Starting phenix.real_space_refine on Sat Aug 23 23:51:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3q_34473/08_2025/8h3q_34473.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3q_34473/08_2025/8h3q_34473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h3q_34473/08_2025/8h3q_34473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3q_34473/08_2025/8h3q_34473.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h3q_34473/08_2025/8h3q_34473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3q_34473/08_2025/8h3q_34473.map" } resolution = 3.76 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= 0.002 sd= 0.033 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 3 6.06 5 S 104 5.16 5 C 9821 2.51 5 N 2682 2.21 5 O 2901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15511 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 8930 Classifications: {'peptide': 1150} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 1095} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 5841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5841 Classifications: {'peptide': 717} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 699} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 737 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14968 SG CYS E 42 58.907 40.541 14.949 1.00135.97 S ATOM 14987 SG CYS E 45 61.101 37.692 13.629 1.00137.74 S ATOM 15282 SG CYS E 83 62.592 40.082 16.293 1.00118.07 S ATOM 15211 SG CYS E 75 54.245 51.033 20.775 1.00115.91 S ATOM 15378 SG CYS E 94 56.392 51.543 18.567 1.00129.19 S ATOM 15054 SG CYS E 53 64.560 36.436 18.063 1.00143.05 S ATOM 15077 SG CYS E 56 66.412 33.863 20.300 1.00146.03 S ATOM 15161 SG CYS E 68 63.508 35.885 21.772 1.00133.77 S Time building chain proxies: 2.61, per 1000 atoms: 0.17 Number of scatterers: 15511 At special positions: 0 Unit cell: (111.708, 128.412, 151.38, 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 3 29.99 S 104 16.00 O 2901 8.00 N 2682 7.00 C 9821 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 581.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E4001 " pdb="ZN ZN E4001 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E4001 " - pdb=" SG CYS E 45 " pdb="ZN ZN E4001 " - pdb=" SG CYS E 42 " pdb="ZN ZN E4001 " - pdb=" SG CYS E 83 " pdb=" ZN E4002 " pdb="ZN ZN E4002 " - pdb=" ND1 HIS E 77 " pdb="ZN ZN E4002 " - pdb=" SG CYS E 75 " pdb="ZN ZN E4002 " - pdb=" SG CYS E 94 " pdb=" ZN E4003 " pdb="ZN ZN E4003 " - pdb=" ND1 HIS E 82 " pdb="ZN ZN E4003 " - pdb=" SG CYS E 56 " pdb="ZN ZN E4003 " - pdb=" SG CYS E 68 " pdb="ZN ZN E4003 " - pdb=" SG CYS E 53 " Number of angles added : 6 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3756 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 4 sheets defined 72.9% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 Processing helix chain 'A' and resid 19 through 38 removed outlier: 3.676A pdb=" N ASP A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.809A pdb=" N LYS A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 79 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 80 through 97 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.516A pdb=" N ARG A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 142 removed outlier: 4.259A pdb=" N ASN A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 Processing helix chain 'A' and resid 172 through 181 Processing helix chain 'A' and resid 182 through 186 removed outlier: 4.180A pdb=" N THR A 185 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER A 186 " --> pdb=" O GLN A 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 182 through 186' Processing helix chain 'A' and resid 188 through 204 removed outlier: 3.972A pdb=" N ARG A 192 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 removed outlier: 3.726A pdb=" N ILE A 211 " --> pdb=" O PHE A 207 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.641A pdb=" N GLY A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 262 Proline residue: A 254 - end of helix removed outlier: 3.705A pdb=" N VAL A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 280 Processing helix chain 'A' and resid 285 through 300 removed outlier: 4.045A pdb=" N HIS A 289 " --> pdb=" O GLU A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 364 removed outlier: 3.826A pdb=" N ARG A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 383 removed outlier: 3.920A pdb=" N PHE A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) Proline residue: A 377 - end of helix Processing helix chain 'A' and resid 389 through 403 Processing helix chain 'A' and resid 423 through 444 Proline residue: A 433 - end of helix Processing helix chain 'A' and resid 447 through 465 Processing helix chain 'A' and resid 472 through 484 Proline residue: A 478 - end of helix Processing helix chain 'A' and resid 492 through 508 removed outlier: 3.512A pdb=" N HIS A 508 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 512 removed outlier: 3.710A pdb=" N VAL A 512 " --> pdb=" O SER A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.958A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 551 Processing helix chain 'A' and resid 561 through 577 Processing helix chain 'A' and resid 582 through 601 Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.837A pdb=" N LYS A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 636 removed outlier: 4.709A pdb=" N THR A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 Proline residue: A 653 - end of helix removed outlier: 3.896A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 681 Processing helix chain 'A' and resid 686 through 701 removed outlier: 3.780A pdb=" N ILE A 690 " --> pdb=" O THR A 686 " (cutoff:3.500A) Proline residue: A 698 - end of helix Processing helix chain 'A' and resid 705 through 721 removed outlier: 3.654A pdb=" N LYS A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 743 removed outlier: 3.777A pdb=" N SER A 728 " --> pdb=" O PRO A 724 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 765 Processing helix chain 'A' and resid 772 through 787 Proline residue: A 782 - end of helix Processing helix chain 'A' and resid 793 through 810 removed outlier: 4.274A pdb=" N TYR A 797 " --> pdb=" O LYS A 793 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 826 Processing helix chain 'A' and resid 831 through 849 removed outlier: 4.099A pdb=" N HIS A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.594A pdb=" N VAL A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 885 removed outlier: 3.673A pdb=" N VAL A 885 " --> pdb=" O GLY A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 900 Proline residue: A 893 - end of helix Processing helix chain 'A' and resid 903 through 919 removed outlier: 3.922A pdb=" N TYR A 907 " --> pdb=" O PRO A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 939 Processing helix chain 'A' and resid 944 through 961 removed outlier: 3.841A pdb=" N ILE A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 977 removed outlier: 3.919A pdb=" N LEU A 966 " --> pdb=" O ASP A 962 " (cutoff:3.500A) Proline residue: A 968 - end of helix Processing helix chain 'A' and resid 978 through 992 Processing helix chain 'A' and resid 1000 through 1015 Processing helix chain 'A' and resid 1019 through 1037 removed outlier: 3.941A pdb=" N VAL A1025 " --> pdb=" O ASN A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1057 removed outlier: 3.810A pdb=" N THR A1047 " --> pdb=" O ASP A1043 " (cutoff:3.500A) Proline residue: A1050 - end of helix removed outlier: 3.784A pdb=" N GLU A1055 " --> pdb=" O HIS A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1096 Processing helix chain 'A' and resid 1101 through 1114 removed outlier: 3.959A pdb=" N PHE A1105 " --> pdb=" O ASP A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1134 Processing helix chain 'A' and resid 1135 through 1140 removed outlier: 3.708A pdb=" N GLN A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1153 Proline residue: A1148 - end of helix Processing helix chain 'A' and resid 1162 through 1185 Processing helix chain 'A' and resid 1203 through 1210 removed outlier: 3.524A pdb=" N GLU A1207 " --> pdb=" O SER A1203 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 46 removed outlier: 3.596A pdb=" N VAL C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 69 through 96 removed outlier: 3.646A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG C 90 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 134 removed outlier: 4.581A pdb=" N MET C 118 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL C 129 " --> pdb=" O TYR C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'C' and resid 156 through 175 removed outlier: 3.610A pdb=" N GLY C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 195 removed outlier: 3.967A pdb=" N LEU C 195 " --> pdb=" O MET C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 225 removed outlier: 3.525A pdb=" N ALA C 207 " --> pdb=" O GLU C 203 " (cutoff:3.500A) Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 230 through 250 removed outlier: 3.609A pdb=" N LYS C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 277 removed outlier: 3.815A pdb=" N SER C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LYS C 274 " --> pdb=" O SER C 270 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL C 277 " --> pdb=" O MET C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 291 removed outlier: 3.570A pdb=" N GLY C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 