6717 (m-80) REVERT: B 151 LYS cc_start: 0.7410 (mtpp) cc_final: 0.7059 (mtmt) REVERT: B 160 TYR cc_start: 0.7871 (m-80) cc_final: 0.7406 (m-80) REVERT: B 265 GLN cc_start: 0.8587 (mt0) cc_final: 0.8264 (mm-40) REVERT: B 299 GLU cc_start: 0.7861 (pt0) cc_final: 0.7542 (tt0) REVERT: B 302 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7716 (mtmt) REVERT: B 309 PHE cc_start: 0.8711 (t80) cc_final: 0.8363 (t80) REVERT: B 334 LYS cc_start: 0.7466 (tppp) cc_final: 0.6854 (ttpp) REVERT: B 450 THR cc_start: 0.8352 (m) cc_final: 0.7990 (p) REVERT: B 529 MET cc_start: 0.9183 (mtp) cc_final: 0.8836 (mtt) REVERT: B 632 LYS cc_start: 0.7675 (mttt) cc_final: 0.7467 (mttp) REVERT: B 721 ARG cc_start: 0.8461 (mmp80) cc_final: 0.8108 (mmp80) REVERT: B 764 MET cc_start: 0.8816 (mtt) cc_final: 0.8585 (mtm) REVERT: B 765 GLU cc_start: 0.8421 (tp30) cc_final: 0.8173 (tp30) REVERT: B 816 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 827 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6854 (mt-10) REVERT: B 965 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8530 (mm) REVERT: C 3 TYR cc_start: 0.8327 (m-80) cc_final: 0.8091 (m-80) REVERT: C 17 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7683 (pt0) REVERT: C 19 VAL cc_start: 0.8413 (t) cc_final: 0.8152 (p) REVERT: E 55 ARG cc_start: 0.6884 (mmm-85) cc_final: 0.6623 (mmt90) REVERT: E 79 GLU cc_start: 0.8650 (mp0) cc_final: 0.8196 (mp0) REVERT: F 124 ILE cc_start: 0.7605 (mt) cc_final: 0.7374 (mp) REVERT: H 20 LYS cc_start: 0.8776 (tttt) cc_final: 0.8293 (mtpt) REVERT: H 54 ASP cc_start: 0.7987 (m-30) cc_final: 0.7481 (m-30) REVERT: H 111 ARG cc_start: 0.7260 (mtp-110) cc_final: 0.7045 (ptm160) REVERT: H 146 LYS cc_start: 0.8169 (tttp) cc_final: 0.7718 (ttpt) REVERT: I 27 LYS cc_start: 0.7270 (ptpt) cc_final: 0.6919 (ptpp) REVERT: I 67 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8150 (mp10) REVERT: I 93 GLU cc_start: 0.8436 (tt0) cc_final: 0.7830 (tt0) REVERT: K 23 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8043 (mptp) REVERT: K 38 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7850 (mm-30) REVERT: K 70 LYS cc_start: 0.8591 (ptpt) cc_final: 0.8355 (ptpp) REVERT: L 15 MET cc_start: 0.6767 (tpp) cc_final: 0.6423 (tpp) REVERT: L 27 GLU cc_start: 0.8136 (tt0) cc_final: 0.7436 (tm-30) REVERT: L 42 ARG cc_start: 0.8592 (mtt-85) cc_final: 0.8153 (mtp85) REVERT: R 76 MET cc_start: 0.6773 (mmp) cc_final: 0.5866 (mmt) REVERT: G 1 MET cc_start: 0.4325 (pmm) cc_final: 0.3582 (ppp) outliers start: 103 outliers final: 35 residues processed: 494 average time/residue: 0.7127 time to fit residues: 404.2640 Evaluate side-chains 433 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 391 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 240 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 315 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 228 optimal weight: 0.0980 chunk 206 optimal weight: 0.6980 chunk 291 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 609 HIS ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN B 582 GLN B 649 ASN B 650 ASN B 842 HIS B 941 GLN B1025 ASN B1040 GLN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN I 22 ASN I 41 ASN ** R 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.182833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116198 restraints weight = 32708.920| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.37 r_work: 0.3426 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 28501 Z= 0.134 Angle : 0.635 17.034 38503 Z= 0.317 Chirality : 0.046 0.212 4304 Planarity : 0.004 0.053 4983 Dihedral : 5.545 54.856 3817 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.32 % Favored : 94.65 % Rotamer: Outliers : 3.69 % Allowed : 15.19 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3441 helix: -0.29 (0.15), residues: 1223 sheet: -1.52 (0.22), residues: 475 loop : -1.64 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 770 TYR 0.012 0.001 TYR G 3 PHE 0.020 0.001 PHE A 592 TRP 0.014 0.002 TRP B 22 HIS 0.005 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00307 (28484) covalent geometry : angle 0.61255 (38477) SS BOND : bond 0.00267 ( 1) SS BOND : angle 0.80996 ( 2) hydrogen bonds : bond 0.03823 ( 1133) hydrogen bonds : angle 5.02424 ( 3237) metal coordination : bond 0.00650 ( 16) metal coordination : angle 6.69407 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 433 time to evaluate : 1.076 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 502 ASN cc_start: 0.8090 (p0) cc_final: 0.7751 (p0) REVERT: A 504 HIS cc_start: 0.7100 (t-90) cc_final: 0.5655 (m90) REVERT: A 508 SER cc_start: 0.7874 (m) cc_final: 0.7505 (p) REVERT: A 509 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6477 (tt) REVERT: A 565 MET cc_start: 0.8667 (mmm) cc_final: 0.8460 (mmm) REVERT: A 637 MET cc_start: 0.8932 (ptm) cc_final: 0.8579 (ptp) REVERT: A 662 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6640 (t70) REVERT: A 711 GLN cc_start: 0.6816 (mt0) cc_final: 0.6396 (tm-30) REVERT: A 859 TYR cc_start: 0.7634 (t80) cc_final: 0.7148 (t80) REVERT: A 927 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: A 947 HIS cc_start: 0.6483 (t70) cc_final: 0.6210 (t-170) REVERT: A 1015 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7340 (mp0) REVERT: A 1102 MET cc_start: 0.6467 (mtp) cc_final: 0.6047 (mtm) REVERT: A 1126 GLU cc_start: 0.7334 (pt0) cc_final: 0.7131 (tm-30) REVERT: A 1150 ASP cc_start: 0.6669 (t70) cc_final: 0.6382 (t0) REVERT: A 1152 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: A 1180 ASN cc_start: 0.8332 (m110) cc_final: 0.8029 (t0) REVERT: A 1211 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6588 (tt) REVERT: A 1228 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8026 (mtt) REVERT: A 1230 GLN cc_start: 0.8963 (mt0) cc_final: 0.8624 (mt0) REVERT: A 1233 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 1269 MET cc_start: 0.1857 (pmm) cc_final: 0.1314 (mmt) REVERT: A 1271 GLU cc_start: 0.1821 (OUTLIER) cc_final: 0.1213 (mm-30) REVERT: A 1279 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6851 (ptp) REVERT: A 1280 ASP cc_start: 0.7829 (m-30) cc_final: 0.7435 (m-30) REVERT: A 1293 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7309 (tt) REVERT: A 1339 ASP cc_start: 0.7633 (t0) cc_final: 0.7019 (m-30) REVERT: A 1362 ILE cc_start: 0.7974 (pt) cc_final: 0.7672 (mp) REVERT: A 1408 ARG cc_start: 0.7651 (mmm160) cc_final: 0.7397 (mmm160) REVERT: B 35 ASP cc_start: 0.8044 (m-30) cc_final: 0.7779 (m-30) REVERT: B 92 TYR cc_start: 0.7466 (m-80) cc_final: 0.6567 (m-80) REVERT: B 151 LYS cc_start: 0.7420 (mtpp) cc_final: 0.7123 (mtmt) REVERT: B 155 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8487 (ttm) REVERT: B 170 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: B 299 GLU cc_start: 0.7920 (pt0) cc_final: 0.7598 (tt0) REVERT: B 302 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7684 (mtmt) REVERT: B 309 PHE cc_start: 0.8755 (t80) cc_final: 0.8433 (t80) REVERT: B 424 ASP cc_start: 0.6204 (OUTLIER) cc_final: 0.5893 (p0) REVERT: B 450 THR cc_start: 0.8358 (m) cc_final: 0.8015 (p) REVERT: B 508 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8015 (mtt) REVERT: B 529 MET cc_start: 0.9176 (mtp) cc_final: 0.8942 (mtt) REVERT: B 617 ASP cc_start: 0.7687 (m-30) cc_final: 0.7398 (m-30) REVERT: B 721 ARG cc_start: 0.8185 (mmp80) cc_final: 0.7881 (mmp80) REVERT: B 764 MET cc_start: 0.8832 (mtm) cc_final: 0.8597 (mtm) REVERT: B 816 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7161 (mm-30) REVERT: B 817 GLN cc_start: 0.8443 (pt0) cc_final: 0.8200 (pt0) REVERT: B 827 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6889 (mt-10) REVERT: B 958 CYS cc_start: 0.8573 (p) cc_final: 0.8316 (m) REVERT: B 965 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8546 (mm) REVERT: C 3 TYR cc_start: 