304 Processing helix chain 'C' and resid 309 through 329 Processing helix chain 'C' and resid 337 through 359 Processing helix chain 'C' and resid 363 through 379 removed outlier: 4.061A pdb=" N ASN C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 398 removed outlier: 4.682A pdb=" N LYS C 398 " --> pdb=" O ASP C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 421 removed outlier: 3.639A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 441 removed outlier: 4.016A pdb=" N PHE C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 460 removed outlier: 3.876A pdb=" N ASN C 453 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 495 Processing helix chain 'C' and resid 525 through 541 removed outlier: 3.957A pdb=" N HIS C 530 " --> pdb=" O PRO C 526 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 531 " --> pdb=" O ALA C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 608 removed outlier: 4.347A pdb=" N ILE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 608 " --> pdb=" O LEU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 619 removed outlier: 3.926A pdb=" N GLU C 619 " --> pdb=" O GLU C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 633 removed outlier: 3.936A pdb=" N ARG C 629 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 633 " --> pdb=" O ARG C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 713 removed outlier: 4.160A pdb=" N ARG C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 730 Processing helix chain 'C' and resid 739 through 745 Processing helix chain 'E' and resid 81 through 88 Processing sheet with id=AA1, first strand: chain 'C' and resid 502 through 503 removed outlier: 7.242A pdb=" N ASP C 502 " --> pdb=" O TRP E 27 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL E 24 " --> pdb=" O ASN C 560 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN C 560 " --> pdb=" O VAL E 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 506 through 509 removed outlier: 5.999A pdb=" N ARG C 506 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TRP E 33 " --> pdb=" O ARG C 506 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU C 508 " --> pdb=" O TRP E 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 645 through 646 Processing sheet with id=AA4, first strand: chain 'E' and resid 78 through 80 984 hydrogen bonds defined for protein. 2940 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: 2.36 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3357 1.33 - 1.45: 3094 1.45 - 1.57: 9149 1.57 - 1.70: 0 1.70 - 1.82: 161 Bond restraints: 15761 Sorted by residual: bond pdb=" N VAL A1138 " pdb=" CA VAL A1138 " ideal model delta sigma weight residual 1.456 1.493 -0.036 9.50e-03 1.11e+04 1.47e+01 bond pdb=" N ARG A 364 " pdb=" CA ARG A 364 " ideal model delta sigma weight residual 1.462 1.517 -0.055 1.44e-02 4.82e+03 1.46e+01 bond pdb=" N GLU A1147 " pdb=" CA GLU A1147 " ideal model delta sigma weight residual 1.462 1.490 -0.028 7.70e-03 1.69e+04 1.29e+01 bond pdb=" C ILE A 296 " pdb=" O ILE A 296 " ideal model delta sigma weight residual 1.237 1.276 -0.039 1.13e-02 7.83e+03 1.21e+01 bond pdb=" N ASP A 222 " pdb=" CA ASP A 222 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.17e+01 ... (remaining 15756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 20345 2.59 - 5.19: 843 5.19 - 7.78: 84 7.78 - 10.38: 13 10.38 - 12.97: 2 Bond angle restraints: 21287 Sorted by residual: angle pdb=" N VAL A1138 " pdb=" CA VAL A1138 " pdb=" C VAL A1138 " ideal model delta sigma weight residual 113.53 107.34 6.19 9.80e-01 1.04e+00 3.99e+01 angle pdb=" N GLN C 465 " pdb=" CA GLN C 465 " pdb=" C GLN C 465 " ideal model delta sigma weight residual 113.02 105.48 7.54 1.20e+00 6.94e-01 3.95e+01 angle pdb=" N ASN A 295 " pdb=" CA ASN A 295 " pdb=" C ASN A 295 " ideal model delta sigma weight residual 111.07 104.79 6.28 1.07e+00 8.73e-01 3.45e+01 angle pdb=" C SER A 488 " pdb=" CA SER A 488 " pdb=" CB SER A 488 " ideal model delta sigma weight residual 116.54 110.15 6.39 1.15e+00 7.56e-01 3.09e+01 angle pdb=" N THR A 405 " pdb=" CA THR A 405 " pdb=" C THR A 405 " ideal model delta sigma weight residual 112.93 106.73 6.20 1.12e+00 7.97e-01 3.07e+01 ... (remaining 21282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7979 17.97 - 35.95: 1183 35.95 - 53.92: 457 53.92 - 71.89: 119 71.89 - 89.87: 28 Dihedral angle restraints: 9766 sinusoidal: 4011 harmonic: 5755 Sorted by residual: dihedral pdb=" C ARG A 364 " pdb=" N ARG A 364 " pdb=" CA ARG A 364 " pdb=" CB ARG A 364 " ideal model delta harmonic sigma weight residual -122.60 -136.91 14.31 0 2.50e+00 1.60e-01 3.28e+01 dihedral pdb=" CA SER A1192 " pdb=" C SER A1192 " pdb=" N PRO A1193 " pdb=" CA PRO A1193 " ideal model delta harmonic sigma weight residual 180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP A 59 " pdb=" C ASP A 59 " pdb=" N LYS A 60 " pdb=" CA LYS A 60 " ideal model delta harmonic sigma weight residual 180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 9763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2131 0.090 - 0.181: 311 0.181 - 0.271: 38 0.271 - 0.362: 8 0.362 - 0.452: 2 Chirality restraints: 2490 Sorted by residual: chirality pdb=" CA ARG A 364 " pdb=" N ARG A 364 " pdb=" C ARG A 364 " pdb=" CB ARG A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CA TYR A 772 " pdb=" N TYR A 772 " pdb=" C TYR A 772 " pdb=" CB TYR A 772 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA THR C 467 " pdb=" N THR C 467 " pdb=" C THR C 467 " pdb=" CB THR C 467 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 2487 not shown) Planarity restraints: 2711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 364 " 0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ARG A 364 " -0.086 2.00e-02 2.50e+03 pdb=" O ARG A 364 " 0.032 2.00e-02 2.50e+03 pdb=" N HIS A 365 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 551 " -0.078 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO A 552 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 552 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 552 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 771 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C GLY A 771 " 0.060 2.00e-02 2.50e+03 pdb=" O GLY A 771 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR A 772 " -0.021 2.00e-02 2.50e+03 ... (remaining 2708 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 149 2.59 - 3.17: 13941 3.17 - 3.75: 26472 3.75 - 4.32: 33340 4.32 - 4.90: 53564 Nonbonded interactions: 127466 Sorted by model distance: nonbonded pdb=" OD2 ASP E 97 " pdb="ZN ZN E4002 " model vdw 2.017 2.230 nonbonded pdb=" OE2 GLU A 915 " pdb=" OG SER A 919 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP A 160 " pdb=" NE ARG A 164 " model vdw 2.204 3.120 nonbonded pdb=" O MET C 477 " pdb=" OG SER C 480 " model vdw 2.205 3.040 nonbonded pdb=" O LEU A 102 " pdb=" OG SER A 106 " model vdw 2.214 3.040 ... (remaining 127461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.620 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 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 : 0.007 0.068 15772 Z= 0.498 Angle : 1.137 12.970 21293 Z= 0.754 Chirality : 0.065 0.452 2490 Planarity : 0.006 0.118 2711 Dihedral : 20.584 89.868 6010 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.93 % Allowed : 11.02 % Favored : 88.05 % Rotamer: Outliers : 10.27 % Allowed : 31.60 % Favored : 58.13 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.84 (0.18), residues: 1942 helix: -0.22 (0.14), residues: 1318 sheet: -1.51 (1.59), residues: 13 loop : -3.44 (0.21), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 629 TYR 0.039 0.002 TYR A 270 PHE 0.045 0.002 PHE A 395 TRP 0.049 0.003 TRP C 513 HIS 0.012 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00699 (15761) covalent geometry : angle 1.13703 (21287) hydrogen bonds : bond 0.13521 ( 984) hydrogen bonds : angle 6.32888 ( 2940) metal coordination : bond 0.00430 ( 11) metal coordination : angle 2.05106 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 526 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: A 14 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6773 (mmmt) REVERT: A 17 SER cc_start: 0.5782 (OUTLIER) cc_final: 0.5422 (p) REVERT: A 70 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7546 (mmtm) REVERT: A 81 GLU cc_start: 0.7647 (pm20) cc_final: 0.7294 (pm20) REVERT: A 95 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7604 (ptm) REVERT: A 114 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7079 (mp) REVERT: A 158 MET cc_start: 0.7604 (tpt) cc_final: 0.7296 (tpt) REVERT: A 209 ASP cc_start: 0.6544 (OUTLIER) cc_final: 0.6238 (t0) REVERT: A 210 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6631 (tt) REVERT: A 218 LEU cc_start: 0.5204 (OUTLIER) cc_final: 0.4578 (pp) REVERT: A 281 ARG cc_start: 0.6264 (OUTLIER) cc_final: 0.2399 (tpt170) REVERT: A 357 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7459 (mt) REVERT: A 358 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6741 (t0) REVERT: A 399 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7484 (mt) REVERT: A 400 SER cc_start: 0.7999 (OUTLIER) cc_final: 0.7667 (p) REVERT: A 427 MET cc_start: 0.7295 (ptt) cc_final: 0.6988 (ptt) REVERT: A 679 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7350 (tttm) REVERT: A 776 LEU cc_start: 0.4634 (OUTLIER) cc_final: 0.4428 (mm) REVERT: A 779 LEU cc_start: 0.5798 (mt) cc_final: 0.4962 (mt) REVERT: A 842 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7901 (tt) REVERT: A 1052 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6869 (tt) REVERT: A 1149 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7561 (pp) REVERT: C 212 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6208 (tmm) REVERT: C 213 SER cc_start: 0.7565 (p) cc_final: 0.6898 (p) REVERT: C 215 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7079 (mt-10) REVERT: C 218 GLN cc_start: 0.7885 (tt0) cc_final: 0.7553 (mt0) REVERT: C 244 GLU cc_start: 0.7373 (tp30) cc_final: 0.6798 (mm-30) REVERT: C 289 LYS cc_start: 0.8215 (tppt) cc_final: 0.7878 (mmtt) REVERT: C 317 MET cc_start: 0.7674 (tpp) cc_final: 0.7389 (mmm) REVERT: C 346 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8066 (mm) REVERT: C 386 GLU cc_start: 0.7012 (tp30) cc_final: 0.6224 (tp30) REVERT: C 420 ARG cc_start: 0.7342 (tpp80) cc_final: 0.7110 (mmm-85) REVERT: C 431 TYR cc_start: 0.7698 (m-10) cc_final: 0.7475 (m-80) REVERT: C 444 LYS cc_start: 0.6257 (OUTLIER) cc_final: 0.5954 (tptp) REVERT: C 459 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7473 (mmmt) REVERT: C 465 GLN cc_start: 0.5723 (OUTLIER) cc_final: 0.4810 (tm130) REVERT: C 473 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7606 (tpp) REVERT: C 533 GLU cc_start: 0.7799 (tp30) cc_final: 0.7476 (tp30) REVERT: C 551 GLN cc_start: 0.6690 (mp10) cc_final: 0.6488 (mp10) REVERT: C 598 GLN cc_start: 0.6974 (mp10) cc_final: 0.6502 (mp10) REVERT: C 632 GLN cc_start: 0.7446 (pp30) cc_final: 0.7115 (pp30) REVERT: C 688 ARG cc_start: 0.6606 (ttm110) cc_final: 0.6018 (mtm110) outliers start: 180 outliers final: 56 residues processed: 631 average time/residue: 0.1185 time to fit residues: 107.2502 Evaluate side-chains 564 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 483 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 284 LYS Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 725 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1042 ARG Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1155 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 354 ARG Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 542 LYS Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 744 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A 456 ASN A 485 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN A 544 GLN A 663 GLN A 998 GLN A1205 ASN C 69 HIS C 84 HIS C 113 GLN C 381 ASN C 593 GLN C 618 GLN C 664 GLN C 718 GLN E 59 ASN E 98 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.149632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127126 restraints weight = 32284.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131284 restraints weight = 17207.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.134072 restraints weight = 10742.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.135905 restraints weight = 7480.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.137210 restraints weight = 5691.751| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15772 Z= 0.173 Angle : 0.780 9.102 21293 Z= 0.405 Chirality : 0.045 0.296 2490 Planarity : 0.006 0.118 2711 Dihedral : 10.865 68.701 2295 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.42 % Favored : 90.16 % Rotamer: Outliers : 7.76 % Allowed : 29.21 % Favored : 63.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.96 (0.19), residues: 1942 helix: 0.54 (0.14), residues: 1335 sheet: -1.27 (1.64), residues: 13 loop : -3.44 (0.21), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 47 TYR 0.027 0.002 TYR A 270 PHE 0.023 0.002 PHE A 395 TRP 0.016 0.002 TRP A 933 HIS 0.008 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00371 (15761) covalent geometry : angle 0.77899 (21287) hydrogen bonds : bond 0.05188 ( 984) hydrogen bonds : angle 5.02518 ( 2940) metal coordination : bond 0.00788 ( 11) metal coordination : angle 1.93365 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 497 time to evaluate : 0.468 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 6 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.7125 (m-80) REVERT: A 17 SER cc_start: 0.6596 (OUTLIER) cc_final: 0.6295 (p) REVERT: A 47 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.6332 (mtm110) REVERT: A 48 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6902 (mtmm) REVERT: A 51 LYS cc_start: 0.8519 (tptp) cc_final: 0.8000 (ttpp) REVERT: A 65 GLN cc_start: 0.8061 (mt0) cc_final: 0.7800 (mt0) REVERT: A 129 ASN cc_start: 0.7536 (t0) cc_final: 0.7324 (t0) REVERT: A 158 MET cc_start: 0.8156 (tpt) cc_final: 0.7601 (tpt) REVERT: A 209 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.6304 (t0) REVERT: A 215 LEU cc_start: 0.7908 (mt) cc_final: 0.7596 (mt) REVERT: A 218 LEU cc_start: 0.6176 (pp) cc_final: 0.5732 (pp) REVERT: A 261 ASN cc_start: 0.8172 (t0) cc_final: 0.7670 (m-40) REVERT: A 275 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6900 (p90) REVERT: A 445 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: A 446 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7821 (mmtm) REVERT: A 551 ARG cc_start: 0.7649 (tpt170) cc_final: 0.7368 (tpm170) REVERT: A 675 ASP cc_start: 0.7432 (t0) cc_final: 0.7198 (t0) REVERT: A 826 LYS cc_start: 0.8104 (tptp) cc_final: 0.7628 (tptt) REVERT: A 836 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8067 (mm) REVERT: A 842 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8366 (tp) REVERT: A 938 LYS cc_start: 0.8051 (tppp) cc_final: 0.7750 (tppp) REVERT: A 967 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7970 (tt) REVERT: A 982 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7400 (mtm-85) REVERT: A 1020 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6628 (pt) REVERT: A 1023 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7323 (mtm110) REVERT: A 1037 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7875 (mmtp) REVERT: A 1083 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8245 (mmmm) REVERT: A 1089 MET cc_start: 0.8070 (mmm) cc_final: 0.7291 (mmm) REVERT: A 1120 LYS cc_start: 0.8424 (mmmm) cc_final: 0.8057 (mmmt) REVERT: A 1121 MET cc_start: 0.8445 (mtp) cc_final: 0.8164 (mmm) REVERT: A 1164 GLN cc_start: 0.7243 (mp10) cc_final: 0.6949 (mp10) REVERT: A 1165 GLU cc_start: 0.7979 (mp0) cc_final: 0.7616 (tp30) REVERT: A 1169 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8269 (mm-40) REVERT: C 176 GLU cc_start: 0.6542 (tm-30) cc_final: 0.6300 (tm-30) REVERT: C 184 ARG cc_start: 0.7156 (ttt180) cc_final: 0.6935 (tpp80) REVERT: C 206 GLU cc_start: 0.5813 (OUTLIER) cc_final: 0.4756 (tt0) REVERT: C 209 PHE cc_start: 0.6190 (t80) cc_final: 0.4933 (t80) REVERT: C 213 SER cc_start: 0.7972 (p) cc_final: 0.7287 (p) REVERT: C 218 GLN cc_start: 0.7970 (tt0) cc_final: 0.7538 (mt0) REVERT: C 228 ASN cc_start: 0.5229 (OUTLIER) cc_final: 0.4822 (m-40) REVERT: C 244 GLU cc_start: 0.7497 (tp30) cc_final: 0.6792 (mm-30) REVERT: C 258 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7044 (mm-30) REVERT: C 289 LYS cc_start: 0.8390 (tppt) cc_final: 0.8086 (tppt) REVERT: C 345 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7603 (tt) REVERT: C 346 LEU cc_start: 0.8455 (mt) cc_final: 0.8037 (mm) REVERT: C 368 GLN cc_start: 0.7074 (tm-30) cc_final: 0.6842 (tm-30) REVERT: C 383 ARG cc_start: 0.7350 (mtp85) cc_final: 0.7143 (mtp85) REVERT: C 386 GLU cc_start: 0.7125 (tp30) cc_final: 0.6025 (tp30) REVERT: C 420 ARG cc_start: 0.7430 (tpp80) cc_final: 0.7033 (mtp85) REVERT: C 431 TYR cc_start: 0.7862 (m-10) cc_final: 0.7468 (m-80) REVERT: C 444 LYS cc_start: 0.6556 (tptp) cc_final: 0.6197 (tptp) REVERT: C 459 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7511 (mmmt) REVERT: C 473 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6756 (ttm) REVERT: C 513 TRP cc_start: 0.7885 (m100) cc_final: 0.7292 (m100) REVERT: C 533 GLU cc_start: 0.7699 (tp30) cc_final: 0.7355 (tp30) REVERT: C 632 GLN cc_start: 0.7356 (pp30) cc_final: 0.7065 (pp30) REVERT: C 673 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7349 (mmtm) REVERT: C 689 LYS cc_start: 0.7793 (ptpp) cc_final: 0.7506 (pttt) REVERT: C 690 GLU cc_start: 0.6832 (pp20) cc_final: 0.6427 (pp20) REVERT: C 693 GLN cc_start: 0.7801 (pp30) cc_final: 0.7319 (pp30) REVERT: C 697 ASP cc_start: 0.7608 (m-30) cc_final: 0.7292 (m-30) REVERT: C 698 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7494 (m-30) REVERT: C 700 LYS cc_start: 0.8356 (mttt) cc_final: 0.7629 (mttt) REVERT: C 707 ILE cc_start: 0.8589 (tp) cc_final: 0.7841 (tp) REVERT: C 711 MET cc_start: 0.5957 (mmt) cc_final: 0.5568 (mmt) REVERT: C 722 LEU cc_start: 0.7587 (pp) cc_final: 0.7348 (mt) REVERT: C 725 GLU cc_start: 0.7408 (tt0) cc_final: 0.6916 (tm-30) REVERT: C 744 ARG cc_start: 0.8147 (ttm170) cc_final: 0.7816 (ttt180) REVERT: E 27 TRP cc_start: 0.7964 (t60) cc_final: 0.7737 (t60) outliers start: 136 outliers final: 64 residues processed: 575 average time/residue: 0.1203 time to fit residues: 100.1162 Evaluate side-chains 558 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 475 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 998 GLN Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 698 ASP Chi-restraints excluded: chain E residue 35 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 103 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 160 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 173 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS A 456 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 707 HIS A 786 GLN C 87 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.145657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.122922 restraints weight = 32359.