0.8243 (m-80) cc_final: 0.8007 (m-80) REVERT: C 17 GLU cc_start: 0.8231 (pt0) cc_final: 0.7563 (pm20) REVERT: C 19 VAL cc_start: 0.8367 (t) cc_final: 0.8138 (p) REVERT: E 79 GLU cc_start: 0.8785 (mp0) cc_final: 0.8082 (pm20) REVERT: F 124 ILE cc_start: 0.7663 (mt) cc_final: 0.7426 (mp) REVERT: H 20 LYS cc_start: 0.8715 (mttt) cc_final: 0.8311 (mtpt) REVERT: H 31 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7846 (mt-10) REVERT: H 54 ASP cc_start: 0.7923 (m-30) cc_final: 0.7328 (m-30) REVERT: H 146 LYS cc_start: 0.8117 (tttp) cc_final: 0.7677 (ttpt) REVERT: I 27 LYS cc_start: 0.7180 (ptpt) cc_final: 0.6844 (ptpp) REVERT: I 51 SER cc_start: 0.7701 (t) cc_final: 0.7300 (p) REVERT: I 93 GLU cc_start: 0.8471 (tt0) cc_final: 0.7866 (tt0) REVERT: K 23 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7944 (mptp) REVERT: K 70 LYS cc_start: 0.8601 (ptpt) cc_final: 0.8374 (ptpp) REVERT: L 15 MET cc_start: 0.7057 (tpp) cc_final: 0.6030 (tpp) REVERT: L 27 GLU cc_start: 0.8146 (tt0) cc_final: 0.7449 (tp30) REVERT: R 104 LEU cc_start: 0.8705 (mm) cc_final: 0.8472 (mp) REVERT: R 170 LEU cc_start: 0.1635 (mt) cc_final: 0.1051 (tm) REVERT: D 33 LEU cc_start: 0.1745 (OUTLIER) cc_final: 0.1395 (mm) REVERT: G 1 MET cc_start: 0.5055 (pmm) cc_final: 0.4270 (ppp) outliers start: 114 outliers final: 40 residues processed: 502 average time/residue: 0.7063 time to fit residues: 406.2000 Evaluate side-chains 452 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 396 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1211 LEU Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 337 optimal weight: 40.0000 chunk 146 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 232 optimal weight: 8.9990 chunk 275 optimal weight: 0.0010 chunk 46 optimal weight: 8.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 GLN B 582 GLN B 649 ASN B 749 HIS ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN I 41 ASN ** R 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.180435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.113137 restraints weight = 32494.894| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.36 r_work: 0.3379 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28501 Z= 0.202 Angle : 0.660 14.123 38503 Z= 0.326 Chirality : 0.047 0.174 4304 Planarity : 0.004 0.048 4983 Dihedral : 5.431 58.252 3813 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.49 % Favored : 94.45 % Rotamer: Outliers : 4.15 % Allowed : 16.46 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.14), residues: 3441 helix: -0.06 (0.15), residues: 1230 sheet: -1.48 (0.22), residues: 478 loop : -1.48 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 169 TYR 0.013 0.001 TYR J 29 PHE 0.024 0.002 PHE A 592 TRP 0.014 0.002 TRP C 49 HIS 0.008 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00488 (28484) covalent geometry : angle 0.64032 (38477) SS BOND : bond 0.00234 ( 1) SS BOND : angle 0.88782 ( 2) hydrogen bonds : bond 0.03975 ( 1133) hydrogen bonds : angle 4.92116 ( 3237) metal coordination : bond 0.00837 ( 16) metal coordination : angle 6.48399 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 411 time to evaluate : 0.962 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 502 ASN cc_start: 0.7898 (p0) cc_final: 0.7566 (p0) REVERT: A 504 HIS cc_start: 0.7047 (t-90) cc_final: 0.5494 (m90) REVERT: A 508 SER cc_start: 0.7959 (OUTLIER) cc_final: 0.7543 (p) REVERT: A 509 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6497 (tt) REVERT: A 520 MET cc_start: 0.6776 (mmm) cc_final: 0.6416 (mmm) REVERT: A 637 MET cc_start: 0.8957 (ptm) cc_final: 0.8569 (ptp) REVERT: A 662 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6643 (t70) REVERT: A 769 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.4747 (mpp) REVERT: A 859 TYR cc_start: 0.7645 (t80) cc_final: 0.7155 (t80) REVERT: A 927 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: A 947 HIS cc_start: 0.6540 (t70) cc_final: 0.6234 (t-170) REVERT: A 1015 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7180 (tm-30) REVERT: A 1031 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6984 (mtt90) REVERT: A 1102 MET cc_start: 0.6592 (mtp) cc_final: 0.6147 (mtm) REVERT: A 1126 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: A 1150 ASP cc_start: 0.6566 (t70) cc_final: 0.6169 (t0) REVERT: A 1152 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7804 (pt0) REVERT: A 1180 ASN cc_start: 0.8116 (m110) cc_final: 0.7762 (t0) REVERT: A 1230 GLN cc_start: 0.8938 (mt0) cc_final: 0.8588 (mt0) REVERT: A 1233 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8076 (mm-30) REVERT: A 1279 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7492 (mtm) REVERT: A 1280 ASP cc_start: 0.7826 (m-30) cc_final: 0.7522 (m-30) REVERT: A 1293 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7267 (tt) REVERT: A 1331 LEU cc_start: 0.7342 (mp) cc_final: 0.7042 (mt) REVERT: A 1339 ASP cc_start: 0.7851 (t0) cc_final: 0.7242 (m-30) REVERT: A 1355 VAL cc_start: 0.8139 (m) cc_final: 0.7889 (t) REVERT: A 1362 ILE cc_start: 0.7914 (pt) cc_final: 0.7674 (mp) REVERT: A 1408 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7371 (mmm160) REVERT: B 35 ASP cc_start: 0.8041 (m-30) cc_final: 0.7786 (m-30) REVERT: B 61 ASP cc_start: 0.7102 (m-30) cc_final: 0.6877 (m-30) REVERT: B 92 TYR cc_start: 0.7455 (m-80) cc_final: 0.6626 (m-80) REVERT: B 151 LYS cc_start: 0.7444 (mtpp) cc_final: 0.7131 (mtmt) REVERT: B 155 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8594 (ttm) REVERT: B 170 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7699 (m-30) REVERT: B 299 GLU cc_start: 0.8040 (pt0) cc_final: 0.7649 (tt0) REVERT: B 302 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7690 (mtmt) REVERT: B 309 PHE cc_start: 0.8740 (t80) cc_final: 0.8419 (t80) REVERT: B 424 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5911 (p0) REVERT: B 450 THR cc_start: 0.8356 (m) cc_final: 0.7988 (p) REVERT: B 617 ASP cc_start: 0.7734 (m-30) cc_final: 0.7478 (m-30) REVERT: B 721 ARG cc_start: 0.8177 (mmp80) cc_final: 0.7955 (mmp80) REVERT: B 765 GLU cc_start: 0.8491 (tp30) cc_final: 0.7893 (tp30) REVERT: B 770 ARG cc_start: 0.8284 (mtm110) cc_final: 0.8058 (mtm110) REVERT: B 816 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7339 (mm-30) REVERT: B 817 GLN cc_start: 0.8543 (pt0) cc_final: 0.8295 (pt0) REVERT: B 913 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: B 958 CYS cc_start: 0.8673 (p) cc_final: 0.8358 (m) REVERT: B 965 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8718 (mm) REVERT: C 3 TYR cc_start: 0.8288 (m-80) cc_final: 0.8055 (m-80) REVERT: C 6 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: C 17 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: C 19 VAL cc_start: 0.8463 (t) cc_final: 0.8249 (p) REVERT: C 262 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6859 (mp10) REVERT: E 79 GLU cc_start: 0.8804 (mp0) cc_final: 0.8030 (pm20) REVERT: F 124 ILE cc_start: 0.7623 (mt) cc_final: 0.7409 (mp) REVERT: H 20 LYS cc_start: 0.8743 (mttt) cc_final: 0.8366 (mtpt) REVERT: H 54 ASP cc_start: 0.7875 (m-30) cc_final: 0.7199 (m-30) REVERT: H 57 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7723 (ttt-90) REVERT: H 89 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8428 (mt-10) REVERT: H 107 GLU cc_start: 0.7473 (pm20) cc_final: 0.7050 (pm20) REVERT: H 146 LYS cc_start: 0.8127 (tttp) cc_final: 0.7649 (ttpt) REVERT: I 51 SER cc_start: 0.7577 (t) cc_final: 0.7187 (p) REVERT: I 67 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: I 93 GLU cc_start: 0.8410 (tt0) cc_final: 0.7956 (tt0) REVERT: K 23 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7941 (mptp) REVERT: K 70 LYS cc_start: 0.8621 (ptpt) cc_final: 0.8376 (ptpp) REVERT: K 96 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7952 (p) REVERT: L 15 MET cc_start: 0.6968 (tpp) cc_final: 0.5897 (tpp) REVERT: L 27 GLU cc_start: 0.8159 (tt0) cc_final: 0.7445 (tp30) REVERT: R 184 LEU cc_start: 0.4180 (tp) cc_final: 0.3608 (tp) REVERT: R 185 CYS cc_start: 0.5162 (OUTLIER) cc_final: 0.3900 (t) REVERT: D 33 LEU cc_start: 0.1880 (OUTLIER) cc_final: 0.1489 (mm) REVERT: G 1 MET cc_start: 0.5467 (pmm) cc_final: 0.4613 (ppp) outliers start: 128 outliers final: 50 residues processed: 492 average time/residue: 0.6982 time to fit residues: 395.2814 Evaluate side-chains 448 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 376 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 211 optimal weight: 0.0670 chunk 261 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 GLN A 735 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN A 780 ASN A 861 GLN A1005 HIS A1332 GLN B 265 GLN B 582 GLN B 649 ASN C 66 HIS E 108 GLN I 18 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.179157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111462 restraints weight = 32577.537| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.35 r_work: 0.3357 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 28501 Z= 0.282 Angle : 0.700 14.440 38503 Z= 0.347 Chirality : 0.049 0.197 4304 Planarity : 0.005 0.051 4983 Dihedral : 5.537 57.729 3813 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.81 % Favored : 94.16 % Rotamer: Outliers : 4.66 % Allowed : 17.04 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.14), residues: 3441 helix: 0.01 (0.15), residues: 1225 sheet: -1.40 (0.23), residues: 477 loop : -1.39 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 169 TYR 0.015 0.002 TYR J 29 PHE 0.027 0.002 PHE A 592 TRP 0.016 0.002 TRP C 49 HIS 0.007 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00692 (28484) covalent geometry : angle 0.68023 (38477) SS BOND : bond 0.00196 ( 1) SS BOND : angle 1.04469 ( 2) hydrogen bonds : bond 0.04270 ( 1133) hydrogen bonds : angle 4.94990 ( 3237) metal coordination : bond 0.01063 ( 16) metal coordination : angle 6.58150 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 397 time to evaluate : 1.070 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 382 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.6950 (mtt180) REVERT: A 502 ASN cc_start: 0.7934 (p0) cc_final: 0.7651 (p0) REVERT: A 504 HIS cc_start: 0.7093 (t-90) cc_final: 0.5528 (m90) REVERT: A 508 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7516 (p) REVERT: A 509 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6528 (tt) REVERT: A 859 TYR cc_start: 0.7680 (t80) cc_final: 0.7191 (t80) REVERT: A 927 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: A 947 HIS cc_start: 0.6623 (t70) cc_final: 0.6275 (t70) REVERT: A 951 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6849 (mt-10) REVERT: A 1015 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7191 (tm-30) REVERT: A 1031 ARG cc_start: 0.7447 (mtt180) cc_final: 0.6906 (mtt90) REVERT: A 1102 MET cc_start: 0.6683 (mtp) cc_final: 0.6230 (mtm) REVERT: A 1126 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: A 1150 ASP cc_start: 0.6568 (t70) cc_final: 0.6168 (t0) REVERT: A 1152 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: A 1180 ASN cc_start: 0.8308 (m110) cc_final: 0.7994 (t0) REVERT: A 1230 GLN cc_start: 0.8958 (mt0) cc_final: 0.8603 (mt0) REVERT: A 1233 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 1269 MET cc_start: 0.1633 (pmm) cc_final: 0.1155 (mmt) REVERT: A 1279 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7702 (mtm) REVERT: A 1280 ASP cc_start: 0.7731 (m-30) cc_final: 0.7477 (m-30) REVERT: A 1293 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7141 (tt) REVERT: A 1331 LEU cc_start: 0.7529 (mp) cc_final: 0.7219 (mt) REVERT: A 1339 ASP cc_start: 0.7974 (t0) cc_final: 0.7274 (m-30) REVERT: A 1355 VAL cc_start: 0.8031 (m) cc_final: 0.7775 (t) REVERT: A 1362 ILE cc_start: 0.7909 (pt) cc_final: 0.7675 (mp) REVERT: A 1408 ARG cc_start: 0.7742 (mmm160) cc_final: 0.7324 (mmm160) REVERT: B 51 ILE cc_start: 0.8748 (tp) cc_final: 0.8483 (tp) REVERT: B 61 ASP cc_start: 0.7113 (m-30) cc_final: 0.6835 (m-30) REVERT: B 92 TYR cc_start: 0.7415 (m-80) cc_final: 0.6630 (m-80) REVERT: B 151 LYS cc_start: 0.7472 (mtpp) cc_final: 0.7164 (mtmt) REVERT: B 155 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8619 (ttm) REVERT: B 160 TYR cc_start: 0.7849 (m-80) cc_final: 0.7317 (m-80) REVERT: B 170 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: B 299 GLU cc_start: 0.8026 (pt0) cc_final: 0.7654 (tt0) REVERT: B 302 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7720 (mtmt) REVERT: B 309 PHE cc_start: 0.8744 (t80) cc_final: 0.8429 (t80) REVERT: B 424 ASP cc_start: 0.6282 (OUTLIER) cc_final: 0.6043 (p0) REVERT: B 433 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7253 (pt) REVERT: B 450 THR cc_start: 0.8417 (m) cc_final: 0.7996 (p) REVERT: B 617 ASP cc_start: 0.7734 (m-30) cc_final: 0.7458 (m-30) REVERT: B 721 ARG cc_start: 0.8245 (mmp80) cc_final: 0.7979 (mmp80) REVERT: B 765 GLU cc_start: 0.8532 (tp30) cc_final: 0.7985 (tp30) REVERT: B 816 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7414 (mm-30) REVERT: B 817 GLN cc_start: 0.8595 (pt0) cc_final: 0.8280 (pt0) REVERT: B 827 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6640 (mt-10) REVERT: B 913 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7797 (tt0) REVERT: B 958 CYS cc_start: 0.8648 (p) cc_final: 0.8387 (m) REVERT: B 965 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8809 (mm) REVERT: C 3 TYR cc_start: 0.8334 (m-80) cc_final: 0.8116 (m-80) REVERT: C 17 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: C 19 VAL cc_start: 0.8499 (t) cc_final: 0.8265 (p) REVERT: C 262 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: E 79 GLU cc_start: 0.8784 (mp0) cc_final: 0.8050 (pm20) REVERT: H 20 LYS cc_start: 0.8745 (mttt) cc_final: 0.8265 (mtpt) REVERT: H 54 ASP cc_start: 0.7880 (m-30) cc_final: 0.7163 (m-30) REVERT: H 57 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7912 (ttt180) REVERT: H 146 LYS cc_start: 0.8123 (tttp) cc_final: 0.7717 (ttpt) REVERT: I 41 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7919 (m110) REVERT: I 67 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8239 (mp10) REVERT: I 93 GLU cc_start: 0.8392 (tt0) cc_final: 0.7884 (tt0) REVERT: K 70 LYS cc_start: 0.8617 (ptpt) cc_final: 0.8355 (ptpp) REVERT: K 110 LYS cc_start: 0.7866 (ttmm) cc_final: 0.7608 (mtpp) REVERT: L 15 MET cc_start: 0.7094 (tpp) cc_final: 0.6581 (tpp) REVERT: L 27 GLU cc_start: 0.8050 (tt0) cc_final: 0.7272 (tm-30) REVERT: R 76 MET cc_start: 0.5482 (mmm) cc_final: 0.4948 (mmm) REVERT: R 104 LEU cc_start: 0.8716 (mm) cc_final: 0.8231 (pp) REVERT: R 170 LEU cc_start: 0.1611 (mt) cc_final: 0.1230 (tm) REVERT: R 184 LEU cc_start: 0.4202 (tp) cc_final: 0.3627 (tp) REVERT: R 185 CYS cc_start: 0.5149 (OUTLIER) cc_final: 0.3795 (t) REVERT: D 33 LEU cc_start: 0.1958 (OUTLIER) cc_final: 0.1578 (mm) REVERT: D 62 MET cc_start: 0.3517 (mmp) cc_final: 0.3018 (mmp) REVERT: G 1 MET cc_start: 0.5591 (pmm) cc_final: 0.4681 (ppp) outliers start: 144 outliers final: 71 residues processed: 492 average time/residue: 0.6793 time to fit residues: 387.0564 Evaluate side-chains 475 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 384 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1126 GLU Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1396 ARG Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 298 MET Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 849 ASP Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 195 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 340 optimal weight: 30.0000 chunk 124 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 334 optimal weight: 50.0000 chunk 341 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 GLN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN B 265 GLN B 452 ASN B 582 GLN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN I 18 GLN I 45 GLN L 26 ASN R 115 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.179729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113212 restraints weight = 32411.695| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.35 r_work: 0.3398 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28501 Z= 0.164 Angle : 0.636 16.451 38503 Z= 0.314 Chirality : 0.046 0.192 4304 Planarity : 0.004 0.052 4983 Dihedral : 5.332 59.046 3813 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 4.15 % Allowed : 17.91 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3441 helix: 0.29 (0.15), residues: 1223 sheet: -1.34 (0.23), residues: 485 loop : -1.25 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 169 TYR 0.021 0.001 TYR E 182 PHE 0.022 0.001 PHE A 592 TRP 0.014 0.002 TRP B 22 HIS 0.008 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00393 (28484) covalent geometry : angle 0.61921 (38477) SS BOND : bond 0.00250 ( 1) SS BOND : angle 0.91431 ( 2) hydrogen bonds : bond 0.03751 ( 1133) hydrogen bonds : angle 4.77599 ( 3237) metal coordination : bond 0.00734 ( 16) metal coordination : angle 5.86543 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 395 time to evaluate : 0.699 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 382 ARG cc_start: 0.7325 (mtm-85) cc_final: 0.6976 (mtt180) REVERT: A 502 ASN cc_start: 0.7876 (p0) cc_final: 0.7575 (p0) REVERT: A 504 HIS cc_start: 0.7080 (t-90) cc_final: 0.5506 (m90) REVERT: A 508 SER cc_start: 0.7976 (m) cc_final: 0.7512 (p) REVERT: A 509 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6497 (tt) REVERT: A 637 MET cc_start: 0.8924 (ptm) cc_final: 0.8551 (ptp) REVERT: A 859 TYR cc_start: 0.7635 (t80) cc_final: 0.7144 (t80) REVERT: A 947 HIS cc_start: 0.6521 (t70) cc_final: 0.6157 (t70) REVERT: A 951 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6725 (mt-10) REVERT: A 954 ARG cc_start: 0.6659 (mtt-85) cc_final: 0.6361 (mtt-85) REVERT: A 1015 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7166 (tm-30) REVERT: A 1031 ARG cc_start: 0.7473 (mtt180) cc_final: 0.6873 (mtt90) REVERT: A 1102 MET cc_start: 0.6707 (mtp) cc_final: 0.6354 (mtm) REVERT: A 1150 ASP cc_start: 0.6397 (t70) cc_final: 0.5926 (t0) REVERT: A 1152 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: A 1180 ASN cc_start: 0.8141 (m110) cc_final: 0.7854 (t0) REVERT: A 1230 GLN cc_start: 0.8971 (mt0) cc_final: 0.8610 (mt0) REVERT: A 1233 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8062 (mm-30) REVERT: A 1279 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7588 (mtm) REVERT: A 1280 ASP cc_start: 0.7691 (m-30) cc_final: 0.7367 (m-30) REVERT: A 1293 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7153 (tt) REVERT: A 1331 LEU cc_start: 0.7579 (mp) cc_final: 0.7258 (mt) REVERT: A 1339 ASP cc_start: 0.7991 (t0) cc_final: 0.7381 (m-30) REVERT: A 1355 VAL cc_start: 0.8117 (m) cc_final: 0.7850 (t) REVERT: A 1408 ARG cc_start: 0.7712 (mmm160) cc_final: 0.7302 (mmm160) REVERT: B 61 ASP cc_start: 0.7004 (m-30) cc_final: 0.6734 (m-30) REVERT: B 92 TYR cc_start: 0.7410 (m-80) cc_final: 0.6554 (m-80) REVERT: B 151 LYS cc_start: 0.7344 (mtpp) cc_final: 0.7073 (mtmt) REVERT: B 155 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8493 (ttm) REVERT: B 160 TYR cc_start: 0.7821 (m-80) cc_final: 0.7244 (m-80) REVERT: B 169 ARG cc_start: 0.7199 (mtp-110) cc_final: 0.6848 (ttt-90) REVERT: B 170 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: B 299 GLU cc_start: 0.7995 (pt0) cc_final: 0.7668 (tt0) REVERT: B 302 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7640 (mtmt) REVERT: B 309 PHE cc_start: 0.8782 (t80) cc_final: 0.8485 (t80) REVERT: B 424 ASP cc_start: 0.6277 (OUTLIER) cc_final: 0.6029 (p0) REVERT: B 433 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7142 (pt) REVERT: B 450 THR cc_start: 0.8365 (m) cc_final: 0.7973 (p) REVERT: B 508 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: B 617 ASP cc_start: 0.7682 (m-30) cc_final: 0.7432 (m-30) REVERT: B 721 ARG cc_start: 0.8010 (mmp80) cc_final: 0.7798 (mmp80) REVERT: B 765 GLU cc_start: 0.8550 (tp30) cc_final: 0.7955 (tp30) REVERT: B 808 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8472 (m) REVERT: B 816 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7240 (mm-30) REVERT: B 817 GLN cc_start: 0.8554 (pt0) cc_final: 0.8281 (pt0) REVERT: B 827 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6704 (mt-10) REVERT: B 913 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: B 965 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8645 (mm) REVERT: C 3 TYR cc_start: 0.8269 (m-80) cc_final: 0.8060 (m-80) REVERT: C 17 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7615 (pm20) REVERT: C 19 VAL cc_start: 0.8427 (t) cc_final: 0.8208 (p) REVERT: C 262 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6872 (mp10) REVERT: E 79 GLU cc_start: 0.8785 (mp0) cc_final: 0.8042 (pm20) REVERT: F 117 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7795 (t0) REVERT: H 20 LYS cc_start: 0.8753 (mttt) cc_final: 0.8390 (mtpt) REVERT: H 54 ASP cc_start: 0.7957 (m-30) cc_final: 0.7176 (m-30) REVERT: H 146 LYS cc_start: 0.8095 (tttp) cc_final: 0.7678 (ttpt) REVERT: I 51 SER cc_start: 0.7526 (t) cc_final: 0.7144 (p) REVERT: I 67 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: I 93 GLU cc_start: 0.8381 (tt0) cc_final: 0.8068 (tt0) REVERT: K 70 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8349 (ptpp) REVERT: K 96 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7944 (p) REVERT: K 110 LYS cc_start: 0.7846 (ttmm) cc_final: 0.7573 (mtpp) REVERT: L 15 MET cc_start: 0.6986 (tpp) cc_final: 0.5798 (tpp) REVERT: L 27 GLU cc_start: 0.8011 (tt0) cc_final: 0.7284 (tp30) REVERT: R 76 MET cc_start: 0.5630 (mmm) cc_final: 0.5085 (mmm) REVERT: R 104 LEU cc_start: 0.8755 (mm) cc_final: 0.8328 (pp) REVERT: R 170 LEU cc_start: 0.1871 (mt) cc_final: 0.1498 (tm) REVERT: R 184 LEU cc_start: 0.4177 (tp) cc_final: 0.3586 (tp) REVERT: R 185 CYS cc_start: 0.5015 (OUTLIER) cc_final: 0.3682 (t) REVERT: R 189 ILE cc_start: 0.4037 (OUTLIER) cc_final: 0.2419 (mt) REVERT: D 33 LEU cc_start: 0.1949 (OUTLIER) cc_final: 0.1553 (mm) REVERT: D 62 MET cc_start: 0.3546 (mmp) cc_final: 0.3037 (mmp) REVERT: G 1 MET cc_start: 0.5571 (pmm) cc_final: 0.4698 (ppp) outliers start: 128 outliers final: 55 residues processed: 478 average time/residue: 0.6983 time to fit residues: 384.9873 Evaluate side-chains 455 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 379 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1152 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 136 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 305 optimal weight: 0.5980 chunk 274 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN B 265 GLN B 582 GLN B 649 ASN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN I 18 GLN L 26 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.179589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112971 restraints weight = 32219.514| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.34 r_work: 0.3392 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28501 Z= 0.176 Angle : 0.636 13.151 38503 Z= 0.315 Chirality : 0.046 0.215 4304 Planarity : 0.004 0.053 4983 Dihedral : 5.235 55.119 3813 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.32 % Favored : 94.65 % Rotamer: Outliers : 4.34 % Allowed : 18.72 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.14), residues: 3441 helix: 0.42 (0.15), residues: 1224 sheet: -1.26 (0.23), residues: 485 loop : -1.18 (0.15), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 770 TYR 0.021 0.001 TYR E 182 PHE 0.023 0.001 PHE A 592 TRP 0.014 0.002 TRP B 27 HIS 0.008 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00427 (28484) covalent geometry : angle 0.62188 (38477) SS BOND : bond 0.00236 ( 1) SS BOND : angle 0.89754 ( 2) hydrogen bonds : bond 0.03738 ( 1133) hydrogen bonds : angle 4.70237 ( 3237) metal coordination : bond 0.00746 ( 16) metal coordination : angle 5.45501 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 393 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ARG cc_start: 0.7296 (mtm-85) cc_final: 0.7016 (mtt180) REVERT: A 401 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6446 (ttp-110) REVERT: A 502 ASN cc_start: 0.7849 (p0) cc_final: 0.7576 (p0) REVERT: A 504 HIS cc_start: 0.7093 (t-90) cc_final: 0.5514 (m90) REVERT: A 508 SER cc_start: 0.7937 (OUTLIER) cc_final: 0.7483 (p) REVERT: A 509 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6489 (tt) REVERT: A 769 MET cc_start: 0.6126 (mtt) cc_final: 0.5885 (mtt) REVERT: A 803 LYS cc_start: 0.7724 (tppp) cc_final: 0.7029 (ttpp) REVERT: A 859 TYR cc_start: 0.7673 (t80) cc_final: 0.7150 (t80) REVERT: A 927 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: A 947 HIS cc_start: 0.6489 (t70) cc_final: 0.6128 (t70) REVERT: A 951 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6714 (mt-10) REVERT: A 1015 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7106 (tm-30) REVERT: A 1031 ARG cc_start: 0.7472 (mtt180) cc_final: 0.6871 (mtt90) REVERT: A 1102 MET cc_start: 0.6806 (mtp) cc_final: 0.6471 (mtm) REVERT: A 1126 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7228 (tt0) REVERT: A 1150 ASP cc_start: 0.6428 (t70) cc_final: 0.5898 (t0) REVERT: A 1180 ASN cc_start: 0.8126 (m110) cc_final: 0.7844 (t0) REVERT: A 1230 GLN cc_start: 0.8945 (mt0) cc_final: 0.8634 (mt0) REVERT: A 1233 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8056 (mm-30) REVERT: A 1279 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7592 (mtm) REVERT: A 1280 ASP cc_start: 0.7669 (m-30) cc_final: 0.7370 (m-30) REVERT: A 1293 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7157 (tt) REVERT: A 1310 HIS cc_start: 0.7320 (p90) cc_final: 0.6948 (p90) REVERT: A 1331 LEU cc_start: 0.7653 (mp) cc_final: 0.7298 (mt) REVERT: A 1339 ASP cc_start: 0.8056 (t0) cc_final: 0.7464 (m-30) REVERT: A 1355 VAL cc_start: 0.8105 (m) cc_final: 0.7833 (t) REVERT: A 1408 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7255 (mmm160) REVERT: B 51 ILE cc_start: 0.8701 (tp) cc_final: 0.8448 (tp) REVERT: B 61 ASP cc_start: 0.7092 (m-30) cc_final: 0.6803 (m-30) REVERT: B 92 TYR cc_start: 0.7396 (m-80) cc_final: 0.6588 (m-80) REVERT: B 151 LYS cc_start: 0.7354 (mtpp) cc_final: 0.7070 (mtmt) REVERT: B 155 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8530 (ttm) REVERT: B 160 TYR cc_start: 0.7801 (m-80) cc_final: 0.7259 (m-80) REVERT: B 169 ARG cc_start: 0.7250 (mtp-110) cc_final: 0.6911 (ttt-90) REVERT: B 170 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: B 299 GLU cc_start: 0.7915 (pt0) cc_final: 0.7678 (tt0) REVERT: B 302 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7650 (mtmt) REVERT: B 309 PHE cc_start: 0.8774 (t80) cc_final: 0.8496 (t80) REVERT: B 334 LYS cc_start: 0.7460 (tppp) cc_final: 0.6893 (ttpp) REVERT: B 388 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.7911 (t80) REVERT: B 424 ASP cc_start: 0.6235 (OUTLIER) cc_final: 0.5999 (p0) REVERT: B 433 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7135 (pt) REVERT: B 450 THR cc_start: 0.8345 (m) cc_final: 0.7961 (p) REVERT: B 508 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: B 617 ASP cc_start: 0.7629 (m-30) cc_final: 0.7382 (m-30) REVERT: B 765 GLU cc_start: 0.8539 (tp30) cc_final: 0.7917 (tp30) REVERT: B 808 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8451 (m) REVERT: B 816 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7223 (mm-30) REVERT: B 817 GLN cc_start: 0.8554 (pt0) cc_final: 0.8281 (pt0) REVERT: B 827 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6622 (mt-10) REVERT: B 913 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: B 965 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8663 (mm) REVERT: C 3 TYR cc_start: 0.8247 (m-80) cc_final: 0.8037 (m-80) REVERT: C 6 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7640 (mt0) REVERT: C 17 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: C 19 VAL cc_start: 0.8436 (t) cc_final: 0.8218 (p) REVERT: C 262 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: E 79 GLU cc_start: 0.8769 (mp0) cc_final: 0.8049 (pm20) REVERT: E 137 ILE cc_start: 0.7692 (pt) cc_final: 0.7488 (pp) REVERT: H 20 LYS cc_start: 0.8747 (mttt) cc_final: 0.8392 (mtpt) REVERT: H 54 ASP cc_start: 0.7979 (m-30) cc_final: 0.7160 (m-30) REVERT: H 146 LYS cc_start: 0.8052 (tttp) cc_final: 0.7676 (ttpt) REVERT: I 51 SER cc_start: 0.7388 (t) cc_final: 0.7015 (p) REVERT: I 93 GLU cc_start: 0.8393 (tt0) cc_final: 0.8041 (tt0) REVERT: K 23 LYS cc_start: 0.8438 (mmtt) cc_final: 0.8135 (mptt) REVERT: K 70 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8349 (ptpp) REVERT: K 96 SER cc_start: 0.8154 (OUTLIER) cc_final: 0.7932 (p) REVERT: K 110 LYS cc_start: 0.7824 (ttmm) cc_final: 0.7526 (mtpp) REVERT: L 15 MET cc_start: 0.6971 (tpp) cc_final: 0.5648 (tpp) REVERT: L 27 GLU cc_start: 0.7961 (tt0) cc_final: 0.7238 (tp30) REVERT: R 76 MET cc_start: 0.5581 (mmm) cc_final: 0.5085 (mmm) REVERT: R 104 LEU cc_start: 0.8743 (mm) cc_final: 0.8358 (pp) REVERT: R 170 LEU cc_start: 0.1650 (mt) cc_final: 0.1301 (tm) REVERT: R 184 LEU cc_start: 0.3986 (tp) cc_final: 0.3394 (tp) REVERT: R 185 CYS cc_start: 0.5001 (OUTLIER) cc_final: 0.3644 (t) REVERT: R 189 ILE cc_start: 0.3994 (OUTLIER) cc_final: 0.2462 (mt) REVERT: D 33 LEU cc_start: 0.2181 (OUTLIER) cc_final: 0.1803 (mm) REVERT: D 62 MET cc_start: 0.3476 (mmp) cc_final: 0.2985 (mmp) REVERT: G 1 MET cc_start: 0.5426 (pmm) cc_final: 0.4565 (ppp) REVERT: G 164 MET cc_start: 0.1394 (mmt) cc_final: 0.0037 (pp-130) outliers start: 134 outliers final: 64 residues processed: 484 average time/residue: 0.6825 time to fit residues: 382.1577 Evaluate side-chains 468 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 381 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 103 GLU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 261 optimal weight: 8.9990 chunk 218 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 217 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 260 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN B 265 GLN B 582 GLN B 649 ASN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN E 108 GLN I 18 GLN L 26 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114323 restraints weight = 32364.704| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.38 r_work: 0.3347 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28501 Z= 0.147 Angle : 0.628 12.785 38503 Z= 0.310 Chirality : 0.046 0.294 4304 Planarity : 0.004 0.057 4983 Dihedral : 5.113 52.739 3813 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.68 % Rotamer: Outliers : 3.73 % Allowed : 19.79 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.14), residues: 3441 helix: 0.60 (0.15), residues: 1221 sheet: -1.15 (0.23), residues: 492 loop : -1.09 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 255 TYR 0.023 0.001 TYR E 182 PHE 0.021 0.001 PHE A 592 TRP 0.013 0.002 TRP A 679 HIS 0.008 0.001 HIS R 177 Details of bonding type rmsd covalent geometry : bond 0.00350 (28484) covalent geometry : angle 0.61569 (38477) SS BOND : bond 0.00246 ( 1) SS BOND : angle 0.85926 ( 2) hydrogen bonds : bond 0.03537 ( 1133) hydrogen bonds : angle 4.62597 ( 3237) metal coordination : bond 0.00626 ( 16) metal coordination : angle 5.01557 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 400 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.7120 (mtt180) REVERT: A 504 HIS cc_start: 0.7140 (t-90) cc_final: 0.5538 (m90) REVERT: A 508 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7378 (p) REVERT: A 509 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6262 (tt) REVERT: A 724 GLU cc_start: 0.8055 (mp0) cc_final: 0.7788 (mp0) REVERT: A 769 MET cc_start: 0.6199 (mtt) cc_final: 0.5990 (mtt) REVERT: A 859 TYR cc_start: 0.7660 (t80) cc_final: 0.7141 (t80) REVERT: A 927 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: A 947 HIS cc_start: 0.6449 (t70) cc_final: 0.6073 (t-170) REVERT: A 951 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6652 (mt-10) REVERT: A 1015 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7118 (tm-30) REVERT: A 1102 MET cc_start: 0.6818 (mtp) cc_final: 0.6612 (mtm) REVERT: A 1150 ASP cc_start: 0.6393 (t70) cc_final: 0.6138 (t0) REVERT: A 1180 ASN cc_start: 0.8114 (m110) cc_final: 0.7849 (t0) REVERT: A 1215 GLU cc_start: 0.7370 (tt0) cc_final: 0.6912 (pt0) REVERT: A 1230 GLN cc_start: 0.8962 (mt0) cc_final: 0.8630 (mt0) REVERT: A 1233 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8039 (mm-30) REVERT: A 1269 MET cc_start: 0.1051 (pmm) cc_final: 0.0648 (ppp) REVERT: A 1279 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7146 (ptp) REVERT: A 1280 ASP cc_start: 0.7662 (m-30) cc_final: 0.7210 (m-30) REVERT: A 1293 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7107 (tt) REVERT: A 1310 HIS cc_start: 0.7288 (p90) cc_final: 0.6973 (p90) REVERT: A 1331 LEU cc_start: 0.7774 (mp) cc_final: 0.7405 (mt) REVERT: A 1337 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6515 (tp30) REVERT: A 1339 ASP cc_start: 0.7872 (t0) cc_final: 0.7235 (m-30) REVERT: A 1408 ARG cc_start: 0.7577 (mmm160) cc_final: 0.7192 (mmm160) REVERT: B 61 ASP cc_start: 0.7055 (m-30) cc_final: 0.6808 (m-30) REVERT: B 92 TYR cc_start: 0.7346 (m-80) cc_final: 0.6531 (m-80) REVERT: B 151 LYS cc_start: 0.7340 (mtpp) cc_final: 0.7127 (mtmt) REVERT: B 155 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8519 (ttm) REVERT: B 169 ARG cc_start: 0.7403 (mtp-110) cc_final: 0.7065 (ttt-90) REVERT: B 170 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: B 264 LYS cc_start: 0.8582 (mptt) cc_final: 0.7921 (mptm) REVERT: B 299 GLU cc_start: 0.7955 (pt0) cc_final: 0.7676 (tt0) REVERT: B 302 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7604 (mtmt) REVERT: B 309 PHE cc_start: 0.8742 (t80) cc_final: 0.8486 (t80) REVERT: B 407 MET cc_start: 0.7108 (mtt) cc_final: 0.6788 (mtt) REVERT: B 424 ASP cc_start: 0.5868 (OUTLIER) cc_final: 0.5647 (p0) REVERT: B 433 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7065 (pt) REVERT: B 450 THR cc_start: 0.8368 (m) cc_final: 0.8006 (p) REVERT: B 508 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8034 (mtt) REVERT: B 617 ASP cc_start: 0.7678 (m-30) cc_final: 0.7410 (m-30) REVERT: B 728 MET cc_start: 0.7852 (mtm) cc_final: 0.7200 (mmp) REVERT: B 765 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: B 770 ARG cc_start: 0.8105 (mtm110) cc_final: 0.7329 (ttp80) REVERT: B 808 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8487 (m) REVERT: B 816 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7163 (mm-30) REVERT: B 817 GLN cc_start: 0.8462 (pt0) cc_final: 0.8196 (pt0) REVERT: B 827 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6661 (mt-10) REVERT: B 913 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: B 965 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8584 (mm) REVERT: C 17 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: C 19 VAL cc_start: 0.8390 (t) cc_final: 0.8152 (p) REVERT: C 262 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6812 (mp10) REVERT: E 79 GLU cc_start: 0.8771 (mp0) cc_final: 0.8051 (pm20) REVERT: H 20 LYS cc_start: 0.8725 (mttt) cc_final: 0.8215 (tptp) REVERT: H 35 PHE cc_start: 0.7868 (m-10) cc_final: 0.7300 (m-80) REVERT: H 54 ASP cc_start: 0.7960 (m-30) cc_final: 0.7103 (m-30) REVERT: H 146 LYS cc_start: 0.8067 (tttp) cc_final: 0.7648 (ttpt) REVERT: I 51 SER cc_start: 0.7311 (t) cc_final: 0.6924 (p) REVERT: I 93 GLU cc_start: 0.8394 (tt0) cc_final: 0.8060 (tt0) REVERT: K 23 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8158 (mptt) REVERT: K 70 LYS cc_start: 0.8600 (ptpt) cc_final: 0.8353 (ptpp) REVERT: K 96 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7963 (p) REVERT: K 110 LYS cc_start: 0.7835 (ttmm) cc_final: 0.7522 (mtpp) REVERT: L 15 MET cc_start: 0.6861 (tpp) cc_final: 0.5477 (tpp) REVERT: L 27 GLU cc_start: 0.7946 (tt0) cc_final: 0.7169 (tp30) REVERT: L 42 ARG cc_start: 0.8559 (mtp85) cc_final: 0.8157 (mmt90) REVERT: R 55 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7352 (pm20) REVERT: R 76 MET cc_start: 0.5709 (mmm) cc_final: 0.5141 (mmm) REVERT: R 104 LEU cc_start: 0.8764 (mm) cc_final: 0.8370 (pp) REVERT: R 170 LEU cc_start: 0.1845 (mt) cc_final: 0.1484 (tm) REVERT: R 184 LEU cc_start: 0.3799 (tp) cc_final: 0.3213 (tp) REVERT: R 185 CYS cc_start: 0.5060 (OUTLIER) cc_final: 0.3682 (t) REVERT: R 189 ILE cc_start: 0.3607 (OUTLIER) cc_final: 0.2305 (mt) REVERT: D 33 LEU cc_start: 0.2147 (OUTLIER) cc_final: 0.1534 (pt) REVERT: G 1 MET cc_start: 0.5511 (pmm) cc_final: 0.4649 (ppp) REVERT: G 164 MET cc_start: 0.1242 (mmt) cc_final: -0.0132 (pp-130) outliers start: 115 outliers final: 65 residues processed: 482 average time/residue: 0.6795 time to fit residues: 378.9533 Evaluate side-chains 474 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 387 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1024 ASN Chi-restraints excluded: chain A residue 1118 THR Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 765 GLU Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 131 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 126 optimal weight: 0.4980 chunk 111 optimal weight: 7.9990 chunk 303 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 327 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 333 optimal weight: 50.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN A1410 HIS B 265 GLN B 582 GLN B 649 ASN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN E 174 GLN I 18 GLN L 26 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.180170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113778 restraints weight = 32476.037| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.34 r_work: 0.3402 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28501 Z= 0.173 Angle : 0.635 13.123 38503 Z= 0.316 Chirality : 0.046 0.266 4304 Planarity : 0.004 0.075 4983 Dihedral : 5.081 52.549 3813 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.32 % Favored : 94.65 % Rotamer: Outliers : 3.85 % Allowed : 19.99 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.14), residues: 3441 helix: 0.62 (0.15), residues: 1228 sheet: -1.08 (0.23), residues: 492 loop : -1.08 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 255 TYR 0.024 0.001 TYR E 182 PHE 0.023 0.002 PHE A 592 TRP 0.015 0.002 TRP B 27 HIS 0.020 0.001 HIS R 60 Details of bonding type rmsd covalent geometry : bond 0.00420 (28484) covalent geometry : angle 0.62294 (38477) SS BOND : bond 0.00225 ( 1) SS BOND : angle 0.86167 ( 2) hydrogen bonds : bond 0.03647 ( 1133) hydrogen bonds : angle 4.60128 ( 3237) metal coordination : bond 0.00688 ( 16) metal coordination : angle 4.93950 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 393 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.7129 (mtt180) REVERT: A 504 HIS cc_start: 0.7128 (t-90) cc_final: 0.5556 (m90) REVERT: A 508 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7363 (p) REVERT: A 509 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6328 (tt) REVERT: A 724 GLU cc_start: 0.8059 (mp0) cc_final: 0.7702 (mp0) REVERT: A 803 LYS cc_start: 0.7744 (tppp) cc_final: 0.7249 (tppt) REVERT: A 859 TYR cc_start: 0.7674 (t80) cc_final: 0.7164 (t80) REVERT: A 902 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7745 (pt0) REVERT: A 927 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7752 (tp30) REVERT: A 947 HIS cc_start: 0.6521 (t70) cc_final: 0.6152 (t-170) REVERT: A 951 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6642 (mt-10) REVERT: A 1015 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7121 (tm-30) REVERT: A 1031 ARG cc_start: 0.7494 (mtt180) cc_final: 0.6896 (mtt90) REVERT: A 1102 MET cc_start: 0.6823 (mtp) cc_final: 0.6516 (mtm) REVERT: A 1150 ASP cc_start: 0.6460 (t70) cc_final: 0.5846 (t0) REVERT: A 1180 ASN cc_start: 0.8318 (m110) cc_final: 0.8094 (t0) REVERT: A 1230 GLN cc_start: 0.8964 (mt0) cc_final: 0.8629 (mt0) REVERT: A 1233 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8048 (mm-30) REVERT: A 1269 MET cc_start: 0.1194 (pmm) cc_final: 0.0843 (ppp) REVERT: A 1279 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7206 (ptp) REVERT: A 1280 ASP cc_start: 0.7686 (m-30) cc_final: 0.7268 (m-30) REVERT: A 1293 LEU cc_start: 0.7446 (tp) cc_final: 0.7099 (tt) REVERT: A 1308 TYR cc_start: 0.6903 (m-80) cc_final: 0.6647 (m-80) REVERT: A 1310 HIS cc_start: 0.7351 (p90) cc_final: 0.7081 (p90) REVERT: A 1331 LEU cc_start: 0.7812 (mp) cc_final: 0.7427 (mt) REVERT: A 1337 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6540 (tp30) REVERT: A 1339 ASP cc_start: 0.8005 (t0) cc_final: 0.7338 (m-30) REVERT: A 1355 VAL cc_start: 0.8032 (m) cc_final: 0.7756 (t) REVERT: A 1408 ARG cc_start: 0.7686 (mmm160) cc_final: 0.7288 (mmm160) REVERT: B 61 ASP cc_start: 0.7122 (m-30) cc_final: 0.6852 (m-30) REVERT: B 92 TYR cc_start: 0.7358 (m-80) cc_final: 0.6552 (m-80) REVERT: B 151 LYS cc_start: 0.7419 (mtpp) cc_final: 0.7146 (mtmt) REVERT: B 155 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8530 (ttm) REVERT: B 160 TYR cc_start: 0.7797 (m-80) cc_final: 0.7157 (m-80) REVERT: B 169 ARG cc_start: 0.7398 (mtp-110) cc_final: 0.7073 (ttt-90) REVERT: B 170 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: B 264 LYS cc_start: 0.8623 (mptt) cc_final: 0.7953 (mptm) REVERT: B 302 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7602 (mtmt) REVERT: B 309 PHE cc_start: 0.8729 (t80) cc_final: 0.8471 (t80) REVERT: B 334 LYS cc_start: 0.7426 (tppp) cc_final: 0.6862 (ttpt) REVERT: B 424 ASP cc_start: 0.5765 (OUTLIER) cc_final: 0.5552 (p0) REVERT: B 433 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7050 (pt) REVERT: B 450 THR cc_start: 0.8329 (m) cc_final: 0.7981 (p) REVERT: B 508 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8049 (mtt) REVERT: B 617 ASP cc_start: 0.7728 (m-30) cc_final: 0.7466 (m-30) REVERT: B 765 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: B 770 ARG cc_start: 0.8113 (mtm110) cc_final: 0.7347 (ttp80) REVERT: B 808 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8441 (m) REVERT: B 816 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7264 (mm-30) REVERT: B 817 GLN cc_start: 0.8534 (pt0) cc_final: 0.8278 (pt0) REVERT: B 827 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6696 (mt-10) REVERT: B 965 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8668 (mm) REVERT: C 17 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: C 126 ARG cc_start: 0.8078 (ptm160) cc_final: 0.7413 (ptm160) REVERT: C 262 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6840 (mp10) REVERT: E 79 GLU cc_start: 0.8777 (mp0) cc_final: 0.8067 (pm20) REVERT: H 20 LYS cc_start: 0.8717 (mttt) cc_final: 0.8198 (tptp) REVERT: H 35 PHE cc_start: 0.7966 (m-10) cc_final: 0.7413 (m-80) REVERT: H 54 ASP cc_start: 0.7979 (m-30) cc_final: 0.7113 (m-30) REVERT: H 146 LYS cc_start: 0.8023 (tttp) cc_final: 0.7673 (ttpt) REVERT: I 51 SER cc_start: 0.7359 (t) cc_final: 0.6960 (p) REVERT: I 93 GLU cc_start: 0.8402 (tt0) cc_final: 0.8068 (tt0) REVERT: K 70 LYS cc_start: 0.8614 (ptpt) cc_final: 0.8369 (ptpp) REVERT: K 96 SER cc_start: 0.8171 (OUTLIER) cc_final: 0.7943 (p) REVERT: K 110 LYS cc_start: 0.7805 (ttmm) cc_final: 0.7069 (mptt) REVERT: L 15 MET cc_start: 0.6928 (tpp) cc_final: 0.5548 (tpp) REVERT: L 27 GLU cc_start: 0.7968 (tt0) cc_final: 0.7191 (tp30) REVERT: L 35 ARG cc_start: 0.8286 (ttt90) cc_final: 0.7496 (ttp-110) REVERT: L 42 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8224 (mmt90) REVERT: L 50 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8167 (mmtm) REVERT: R 55 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: R 76 MET cc_start: 0.5490 (mmm) cc_final: 0.5017 (mmm) REVERT: R 104 LEU cc_start: 0.8754 (mm) cc_final: 0.8374 (pp) REVERT: R 170 LEU cc_start: 0.1928 (mt) cc_final: 0.1497 (tm) REVERT: R 184 LEU cc_start: 0.3684 (tp) cc_final: 0.3153 (tp) REVERT: R 185 CYS cc_start: 0.5000 (OUTLIER) cc_final: 0.3623 (t) REVERT: R 189 ILE cc_start: 0.3415 (OUTLIER) cc_final: 0.2361 (mt) REVERT: D 33 LEU cc_start: 0.2044 (OUTLIER) cc_final: 0.1566 (pt) REVERT: D 62 MET cc_start: 0.3257 (mmp) cc_final: 0.2718 (mmp) REVERT: G 1 MET cc_start: 0.5522 (pmm) cc_final: 0.4640 (ppp) REVERT: G 164 MET cc_start: 0.1291 (mmt) cc_final: -0.0109 (pp-130) outliers start: 119 outliers final: 64 residues processed: 475 average time/residue: 0.6761 time to fit residues: 371.3064 Evaluate side-chains 464 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 378 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 765 GLU Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1007 ASN Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 42 ARG Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 30.0000 chunk 65 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 80 optimal weight: 0.0870 chunk 175 optimal weight: 0.6980 chunk 264 optimal weight: 0.9980 chunk 127 optimal weight: 0.2980 chunk 172 optimal weight: 0.7980 chunk 149 optimal weight: 0.0470 chunk 284 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A 502 ASN A 539 GLN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN A 861 GLN A1384 HIS B 265 GLN B 582 GLN B 649 ASN B 941 GLN B1049 GLN C 18 ASN C 66 HIS E 92 GLN E 108 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 GLN K 84 GLN L 26 ASN G 14 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.182786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116820 restraints weight = 32293.147| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.37 r_work: 0.3445 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28501 Z= 0.117 Angle : 0.613 12.841 38503 Z= 0.304 Chirality : 0.045 0.245 4304 Planarity : 0.004 0.077 4983 Dihedral : 4.879 54.194 3811 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 2.92 % Allowed : 21.09 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.15), residues: 3441 helix: 0.80 (0.15), residues: 1229 sheet: -1.05 (0.23), residues: 501 loop : -0.96 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG B 255 TYR 0.019 0.001 TYR B 388 PHE 0.018 0.001 PHE A 592 TRP 0.013 0.001 TRP C 203 HIS 0.008 0.001 HIS R 60 Details of bonding type rmsd covalent geometry : bond 0.00269 (28484) covalent geometry : angle 0.60401 (38477) SS BOND : bond 0.00271 ( 1) SS BOND : angle 0.76746 ( 2) hydrogen bonds : bond 0.03276 ( 1133) hydrogen bonds : angle 4.49785 ( 3237) metal coordination : bond 0.00547 ( 16) metal coordination : angle 4.32667 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6882 Ramachandran restraints generated. 