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.127001 restraints weight = 17235.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.129751 restraints weight = 10796.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.131698 restraints weight = 7523.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132890 restraints weight = 5696.382| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15772 Z= 0.185 Angle : 0.771 11.199 21293 Z= 0.396 Chirality : 0.044 0.200 2490 Planarity : 0.006 0.119 2711 Dihedral : 8.985 59.867 2201 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.27 % Favored : 90.37 % Rotamer: Outliers : 7.70 % Allowed : 28.86 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.69 (0.19), residues: 1942 helix: 0.78 (0.14), residues: 1338 sheet: -1.13 (1.59), residues: 13 loop : -3.44 (0.21), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 629 TYR 0.020 0.002 TYR C 341 PHE 0.027 0.002 PHE A 395 TRP 0.013 0.001 TRP E 72 HIS 0.004 0.001 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00398 (15761) covalent geometry : angle 0.77001 (21287) hydrogen bonds : bond 0.05049 ( 984) hydrogen bonds : angle 4.90298 ( 2940) metal coordination : bond 0.00741 ( 11) metal coordination : angle 2.24054 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 502 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: A 47 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.6269 (mpp-170) REVERT: A 51 LYS cc_start: 0.8512 (tptp) cc_final: 0.8188 (ptmm) REVERT: A 65 GLN cc_start: 0.8298 (mt0) cc_final: 0.8085 (mt0) REVERT: A 129 ASN cc_start: 0.7539 (t0) cc_final: 0.7309 (t0) REVERT: A 153 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6977 (mm-30) REVERT: A 155 LEU cc_start: 0.8566 (mm) cc_final: 0.8288 (mm) REVERT: A 157 ILE cc_start: 0.8748 (mt) cc_final: 0.8476 (mt) REVERT: A 158 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7848 (tpt) REVERT: A 209 ASP cc_start: 0.6806 (OUTLIER) cc_final: 0.6438 (t0) REVERT: A 215 LEU cc_start: 0.7999 (mt) cc_final: 0.7673 (mt) REVERT: A 218 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5518 (pp) REVERT: A 233 CYS cc_start: 0.8193 (t) cc_final: 0.7940 (t) REVERT: A 261 ASN cc_start: 0.8200 (t0) cc_final: 0.7797 (m-40) REVERT: A 275 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6956 (p90) REVERT: A 358 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7359 (t0) REVERT: A 387 GLU cc_start: 0.4944 (OUTLIER) cc_final: 0.4156 (pm20) REVERT: A 403 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7983 (mmmt) REVERT: A 429 GLN cc_start: 0.7488 (pp30) cc_final: 0.7276 (pp30) REVERT: A 442 GLN cc_start: 0.7684 (mm-40) cc_final: 0.6592 (mm-40) REVERT: A 445 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6108 (mp0) REVERT: A 500 CYS cc_start: 0.8127 (t) cc_final: 0.7764 (p) REVERT: A 551 ARG cc_start: 0.7782 (tpt170) cc_final: 0.7486 (tpm170) REVERT: A 580 ASP cc_start: 0.6033 (OUTLIER) cc_final: 0.5602 (t70) REVERT: A 590 ILE cc_start: 0.8560 (mm) cc_final: 0.7980 (mm) REVERT: A 615 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7525 (m-80) REVERT: A 633 THR cc_start: 0.8493 (m) cc_final: 0.8069 (p) REVERT: A 662 ASN cc_start: 0.7379 (p0) cc_final: 0.7113 (t0) REVERT: A 675 ASP cc_start: 0.7445 (t0) cc_final: 0.7220 (t0) REVERT: A 689 MET cc_start: 0.7032 (pmm) cc_final: 0.5639 (ptt) REVERT: A 776 LEU cc_start: 0.5989 (mm) cc_final: 0.5665 (mm) REVERT: A 826 LYS cc_start: 0.8171 (tptp) cc_final: 0.7632 (tptt) REVERT: A 836 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 842 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8425 (tp) REVERT: A 854 GLN cc_start: 0.7163 (pp30) cc_final: 0.6353 (tm-30) REVERT: A 915 GLU cc_start: 0.7441 (tp30) cc_final: 0.7206 (tp30) REVERT: A 938 LYS cc_start: 0.8084 (tppp) cc_final: 0.7565 (tppp) REVERT: A 1023 ARG cc_start: 0.7952 (ttm110) cc_final: 0.7462 (ttm110) REVERT: A 1037 LYS cc_start: 0.8032 (mmtp) cc_final: 0.7830 (mmtp) REVERT: A 1083 LYS cc_start: 0.8603 (mmmm) cc_final: 0.8397 (mmmm) REVERT: A 1087 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7978 (tt0) REVERT: A 1089 MET cc_start: 0.8066 (mmm) cc_final: 0.7290 (mmm) REVERT: A 1108 HIS cc_start: 0.7880 (m90) cc_final: 0.7648 (m170) REVERT: A 1117 TYR cc_start: 0.8126 (t80) cc_final: 0.7732 (t80) REVERT: A 1121 MET cc_start: 0.8526 (mtp) cc_final: 0.8202 (mmm) REVERT: A 1156 LYS cc_start: 0.8572 (tppt) cc_final: 0.8140 (mmtt) REVERT: A 1164 GLN cc_start: 0.7361 (mp10) cc_final: 0.7068 (mp10) REVERT: A 1165 GLU cc_start: 0.7962 (mp0) cc_final: 0.7623 (tp30) REVERT: A 1169 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8087 (mm-40) REVERT: A 1174 ARG cc_start: 0.8322 (ttm110) cc_final: 0.8117 (ttm110) REVERT: C 59 ARG cc_start: 0.7369 (ttp-170) cc_final: 0.7037 (ttp-170) REVERT: C 109 TRP cc_start: 0.8172 (t-100) cc_final: 0.7855 (t-100) REVERT: C 112 HIS cc_start: 0.7683 (t70) cc_final: 0.7203 (t70) REVERT: C 126 MET cc_start: 0.7699 (ppp) cc_final: 0.7437 (ppp) REVERT: C 184 ARG cc_start: 0.7295 (ttt180) cc_final: 0.6516 (ttm-80) REVERT: C 187 CYS cc_start: 0.7576 (m) cc_final: 0.7304 (m) REVERT: C 204 ASP cc_start: 0.2658 (OUTLIER) cc_final: 0.2296 (m-30) REVERT: C 206 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5116 (tt0) REVERT: C 213 SER cc_start: 0.8083 (p) cc_final: 0.7851 (t) REVERT: C 218 GLN cc_start: 0.8057 (tt0) cc_final: 0.7565 (mt0) REVERT: C 228 ASN cc_start: 0.5456 (OUTLIER) cc_final: 0.5035 (m-40) REVERT: C 244 GLU cc_start: 0.7433 (tp30) cc_final: 0.6666 (mm-30) REVERT: C 258 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7074 (mm-30) REVERT: C 289 LYS cc_start: 0.8475 (tppt) cc_final: 0.8214 (tppt) REVERT: C 313 MET cc_start: 0.7836 (ttm) cc_final: 0.7568 (ttm) REVERT: C 354 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7425 (ttp80) REVERT: C 368 GLN cc_start: 0.7241 (tm-30) cc_final: 0.7027 (tm-30) REVERT: C 414 LYS cc_start: 0.8296 (mmmt) cc_final: 0.8094 (mmmt) REVERT: C 422 MET cc_start: 0.8584 (ttp) cc_final: 0.8356 (ttm) REVERT: C 459 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7826 (mmmt) REVERT: C 460 THR cc_start: 0.7839 (t) cc_final: 0.7560 (p) REVERT: C 469 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7751 (mmmt) REVERT: C 473 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.5921 (ttm) REVERT: C 513 TRP cc_start: 0.7907 (m100) cc_final: 0.7427 (m100) REVERT: C 533 GLU cc_start: 0.7801 (tp30) cc_final: 0.7401 (tp30) REVERT: C 673 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7237 (mmtm) REVERT: C 689 LYS cc_start: 0.7965 (ptpp) cc_final: 0.7624 (ptpt) REVERT: C 690 GLU cc_start: 0.6927 (pp20) cc_final: 0.6403 (pp20) REVERT: C 693 GLN cc_start: 0.7895 (pp30) cc_final: 0.7348 (pp30) REVERT: C 697 ASP cc_start: 0.7639 (m-30) cc_final: 0.7327 (m-30) REVERT: C 700 LYS cc_start: 0.8353 (mttt) cc_final: 0.7548 (mttt) REVERT: C 710 ILE cc_start: 0.7756 (tp) cc_final: 0.7233 (tt) REVERT: C 711 MET cc_start: 0.6233 (mmt) cc_final: 0.5601 (mmt) REVERT: C 731 LYS cc_start: 0.8377 (ttmm) cc_final: 0.7928 (ttmm) REVERT: C 744 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7702 (ttt180) REVERT: C 748 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6262 (tt) outliers start: 135 outliers final: 68 residues processed: 581 average time/residue: 0.1247 time to fit residues: 103.8945 Evaluate side-chains 574 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 484 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain E residue 35 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 0.4980 chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 471 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.144708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.121855 restraints weight = 32083.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.126021 restraints weight = 16998.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.128758 restraints weight = 10602.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.130547 restraints weight = 7409.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.131963 restraints weight = 5684.344| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15772 Z= 0.162 Angle : 0.740 15.086 21293 Z= 0.378 Chirality : 0.044 0.250 2490 Planarity : 0.006 0.118 2711 Dihedral : 7.771 58.857 2171 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.37 % Favored : 90.32 % Rotamer: Outliers : 7.30 % Allowed : 29.44 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.56 (0.19), residues: 1942 helix: 0.90 (0.14), residues: 1342 sheet: -1.17 (1.46), residues: 13 loop : -3.51 (0.21), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 629 TYR 0.028 0.002 TYR C 154 PHE 0.021 0.002 PHE A 395 TRP 0.011 0.001 TRP E 72 HIS 0.006 0.001 HIS A 516 Details of bonding type rmsd covalent geometry : bond 0.00349 (15761) covalent geometry : angle 0.73940 (21287) hydrogen bonds : bond 0.04766 ( 984) hydrogen bonds : angle 4.82763 ( 2940) metal coordination : bond 0.00655 ( 11) metal coordination : angle 2.11032 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 497 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: A 47 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6188 (mpp-170) REVERT: A 51 LYS cc_start: 0.8486 (tptp) cc_final: 0.8177 (ptmm) REVERT: A 63 GLU cc_start: 0.7799 (mp0) cc_final: 0.7562 (mp0) REVERT: A 65 GLN cc_start: 0.8382 (mt0) cc_final: 0.7902 (mm-40) REVERT: A 67 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7499 (mm) REVERT: A 129 ASN cc_start: 0.7582 (t0) cc_final: 0.7380 (t0) REVERT: A 153 GLU cc_start: 0.7364 (mm-30) cc_final: 0.7008 (mm-30) REVERT: A 155 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8335 (mm) REVERT: A 158 MET cc_start: 0.8134 (tpt) cc_final: 0.7747 (tpt) REVERT: A 164 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.6180 (mpp80) REVERT: A 209 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6423 (t0) REVERT: A 215 LEU cc_start: 0.8006 (mt) cc_final: 0.7671 (mt) REVERT: A 218 LEU cc_start: 0.6260 (pp) cc_final: 0.5629 (pp) REVERT: A 261 ASN cc_start: 0.8212 (t0) cc_final: 0.7815 (m-40) REVERT: A 275 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6863 (p90) REVERT: A 358 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7329 (t0) REVERT: A 403 LYS cc_start: 0.8394 (mtmm) cc_final: 0.7987 (mmmt) REVERT: A 429 GLN cc_start: 0.7602 (pp30) cc_final: 0.7392 (pp30) REVERT: A 444 LYS cc_start: 0.8637 (mmmm) cc_final: 0.8418 (mmmm) REVERT: A 446 LYS cc_start: 0.8334 (mmtt) cc_final: 0.7911 (mmtm) REVERT: A 471 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8699 (mp10) REVERT: A 500 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7747 (p) REVERT: A 527 CYS cc_start: 0.8187 (m) cc_final: 0.7308 (t) REVERT: A 551 ARG cc_start: 0.7793 (tpt170) cc_final: 0.7564 (tpm170) REVERT: A 566 LYS cc_start: 0.8883 (tptp) cc_final: 0.8677 (tppt) REVERT: A 580 ASP cc_start: 0.6066 (OUTLIER) cc_final: 0.5625 (t70) REVERT: A 590 ILE cc_start: 0.8505 (mm) cc_final: 0.7970 (mm) REVERT: A 633 THR cc_start: 0.8501 (m) cc_final: 0.8097 (p) REVERT: A 662 ASN cc_start: 0.7372 (p0) cc_final: 0.7126 (t0) REVERT: A 675 ASP cc_start: 0.7471 (t0) cc_final: 0.7220 (t0) REVERT: A 689 MET cc_start: 0.7084 (pmm) cc_final: 0.5919 (ptt) REVERT: A 703 GLU cc_start: 0.7605 (tp30) cc_final: 0.7110 (tp30) REVERT: A 776 LEU cc_start: 0.6011 (mm) cc_final: 0.5699 (mm) REVERT: A 826 LYS cc_start: 0.8120 (tptp) cc_final: 0.7596 (tptt) REVERT: A 836 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8110 (mm) REVERT: A 854 GLN cc_start: 0.7382 (pp30) cc_final: 0.7103 (pp30) REVERT: A 915 GLU cc_start: 0.7464 (tp30) cc_final: 0.7148 (tp30) REVERT: A 938 LYS cc_start: 0.8077 (tppp) cc_final: 0.7578 (tppp) REVERT: A 953 GLU cc_start: 0.6566 (mm-30) cc_final: 0.6059 (mm-30) REVERT: A 1023 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7329 (ttm110) REVERT: A 1087 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7988 (tt0) REVERT: A 1089 MET cc_start: 0.8118 (mmm) cc_final: 0.7269 (mmm) REVERT: A 1117 TYR cc_start: 0.8102 (t80) cc_final: 0.7761 (t80) REVERT: A 1120 LYS cc_start: 0.8429 (mmmm) cc_final: 0.7983 (mttm) REVERT: A 1121 MET cc_start: 0.8471 (mtp) cc_final: 0.8034 (mmm) REVERT: A 1156 LYS cc_start: 0.8494 (tppt) cc_final: 0.8091 (mmmt) REVERT: A 1164 GLN cc_start: 0.7480 (mp10) cc_final: 0.7151 (mp10) REVERT: A 1165 GLU cc_start: 0.7949 (mp0) cc_final: 0.7616 (tp30) REVERT: A 1169 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8089 (mm-40) REVERT: A 1170 ASP cc_start: 0.7885 (m-30) cc_final: 0.7538 (m-30) REVERT: A 1171 GLU cc_start: 0.7839 (tp30) cc_final: 0.7462 (tp30) REVERT: C 59 ARG cc_start: 0.7388 (ttp-170) cc_final: 0.7013 (ttp-170) REVERT: C 79 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7264 (pp20) REVERT: C 126 MET cc_start: 0.7723 (ppp) cc_final: 0.7429 (ppp) REVERT: C 187 CYS cc_start: 0.7785 (m) cc_final: 0.7460 (m) REVERT: C 191 MET cc_start: 0.7080 (mmm) cc_final: 0.6745 (mmt) REVERT: C 204 ASP cc_start: 0.2935 (OUTLIER) cc_final: 0.2616 (m-30) REVERT: C 206 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5086 (tt0) REVERT: C 213 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7837 (t) REVERT: C 218 GLN cc_start: 0.8021 (tt0) cc_final: 0.7556 (mt0) REVERT: C 228 ASN cc_start: 0.5361 (OUTLIER) cc_final: 0.4991 (m-40) REVERT: C 244 GLU cc_start: 0.7436 (tp30) cc_final: 0.6685 (mm-30) REVERT: C 266 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7532 (ttp80) REVERT: C 288 LEU cc_start: 0.8988 (mm) cc_final: 0.8768 (mt) REVERT: C 289 LYS cc_start: 0.8470 (tppt) cc_final: 0.8241 (tppt) REVERT: C 300 TYR cc_start: 0.7940 (t80) cc_final: 0.7689 (t80) REVERT: C 313 MET cc_start: 0.7848 (ttm) cc_final: 0.7578 (ttm) REVERT: C 317 MET cc_start: 0.8192 (tpp) cc_final: 0.7787 (mmm) REVERT: C 361 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8126 (p0) REVERT: C 368 GLN cc_start: 0.7347 (tm-30) cc_final: 0.7101 (tm-30) REVERT: C 386 GLU cc_start: 0.7395 (tp30) cc_final: 0.6954 (tp30) REVERT: C 416 MET cc_start: 0.7818 (mmm) cc_final: 0.7452 (mmp) REVERT: C 422 MET cc_start: 0.8657 (ttp) cc_final: 0.8365 (ttm) REVERT: C 429 GLU cc_start: 0.7478 (tt0) cc_final: 0.7242 (tt0) REVERT: C 440 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8168 (tt) REVERT: C 444 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.6064 (tptp) REVERT: C 459 LYS cc_start: 0.8375 (mmmt) cc_final: 0.7787 (ttmm) REVERT: C 460 THR cc_start: 0.7831 (t) cc_final: 0.7526 (p) REVERT: C 469 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7739 (mmmt) REVERT: C 505 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7671 (p) REVERT: C 506 ARG cc_start: 0.7395 (mmm-85) cc_final: 0.7135 (mtp85) REVERT: C 533 GLU cc_start: 0.7819 (tp30) cc_final: 0.7430 (tp30) REVERT: C 673 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7225 (mmtm) REVERT: C 689 LYS cc_start: 0.7977 (ptpp) cc_final: 0.7663 (ptpt) REVERT: C 690 GLU cc_start: 0.6951 (pp20) cc_final: 0.6475 (pp20) REVERT: C 693 GLN cc_start: 0.7892 (pp30) cc_final: 0.7353 (pp30) REVERT: C 697 ASP cc_start: 0.7603 (m-30) cc_final: 0.7297 (m-30) REVERT: C 700 LYS cc_start: 0.8334 (mttt) cc_final: 0.7466 (mttt) REVERT: C 701 HIS cc_start: 0.7755 (m170) cc_final: 0.7259 (m170) REVERT: C 710 ILE cc_start: 0.7547 (tp) cc_final: 0.6927 (tt) REVERT: C 711 MET cc_start: 0.6125 (mmt) cc_final: 0.5639 (mmt) REVERT: C 731 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7860 (ttmm) REVERT: C 744 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7654 (ttt180) REVERT: C 748 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6266 (tt) REVERT: E 100 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7023 (tt0) outliers start: 128 outliers final: 62 residues processed: 570 average time/residue: 0.1207 time to fit residues: 98.5671 Evaluate side-chains 565 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 479 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1172 LEU Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 100 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 16 optimal weight: 0.0040 chunk 106 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 chunk 150 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 HIS C 188 GLN C 222 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.144487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.121636 restraints weight = 31931.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.125806 restraints weight = 16884.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.128514 restraints weight = 10490.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.130287 restraints weight = 7338.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.131642 restraints weight = 5618.684| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15772 Z= 0.161 Angle : 0.747 12.441 21293 Z= 0.379 Chirality : 0.044 0.212 2490 Planarity : 0.006 0.117 2711 Dihedral : 7.172 54.596 2153 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.47 % Favored : 90.27 % Rotamer: Outliers : 7.24 % Allowed : 30.75 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.48 (0.19), residues: 1942 helix: 0.95 (0.14), residues: 1342 sheet: -1.04 (1.46), residues: 13 loop : -3.43 (0.21), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1174 TYR 0.025 0.002 TYR C 154 PHE 0.019 0.002 PHE A 395 TRP 0.012 0.001 TRP C 513 HIS 0.009 0.001 HIS A 847 Details of bonding type rmsd covalent geometry : bond 0.00350 (15761) covalent geometry : angle 0.74646 (21287) hydrogen bonds : bond 0.04724 ( 984) hydrogen bonds : angle 4.78556 ( 2940) metal coordination : bond 0.00641 ( 11) metal coordination : angle 2.03318 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 507 time to evaluate : 0.614 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 47 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6586 (mtm-85) REVERT: A 51 LYS cc_start: 0.8484 (tptp) cc_final: 0.8174 (ptmm) REVERT: A 65 GLN cc_start: 0.8398 (mt0) cc_final: 0.7885 (mm-40) REVERT: A 70 LYS cc_start: 0.7391 (mmtt) cc_final: 0.7122 (mmtt) REVERT: A 129 ASN cc_start: 0.7621 (t0) cc_final: 0.7388 (t0) REVERT: A 153 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7123 (mm-30) REVERT: A 155 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8359 (mm) REVERT: A 158 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7794 (tpt) REVERT: A 164 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6261 (mpp80) REVERT: A 209 ASP cc_start: 0.6927 (OUTLIER) cc_final: 0.6482 (t0) REVERT: A 215 LEU cc_start: 0.8062 (mt) cc_final: 0.7724 (mt) REVERT: A 218 LEU cc_start: 0.6311 (pp) cc_final: 0.5761 (pp) REVERT: A 233 CYS cc_start: 0.8343 (t) cc_final: 0.7947 (t) REVERT: A 261 ASN cc_start: 0.8239 (t0) cc_final: 0.7829 (m-40) REVERT: A 268 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6854 (ptm-80) REVERT: A 275 