3441 Oldfield, 0 Emsley, 3441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 390 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.7030 (mtt180) REVERT: A 504 HIS cc_start: 0.7132 (t-90) cc_final: 0.5536 (m90) REVERT: A 508 SER cc_start: 0.7638 (OUTLIER) cc_final: 0.7389 (p) REVERT: A 509 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6301 (tt) REVERT: A 637 MET cc_start: 0.8856 (ptm) cc_final: 0.8477 (ptp) REVERT: A 724 GLU cc_start: 0.8031 (mp0) cc_final: 0.7793 (mp0) REVERT: A 859 TYR cc_start: 0.7641 (t80) cc_final: 0.7148 (t80) REVERT: A 927 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: A 947 HIS cc_start: 0.6331 (t70) cc_final: 0.5978 (t-170) REVERT: A 951 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6647 (mt-10) REVERT: A 976 LYS cc_start: 0.8421 (ttmm) cc_final: 0.7835 (ttpt) REVERT: A 1015 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7061 (tm-30) REVERT: A 1054 MET cc_start: 0.8727 (tpp) cc_final: 0.8501 (mmm) REVERT: A 1150 ASP cc_start: 0.6215 (t70) cc_final: 0.5935 (t0) REVERT: A 1180 ASN cc_start: 0.8071 (m110) cc_final: 0.7869 (t0) REVERT: A 1215 GLU cc_start: 0.7421 (tt0) cc_final: 0.6999 (pt0) REVERT: A 1230 GLN cc_start: 0.8937 (mt0) cc_final: 0.8607 (mt0) REVERT: A 1233 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8047 (mm-30) REVERT: A 1269 MET cc_start: 0.1224 (pmm) cc_final: 0.0889 (ppp) REVERT: A 1279 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6992 (ptp) REVERT: A 1280 ASP cc_start: 0.7689 (m-30) cc_final: 0.7283 (m-30) REVERT: A 1293 LEU cc_start: 0.7392 (tp) cc_final: 0.7047 (tt) REVERT: A 1296 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.6103 (tpt) REVERT: A 1308 TYR cc_start: 0.6904 (m-80) cc_final: 0.6683 (m-80) REVERT: A 1310 HIS cc_start: 0.7321 (p90) cc_final: 0.7051 (p90) REVERT: A 1331 LEU cc_start: 0.7822 (mp) cc_final: 0.7460 (mt) REVERT: A 1337 GLU cc_start: 0.7496 (mm-30) cc_final: 0.6457 (tp30) REVERT: A 1339 ASP cc_start: 0.7955 (t0) cc_final: 0.7306 (m-30) REVERT: A 1355 VAL cc_start: 0.8031 (m) cc_final: 0.7743 (t) REVERT: A 1408 ARG cc_start: 0.7557 (mmm160) cc_final: 0.7160 (mmm160) REVERT: B 61 ASP cc_start: 0.7127 (m-30) cc_final: 0.6776 (m-30) REVERT: B 92 TYR cc_start: 0.7360 (m-80) cc_final: 0.6492 (m-80) REVERT: B 151 LYS cc_start: 0.7295 (mtpp) cc_final: 0.7032 (mtmm) REVERT: B 155 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8468 (ttm) REVERT: B 169 ARG cc_start: 0.7412 (mtp-110) cc_final: 0.7120 (ttt-90) REVERT: B 170 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: B 211 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6679 (pttt) REVERT: B 254 GLN cc_start: 0.7876 (mt0) cc_final: 0.7526 (mt0) REVERT: B 264 LYS cc_start: 0.8659 (mptt) cc_final: 0.7970 (mptm) REVERT: B 298 MET cc_start: 0.8016 (mtm) cc_final: 0.7813 (mtp) REVERT: B 302 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7568 (mtmt) REVERT: B 309 PHE cc_start: 0.8701 (t80) cc_final: 0.8478 (t80) REVERT: B 334 LYS cc_start: 0.7443 (tppp) cc_final: 0.6878 (ttpt) REVERT: B 424 ASP cc_start: 0.5604 (OUTLIER) cc_final: 0.5374 (p0) REVERT: B 433 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7051 (pt) REVERT: B 450 THR cc_start: 0.8324 (m) cc_final: 0.8015 (p) REVERT: B 508 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.7867 (mtt) REVERT: B 617 ASP cc_start: 0.7644 (m-30) cc_final: 0.7405 (m-30) REVERT: B 728 MET cc_start: 0.7621 (mtm) cc_final: 0.7025 (mmp) REVERT: B 765 GLU cc_start: 0.8533 (tp30) cc_final: 0.7968 (tp30) REVERT: B 770 ARG cc_start: 0.8073 (mtm110) cc_final: 0.7349 (ttp80) REVERT: B 791 GLU cc_start: 0.7260 (pm20) cc_final: 0.6674 (mp0) REVERT: B 808 SER cc_start: 0.8877 (OUTLIER) cc_final: 0.8499 (m) REVERT: B 816 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7098 (mm-30) REVERT: B 817 GLN cc_start: 0.8377 (pt0) cc_final: 0.8106 (pt0) REVERT: B 827 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6735 (mt-10) REVERT: B 965 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8463 (mm) REVERT: C 17 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: C 41 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8114 (mt-10) REVERT: C 262 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6822 (mp10) REVERT: E 79 GLU cc_start: 0.8791 (mp0) cc_final: 0.8097 (pm20) REVERT: E 92 GLN cc_start: 0.8167 (pt0) cc_final: 0.7637 (pp30) REVERT: F 95 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8123 (ptpp) REVERT: H 20 LYS cc_start: 0.8701 (mttt) cc_final: 0.8441 (mtpt) REVERT: H 35 PHE cc_start: 0.7905 (m-10) cc_final: 0.7366 (m-80) REVERT: H 54 ASP cc_start: 0.7967 (m-30) cc_final: 0.7111 (m-30) REVERT: H 146 LYS cc_start: 0.8097 (tttp) cc_final: 0.7672 (ttpt) REVERT: I 51 SER cc_start: 0.7353 (t) cc_final: 0.6927 (p) REVERT: I 93 GLU cc_start: 0.8366 (tt0) cc_final: 0.7936 (tt0) REVERT: K 103 GLU cc_start: 0.7564 (pt0) cc_final: 0.7186 (mt-10) REVERT: K 110 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7060 (mptt) REVERT: L 15 MET cc_start: 0.6819 (tpp) cc_final: 0.5454 (tpp) REVERT: L 27 GLU cc_start: 0.7981 (tt0) cc_final: 0.7314 (tp30) REVERT: L 35 ARG cc_start: 0.8232 (ttt90) cc_final: 0.7464 (ttp-110) REVERT: L 42 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8251 (mmt90) REVERT: L 50 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8127 (mmtm) REVERT: R 55 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: R 76 MET cc_start: 0.5490 (mmm) cc_final: 0.5010 (mmm) REVERT: R 104 LEU cc_start: 0.8700 (mm) cc_final: 0.8318 (pp) REVERT: R 170 LEU cc_start: 0.1849 (mt) cc_final: 0.1387 (tm) REVERT: R 184 LEU cc_start: 0.3630 (tp) cc_final: 0.3076 (tp) REVERT: R 185 CYS cc_start: 0.4740 (OUTLIER) cc_final: 0.3513 (t) REVERT: R 189 ILE cc_start: 0.3296 (OUTLIER) cc_final: 0.2364 (mt) REVERT: D 33 LEU cc_start: 0.2213 (OUTLIER) cc_final: 0.1722 (pt) REVERT: D 62 MET cc_start: 0.3248 (mmp) cc_final: 0.2786 (mmm) REVERT: G 1 MET cc_start: 0.5475 (pmm) cc_final: 0.4603 (ppp) REVERT: G 164 MET cc_start: 0.1290 (mmt) cc_final: -0.0008 (pp-130) outliers start: 90 outliers final: 47 residues processed: 453 average time/residue: 0.6682 time to fit residues: 350.7919 Evaluate side-chains 448 residues out of total 3114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 380 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1186 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1296 MET Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 687 VAL Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 941 GLN Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 1000 THR Chi-restraints excluded: chain B residue 1028 LEU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 116 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 42 ARG Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 114 LYS Chi-restraints excluded: chain R residue 119 ILE Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 200 PHE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 49 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 195 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 297 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN A 502 ASN ** A 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1384 HIS B 265 GLN B 582 GLN B 649 ASN ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 ASN E 92 GLN E 108 GLN H 44 ASN I 18 GLN L 26 ASN ** R 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114568 restraints weight = 32317.477| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.37 r_work: 0.3381 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28501 Z= 0.170 Angle : 0.637 14.389 38503 Z= 0.316 Chirality : 0.046 0.273 4304 Planarity : 0.004 0.077 4983 Dihedral : 4.932 53.270 3811 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 2.88 % Allowed : 21.12 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.14), residues: 3441 helix: 0.80 (0.15), residues: 1220 sheet: -0.94 (0.23), residues: 491 loop : -0.97 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 255 TYR 0.019 0.001 TYR B 388 PHE 0.021 0.001 PHE A 592 TRP 0.014 0.002 TRP B 27 HIS 0.019 0.001 HIS R 60 Details of bonding type rmsd covalent geometry : bond 0.00412 (28484) covalent geometry : angle 0.62665 (38477) SS BOND : bond 0.00210 ( 1) SS BOND : angle 0.80042 ( 2) hydrogen bonds : bond 0.03559 ( 1133) hydrogen bonds : angle 4.51833 ( 3237) metal coordination : bond 0.00623 ( 16) metal coordination : angle 4.52255 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13560.88 seconds wall clock time: 230 minutes 24.53 seconds (13824.53 seconds total)