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6881 (p90) REVERT: A 358 ASP cc_start: 0.7584 (t70) cc_final: 0.7373 (t0) REVERT: A 387 GLU cc_start: 0.4236 (OUTLIER) cc_final: 0.3879 (pm20) REVERT: A 391 LYS cc_start: 0.8097 (tmtt) cc_final: 0.7450 (tptp) REVERT: A 395 PHE cc_start: 0.8359 (m-10) cc_final: 0.7689 (m-10) REVERT: A 403 LYS cc_start: 0.8429 (mtmm) cc_final: 0.7992 (mmmt) REVERT: A 429 GLN cc_start: 0.7610 (pp30) cc_final: 0.7375 (pp30) REVERT: A 444 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8338 (mmmm) REVERT: A 446 LYS cc_start: 0.8349 (mmtt) cc_final: 0.7914 (mmtm) REVERT: A 500 CYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7731 (p) REVERT: A 527 CYS cc_start: 0.8217 (m) cc_final: 0.7318 (t) REVERT: A 551 ARG cc_start: 0.7784 (tpt170) cc_final: 0.7575 (tpm170) REVERT: A 580 ASP cc_start: 0.6118 (OUTLIER) cc_final: 0.5651 (t70) REVERT: A 590 ILE cc_start: 0.8492 (mm) cc_final: 0.7962 (mm) REVERT: A 647 VAL cc_start: 0.8391 (m) cc_final: 0.8039 (p) REVERT: A 662 ASN cc_start: 0.7490 (p0) cc_final: 0.7228 (t0) REVERT: A 675 ASP cc_start: 0.7495 (t0) cc_final: 0.7217 (t0) REVERT: A 689 MET cc_start: 0.7040 (pmm) cc_final: 0.6066 (ptt) REVERT: A 776 LEU cc_start: 0.6052 (mm) cc_final: 0.5712 (mm) REVERT: A 826 LYS cc_start: 0.8161 (tptp) cc_final: 0.7608 (tptt) REVERT: A 836 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8154 (mm) REVERT: A 854 GLN cc_start: 0.7305 (pp30) cc_final: 0.6901 (pp30) REVERT: A 915 GLU cc_start: 0.7467 (tp30) cc_final: 0.7192 (tp30) REVERT: A 938 LYS cc_start: 0.8114 (tppp) cc_final: 0.7608 (tppp) REVERT: A 945 GLU cc_start: 0.6232 (tm-30) cc_final: 0.5943 (tm-30) REVERT: A 953 GLU cc_start: 0.6437 (mm-30) cc_final: 0.5950 (mm-30) REVERT: A 982 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7855 (mtt90) REVERT: A 1023 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7324 (ttm110) REVERT: A 1037 LYS cc_start: 0.8190 (mttt) cc_final: 0.7716 (mttm) REVERT: A 1055 GLU cc_start: 0.7562 (pm20) cc_final: 0.7354 (pm20) REVERT: A 1087 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8022 (tt0) REVERT: A 1106 LEU cc_start: 0.8369 (mm) cc_final: 0.8161 (mm) REVERT: A 1117 TYR cc_start: 0.8066 (t80) cc_final: 0.7657 (t80) REVERT: A 1120 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8006 (mttm) REVERT: A 1144 ARG cc_start: 0.6995 (mtp85) cc_final: 0.6564 (mtp85) REVERT: A 1156 LYS cc_start: 0.8463 (tppt) cc_final: 0.8159 (mmtt) REVERT: A 1164 GLN cc_start: 0.7512 (mp10) cc_final: 0.7165 (mp10) REVERT: A 1165 GLU cc_start: 0.7972 (mp0) cc_final: 0.7624 (tp30) REVERT: A 1169 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8097 (mm-40) REVERT: A 1170 ASP cc_start: 0.7866 (m-30) cc_final: 0.7542 (m-30) REVERT: A 1171 GLU cc_start: 0.7839 (tp30) cc_final: 0.7368 (tp30) REVERT: C 45 GLN cc_start: 0.7890 (tt0) cc_final: 0.7491 (tm-30) REVERT: C 59 ARG cc_start: 0.7339 (ttp-170) cc_final: 0.6952 (ttp-170) REVERT: C 79 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7305 (pp20) REVERT: C 90 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7673 (mtp-110) REVERT: C 126 MET cc_start: 0.7737 (ppp) cc_final: 0.7412 (ppp) REVERT: C 153 ARG cc_start: 0.7653 (mtt-85) cc_final: 0.7419 (mtp85) REVERT: C 176 GLU cc_start: 0.6414 (tm-30) cc_final: 0.6185 (tm-30) REVERT: C 184 ARG cc_start: 0.7270 (ttt180) cc_final: 0.6610 (ttm-80) REVERT: C 187 CYS cc_start: 0.7846 (m) cc_final: 0.7570 (m) REVERT: C 191 MET cc_start: 0.7141 (mmm) cc_final: 0.6887 (mmt) REVERT: C 204 ASP cc_start: 0.2987 (OUTLIER) cc_final: 0.2760 (m-30) REVERT: C 213 SER cc_start: 0.8158 (OUTLIER) cc_final: 0.7704 (t) REVERT: C 218 GLN cc_start: 0.8049 (tt0) cc_final: 0.7531 (mt0) REVERT: C 228 ASN cc_start: 0.5360 (OUTLIER) cc_final: 0.5009 (m-40) REVERT: C 244 GLU cc_start: 0.7417 (tp30) cc_final: 0.6732 (mm-30) REVERT: C 266 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7493 (ttp80) REVERT: C 288 LEU cc_start: 0.8992 (mm) cc_final: 0.8628 (mt) REVERT: C 289 LYS cc_start: 0.8514 (tppt) cc_final: 0.7791 (tppt) REVERT: C 313 MET cc_start: 0.7875 (ttm) cc_final: 0.7556 (ttm) REVERT: C 320 TYR cc_start: 0.8188 (t80) cc_final: 0.7554 (t80) REVERT: C 326 LYS cc_start: 0.7028 (mmmt) cc_final: 0.6800 (mptt) REVERT: C 368 GLN cc_start: 0.7279 (tm-30) cc_final: 0.7001 (tm-30) REVERT: C 383 ARG cc_start: 0.7538 (mtp85) cc_final: 0.7307 (mtp85) REVERT: C 386 GLU cc_start: 0.7307 (tp30) cc_final: 0.6845 (tp30) REVERT: C 416 MET cc_start: 0.7819 (mmm) cc_final: 0.7515 (mmp) REVERT: C 422 MET cc_start: 0.8662 (ttp) cc_final: 0.8391 (ttm) REVERT: C 424 GLU cc_start: 0.7366 (mp0) cc_final: 0.7141 (mp0) REVERT: C 429 GLU cc_start: 0.7566 (tt0) cc_final: 0.7331 (tt0) REVERT: C 444 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.6173 (tptp) REVERT: C 454 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.6901 (tmm) REVERT: C 459 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7885 (ttmm) REVERT: C 469 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7806 (mmmt) REVERT: C 473 MET cc_start: 0.7749 (ttt) cc_final: 0.7491 (tpt) REVERT: C 506 ARG cc_start: 0.7395 (mmm-85) cc_final: 0.7129 (mtp85) REVERT: C 533 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: C 673 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7198 (mmtm) REVERT: C 688 ARG cc_start: 0.6814 (ttm110) cc_final: 0.6221 (ttm110) REVERT: C 689 LYS cc_start: 0.7994 (ptpp) cc_final: 0.7652 (ptpt) REVERT: C 690 GLU cc_start: 0.6988 (pp20) cc_final: 0.6434 (pp20) REVERT: C 693 GLN cc_start: 0.7959 (pp30) cc_final: 0.7359 (pp30) REVERT: C 697 ASP cc_start: 0.7610 (m-30) cc_final: 0.7329 (m-30) REVERT: C 700 LYS cc_start: 0.8341 (mttt) cc_final: 0.7239 (mttt) REVERT: C 701 HIS cc_start: 0.7687 (m170) cc_final: 0.7097 (m170) REVERT: C 707 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.7348 (tp) REVERT: C 710 ILE cc_start: 0.7532 (tp) cc_final: 0.7006 (tt) REVERT: C 711 MET cc_start: 0.6151 (mmt) cc_final: 0.5572 (mmt) REVERT: C 731 LYS cc_start: 0.8371 (ttmm) cc_final: 0.7874 (ttmm) REVERT: C 744 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7411 (tpt-90) REVERT: C 748 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6268 (tt) REVERT: E 100 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6950 (tt0) outliers start: 127 outliers final: 77 residues processed: 575 average time/residue: 0.1255 time to fit residues: 103.7776 Evaluate side-chains 600 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 500 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 453 CYS Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 904 LYS Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 533 GLU Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 729 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain E residue 35 TRP Chi-restraints excluded: chain E residue 100 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 118 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 471 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 HIS C 48 ASN C 188 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 423 GLN ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.137523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.114406 restraints weight = 31519.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.118458 restraints weight = 16594.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.121135 restraints weight = 10301.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.122963 restraints weight = 7223.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124017 restraints weight = 5505.490| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 15772 Z= 0.264 Angle : 0.836 11.913 21293 Z= 0.436 Chirality : 0.048 0.206 2490 Planarity : 0.007 0.120 2711 Dihedral : 7.044 59.531 2141 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.63 % Favored : 90.01 % Rotamer: Outliers : 7.82 % Allowed : 30.92 % Favored : 61.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.77 (0.19), residues: 1942 helix: 0.64 (0.14), residues: 1340 sheet: -0.38 (1.64), residues: 13 loop : -3.30 (0.22), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 629 TYR 0.031 0.003 TYR C 62 PHE 0.030 0.002 PHE A 395 TRP 0.012 0.002 TRP E 72 HIS 0.009 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00550 (15761) covalent geometry : angle 0.83572 (21287) hydrogen bonds : bond 0.05865 ( 984) hydrogen bonds : angle 5.13600 ( 2940) metal coordination : bond 0.01087 ( 11) metal coordination : angle 2.29840 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 530 time to evaluate : 0.529 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 6 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: A 47 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6636 (mpt-90) REVERT: A 51 LYS cc_start: 0.8512 (tptp) cc_final: 0.8176 (ptmm) REVERT: A 65 GLN cc_start: 0.8447 (mt0) cc_final: 0.7897 (mm-40) REVERT: A 67 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7744 (mm) REVERT: A 129 ASN cc_start: 0.7674 (t0) cc_final: 0.7457 (t0) REVERT: A 155 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8322 (mm) REVERT: A 158 MET cc_start: 0.8168 (tpt) cc_final: 0.7583 (tpt) REVERT: A 160 ASP cc_start: 0.8056 (m-30) cc_final: 0.7367 (m-30) REVERT: A 162 LEU cc_start: 0.8509 (mt) cc_final: 0.8207 (mt) REVERT: A 164 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6478 (mpp80) REVERT: A 233 CYS cc_start: 0.8313 (t) cc_final: 0.8041 (t) REVERT: A 261 ASN cc_start: 0.8268 (t0) cc_final: 0.7804 (m-40) REVERT: A 275 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7067 (p90) REVERT: A 387 GLU cc_start: 0.4689 (OUTLIER) cc_final: 0.4289 (pm20) REVERT: A 391 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7554 (tmtt) REVERT: A 403 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8052 (mmmt) REVERT: A 429 GLN cc_start: 0.7726 (pp30) cc_final: 0.7433 (pp30) REVERT: A 444 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8494 (mmmm) REVERT: A 446 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8343 (mmtm) REVERT: A 452 GLN cc_start: 0.7321 (mt0) cc_final: 0.6422 (tm-30) REVERT: A 471 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8693 (mp10) REVERT: A 500 CYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7600 (p) REVERT: A 527 CYS cc_start: 0.8387 (m) cc_final: 0.7438 (t) REVERT: A 566 LYS cc_start: 0.8946 (tppt) cc_final: 0.8636 (tptp) REVERT: A 587 GLU cc_start: 0.7387 (pp20) cc_final: 0.6975 (pp20) REVERT: A 647 VAL cc_start: 0.8555 (m) cc_final: 0.8247 (p) REVERT: A 650 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6568 (mm-30) REVERT: A 675 ASP cc_start: 0.7528 (t0) cc_final: 0.7326 (t0) REVERT: A 689 MET cc_start: 0.7100 (pmm) cc_final: 0.6300 (ptt) REVERT: A 703 GLU cc_start: 0.7572 (tp30) cc_final: 0.7072 (tp30) REVERT: A 776 LEU cc_start: 0.6904 (mm) cc_final: 0.6535 (mm) REVERT: A 826 LYS cc_start: 0.8358 (tptp) cc_final: 0.7793 (tptt) REVERT: A 836 LEU cc_start: 0.8502 (mt) cc_final: 0.8235 (mm) REVERT: A 854 GLN cc_start: 0.7428 (pp30) cc_final: 0.6909 (pp30) REVERT: A 915 GLU cc_start: 0.7531 (tp30) cc_final: 0.7277 (tp30) REVERT: A 938 LYS cc_start: 0.8147 (tppp) cc_final: 0.7669 (tppp) REVERT: A 945 GLU cc_start: 0.6241 (tm-30) cc_final: 0.5897 (tm-30) REVERT: A 1023 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7602 (ttm110) REVERT: A 1024 ARG cc_start: 0.8147 (ptm-80) cc_final: 0.7429 (tmm-80) REVERT: A 1080 ASP cc_start: 0.8291 (p0) cc_final: 0.8049 (p0) REVERT: A 1081 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8583 (mm) REVERT: A 1083 LYS cc_start: 0.8627 (mmmm) cc_final: 0.8013 (mmmm) REVERT: A 1086 PHE cc_start: 0.8445 (m-80) cc_final: 0.8173 (m-80) REVERT: A 1087 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8069 (tt0) REVERT: A 1164 GLN cc_start: 0.7791 (mp10) cc_final: 0.7401 (mp10) REVERT: A 1165 GLU cc_start: 0.7952 (mp0) cc_final: 0.7587 (tp30) REVERT: A 1171 GLU cc_start: 0.7760 (tp30) cc_final: 0.7214 (tp30) REVERT: C 42 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8092 (tm-30) REVERT: C 45 GLN cc_start: 0.8042 (tt0) cc_final: 0.7596 (tm-30) REVERT: C 59 ARG cc_start: 0.7410 (ttp-170) cc_final: 0.7011 (ttp-170) REVERT: C 83 GLU cc_start: 0.8032 (pp20) cc_final: 0.7670 (pp20) REVERT: C 84 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7393 (t70) REVERT: C 126 MET cc_start: 0.7589 (ppp) cc_final: 0.7382 (ppp) REVERT: C 153 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.7468 (mtp85) REVERT: C 176 GLU cc_start: 0.6531 (tm-30) cc_final: 0.5971 (tm-30) REVERT: C 184 ARG cc_start: 0.7282 (ttt180) cc_final: 0.6913 (ttm-80) REVERT: C 188 GLN cc_start: 0.7564 (mt0) cc_final: 0.7182 (mm-40) REVERT: C 191 MET cc_start: 0.7426 (mmm) cc_final: 0.7131 (tpp) REVERT: C 206 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5896 (tt0) REVERT: C 213 SER cc_start: 0.8200 (p) cc_final: 0.7876 (t) REVERT: C 218 GLN cc_start: 0.8066 (tt0) cc_final: 0.7860 (tt0) REVERT: C 228 ASN cc_start: 0.5879 (OUTLIER) cc_final: 0.5436 (m-40) REVERT: C 235 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7865 (mtpp) REVERT: C 236 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7499 (ttmt) REVERT: C 246 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7108 (mm-30) REVERT: C 288 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8450 (mt) REVERT: C 289 LYS cc_start: 0.8625 (tppt) cc_final: 0.8279 (tppt) REVERT: C 313 MET cc_start: 0.8073 (ttm) cc_final: 0.7851 (ttm) REVERT: C 326 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7651 (mmtt) REVERT: C 354 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7129 (ttp80) REVERT: C 359 SER cc_start: 0.8215 (p) cc_final: 0.7813 (m) REVERT: C 366 PHE cc_start: 0.8235 (m-80) cc_final: 0.7675 (m-80) REVERT: C 368 GLN cc_start: 0.7344 (tm-30) cc_final: 0.7098 (tm-30) REVERT: C 375 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7059 (tm-30) REVERT: C 386 GLU cc_start: 0.7505 (tp30) cc_final: 0.7089 (tp30) REVERT: C 387 TYR cc_start: 0.8110 (m-80) cc_final: 0.7758 (m-80) REVERT: C 393 ASP cc_start: 0.7401 (t0) cc_final: 0.7026 (t70) REVERT: C 416 MET cc_start: 0.7840 (mmm) cc_final: 0.7435 (mmp) REVERT: C 429 GLU cc_start: 0.7668 (tt0) cc_final: 0.7306 (tp30) REVERT: C 444 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6629 (tptp) REVERT: C 454 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7079 (tmm) REVERT: C 459 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8064 (ttmm) REVERT: C 473 MET cc_start: 0.7918 (ttt) cc_final: 0.7467 (tpt) REVERT: C 506 ARG cc_start: 0.7488 (mmm-85) cc_final: 0.7227 (mtp85) REVERT: C 533 GLU cc_start: 0.7843 (tp30) cc_final: 0.7460 (tp30) REVERT: C 689 LYS cc_start: 0.8187 (ptpp) cc_final: 0.7957 (ptpt) REVERT: C 690 GLU cc_start: 0.7094 (pp20) cc_final: 0.6536 (pp20) REVERT: C 693 GLN cc_start: 0.8051 (pp30) cc_final: 0.7495 (pp30) REVERT: C 697 ASP cc_start: 0.7696 (m-30) cc_final: 0.7412 (m-30) REVERT: C 700 LYS cc_start: 0.8486 (mttt) cc_final: 0.7782 (mttt) REVERT: C 707 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.7561 (mm) REVERT: C 711 MET cc_start: 0.6414 (mmt) cc_final: 0.5909 (mmt) REVERT: C 725 GLU cc_start: 0.7576 (tt0) cc_final: 0.7094 (tp30) REVERT: C 731 LYS cc_start: 0.8394 (ttmm) cc_final: 0.7919 (ttmm) REVERT: C 744 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7721 (ttm170) REVERT: C 748 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6544 (tt) REVERT: E 87 TRP cc_start: 0.7460 (t60) cc_final: 0.6634 (t60) outliers start: 137 outliers final: 78 residues processed: 607 average time/residue: 0.1231 time to fit residues: 107.4570 Evaluate side-chains 611 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 514 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 508 HIS Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 992 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 613 PHE Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 729 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain E residue 35 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 25 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN A 680 ASN ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 113 GLN C 188 GLN C 222 GLN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.138767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.115081 restraints weight = 31730.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.119186 restraints weight = 16975.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121848 restraints weight = 10707.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.123483 restraints weight = 7592.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.124740 restraints weight = 5935.630| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15772 Z= 0.211 Angle : 0.827 11.994 21293 Z= 0.423 Chirality : 0.047 0.211 2490 Planarity : 0.006 0.118 2711 Dihedral : 6.075 57.012 2119 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.91 % Favored : 90.73 % Rotamer: Outliers : 6.90 % Allowed : 32.92 % Favored : 60.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.66 (0.19), residues: 1942 helix: 0.74 (0.14), residues: 1343 sheet: -0.59 (1.58), residues: 13 loop : -3.34 (0.22), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 629 TYR 0.016 0.002 TYR C 62 PHE 0.020 0.002 PHE C 734 TRP 0.013 0.002 TRP A 347 HIS 0.008 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00448 (15761) covalent geometry : angle 0.82665 (21287) hydrogen bonds : bond 0.05319 ( 984) hydrogen bonds : angle 5.01460 ( 2940) metal coordination : bond 0.00812 ( 11) metal coordination : angle 2.23340 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 528 time to evaluate : 0.501 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 6 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: A 47 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6599 (mpt-90) REVERT: A 51 LYS cc_start: 0.8478 (tptp) cc_final: 0.8145 (ptmm) REVERT: A 55 LYS cc_start: 0.8326 (tppt) cc_final: 0.7812 (ttpp) REVERT: A 65 GLN cc_start: 0.8426 (mt0) cc_final: 0.7880 (mm-40) REVERT: A 67 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7798 (mm) REVERT: A 78 LYS cc_start: 0.8400 (mmmt) cc_final: 0.8064 (tppt) REVERT: A 129 ASN cc_start: 0.7613 (t0) cc_final: 0.7378 (t0) REVERT: A 153 GLU cc_start: 0.7686 (mp0) cc_final: 0.7314 (mp0) REVERT: A 155 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8504 (mm) REVERT: A 158 MET cc_start: 0.8103 (tpt) cc_final: 0.7523 (tpt) REVERT: A 160 ASP cc_start: 0.8047 (m-30) cc_final: 0.7314 (m-30) REVERT: A 162 LEU cc_start: 0.8495 (mt) cc_final: 0.8181 (mt) REVERT: A 164 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6461 (mpp80) REVERT: A 215 LEU cc_start: 0.8336 (mt) cc_final: 0.8107 (mt) REVERT: A 218 LEU cc_start: 0.7017 (pp) cc_final: 0.6604 (pp) REVERT: A 233 CYS cc_start: 0.8191 (t) cc_final: 0.7912 (t) REVERT: A 239 ARG cc_start: 0.7685 (ttm110) cc_final: 0.6819 (ttm110) REVERT: A 258 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8047 (ttpt) REVERT: A 261 ASN cc_start: 0.8266 (t0) cc_final: 0.7842 (m-40) REVERT: A 275 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6940 (p90) REVERT: A 387 GLU cc_start: 0.4085 (OUTLIER) cc_final: 0.3508 (pm20) REVERT: A 403 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8012 (mmmt) REVERT: A 429 GLN cc_start: 0.7651 (pp30) cc_final: 0.7343 (pp30) REVERT: A 444 LYS cc_start: 0.8731 (mmmm) cc_final: 0.8437 (mmmm) REVERT: A 446 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8301 (mmtm) REVERT: A 452 GLN cc_start: 0.7384 (mt0) cc_final: 0.6430 (tm-30) REVERT: A 471 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8630 (mp10) REVERT: A 500 CYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7569 (p) REVERT: A 527 CYS cc_start: 0.8247 (m) cc_final: 0.7385 (t) REVERT: A 551 ARG cc_start: 0.7839 (tpt170) cc_final: 0.7577 (tpm170) REVERT: A 566 LYS cc_start: 0.8941 (tppt) cc_final: 0.8573 (tptp) REVERT: A 621 ASN cc_start: 0.7259 (OUTLIER) cc_final: 0.7034 (m-40) REVERT: A 633 THR cc_start: 0.8495 (m) cc_final: 0.8076 (p) REVERT: A 647 VAL cc_start: 0.8535 (m) cc_final: 0.8224 (p) REVERT: A 650 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6498 (mm-30) REVERT: A 675 ASP cc_start: 0.7495 (t0) cc_final: 0.7292 (t0) REVERT: A 689 MET cc_start: 0.7057 (pmm) cc_final: 0.6296 (ptt) REVERT: A 703 GLU cc_start: 0.7517 (tp30) cc_final: 0.7118 (tp30) REVERT: A 755 MET cc_start: 0.8152 (ttm) cc_final: 0.7746 (ttm) REVERT: A 776 LEU cc_start: 0.6849 (mm) cc_final: 0.6480 (mm) REVERT: A 826 LYS cc_start: 0.8341 (tptp) cc_final: 0.7766 (tptt) REVERT: A 836 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8169 (mm) REVERT: A 854 GLN cc_start: 0.7314 (pp30) cc_final: 0.6821 (pp30) REVERT: A 915 GLU cc_start: 0.7458 (tp30) cc_final: 0.7114 (tp30) REVERT: A 938 LYS cc_start: 0.8144 (tppp) cc_final: 0.7689 (tppp) REVERT: A 945 GLU cc_start: 0.6260 (tm-30) cc_final: 0.5841 (tm-30) REVERT: A 982 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7429 (mtm-85) REVERT: A 1023 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7606 (ttm110) REVERT: A 1081 ILE cc_start: 0.8936 (mt) cc_final: 0.8730 (mm) REVERT: A 1083 LYS cc_start: 0.8594 (mmmm) cc_final: 0.7990 (mmmm) REVERT: A 1086 PHE cc_start: 0.8387 (m-80) cc_final: 0.8080 (m-80) REVERT: A 1087 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8072 (tt0) REVERT: A 1089 MET cc_start: 0.8098 (mmm) cc_final: 0.7161 (mmm) REVERT: A 1120 LYS cc_start: 0.8580 (mmmm) cc_final: 0.7977 (mmtm) REVERT: A 1121 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8232 (mpp) REVERT: A 1164 GLN cc_start: 0.7741 (mp10) cc_final: 0.7353 (mp10) REVERT: A 1165 GLU cc_start: 0.8012 (mp0) cc_final: 0.7561 (tp30) REVERT: A 1168 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8257 (ttmt) REVERT: A 1171 GLU cc_start: 0.7801 (tp30) cc_final: 0.7237 (tp30) REVERT: C 42 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8126 (tm-30) REVERT: C 45 GLN cc_start: 0.8073 (tt0) cc_final: 0.7553 (tm-30) REVERT: C 59 ARG cc_start: 0.7398 (ttp-170) cc_final: 0.6974 (ttp-170) REVERT: C 83 GLU cc_start: 0.7989 (pp20) cc_final: 0.7644 (pp20) REVERT: C 88 LYS cc_start: 0.8278 (tptt) cc_final: 0.7701 (tppp) REVERT: C 91 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7401 (tm-30) REVERT: C 124 MET cc_start: 0.3942 (tmm) cc_final: 0.3534 (tmm) REVERT: C 153 ARG cc_start: 0.7759 (mtt-85) cc_final: 0.7366 (mmm-85) REVERT: C 176 GLU cc_start: 0.6543 (tm-30) cc_final: 0.6283 (tm-30) REVERT: C 188 GLN cc_start: 0.7616 (mt0) cc_final: 0.7225 (mm-40) REVERT: C 191 MET cc_start: 0.7435 (mmm) cc_final: 0.7224 (tpp) REVERT: C 211 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6443 (mt-10) REVERT: C 213 SER cc_start: 0.8154 (p) cc_final: 0.7820 (t) REVERT: C 228 ASN cc_start: 0.5749 (OUTLIER) cc_final: 0.5167 (m-40) REVERT: C 235 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7822 (mtpp) REVERT: C 236 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7386 (mtmt) REVERT: C 246 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7112 (mm-30) REVERT: C 288 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8603 (mt) REVERT: C 289 LYS cc_start: 0.8617 (tppt) cc_final: 0.8236 (tppt) REVERT: C 313 MET cc_start: 0.8109 (ttm) cc_final: 0.7791 (ttm) REVERT: C 326 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7768 (mmtm) REVERT: C 340 ASP cc_start: 0.7518 (m-30) cc_final: 0.7147 (m-30) REVERT: C 366 PHE cc_start: 0.8123 (m-80) cc_final: 0.7498 (m-80) REVERT: C 368 GLN cc_start: 0.7328 (tm-30) cc_final: 0.7061 (tm-30) REVERT: C 369 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.7621 (t) REVERT: C 375 GLU cc_start: 0.7433 (tm-30) cc_final: 0.7023 (tm-30) REVERT: C 386 GLU cc_start: 0.7445 (tp30) cc_final: 0.6950 (tp30) REVERT: C 387 TYR cc_start: 0.8052 (m-80) cc_final: 0.7714 (m-80) REVERT: C 393 ASP cc_start: 0.7225 (t0) cc_final: 0.6895 (t70) REVERT: C 444 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6530 (tptp) REVERT: C 454 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6951 (tmm) REVERT: C 459 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8064 (ttmm) REVERT: C 473 MET cc_start: 0.7869 (ttt) cc_final: 0.6572 (tpp) REVERT: C 506 ARG cc_start: 0.7414 (mmm-85) cc_final: 0.7157 (mtp85) REVERT: C 513 TRP cc_start: 0.8222 (m100) cc_final: 0.7439 (m100) REVERT: C 533 GLU cc_start: 0.7875 (tp30) cc_final: 0.7419 (tp30) REVERT: C 689 LYS cc_start: 0.8195 (ptpp) cc_final: 0.7967 (ptpt) REVERT: C 690 GLU cc_start: 0.7027 (pp20) cc_final: 0.6465 (pp20) REVERT: C 693 GLN cc_start: 0.8047 (pp30) cc_final: 0.7453 (pp30) REVERT: C 697 ASP cc_start: 0.7654 (m-30) cc_final: 0.7338 (m-30) REVERT: C 707 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.7592 (mm) REVERT: C 711 MET cc_start: 0.6322 (mmt) cc_final: 0.5936 (mmt) REVERT: C 725 GLU cc_start: 0.7550 (tt0) cc_final: 0.7153 (tm-30) REVERT: C 731 LYS cc_start: 0.8371 (ttmm) cc_final: 0.7875 (ttmm) REVERT: C 744 ARG cc_start: 0.8174 (ttm170) cc_final: 0.7791 (ttt180) REVERT: C 748 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6547 (tt) REVERT: E 87 TRP cc_start: 0.7508 (t60) cc_final: 0.6702 (t60) REVERT: E 101 TRP cc_start: 0.6935 (t-100) cc_final: 0.6317 (t-100) outliers start: 121 outliers final: 75 residues processed: 587 average time/residue: 0.1229 time to fit residues: 103.2820 Evaluate side-chains 616 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 520 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 400 SER Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 992 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1121 MET Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 613 PHE Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 685 ASP Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 729 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain E residue 35 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 22 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 53 optimal weight: 0.1980 chunk 171 optimal weight: 0.0010 chunk 145 optimal weight: 1.9990 chunk 98 optimal weight: 0.0020 chunk 9 optimal weight: 0.0970 chunk 141 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.0170 chunk 85 optimal weight: 2.9990 overall best weight: 0.0630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 ASN A 471 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS C 222 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 HIS ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.144097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.120640 restraints weight = 32073.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.124779 restraints weight = 17125.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.127498 restraints weight = 10807.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129353 restraints weight = 7665.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.130470 restraints weight = 5896.047| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15772 Z= 0.165 Angle : 0.820 11.632 21293 Z= 0.409 Chirality : 0.045 0.196 2490 Planarity : 0.006 0.116 2711 Dihedral : 5.849 57.410 2119 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.86 % Favored : 90.94 % Rotamer: Outliers : 5.08 % Allowed : 34.57 % Favored : 60.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.40 (0.19), residues: 1942 helix: 0.97 (0.14), residues: 1338 sheet: -0.74 (1.44), residues: 13 loop : -3.28 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG C 629 TYR 0.030 0.002 TYR C 341 PHE 0.018 0.002 PHE C 538 TRP 0.015 0.002 TRP A 347 HIS 0.007 0.001 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00346 (15761) covalent geometry : angle 0.81926 (21287) hydrogen bonds : bond 0.04604 ( 984) hydrogen bonds : angle 4.81461 ( 2940) metal coordination : bond 0.00492 ( 11) metal coordination : angle 2.12062 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 525 time to evaluate : 0.512 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 6 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7328 (m-80) REVERT: A 47 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6375 (mpp-170) REVERT: A 51 LYS cc_start: 0.8456 (tptp) cc_final: 0.8123 (ptmm) REVERT: A 65 GLN cc_start: 0.8352 (mt0) cc_final: 0.7773 (mm-40) REVERT: A 67 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7609 (mm) REVERT: A 78 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8038 (tppt) REVERT: A 95 MET cc_start: 0.7926 (ptp) cc_final: 0.7711 (ptm) REVERT: A 129 ASN cc_start: 0.7501 (t0) cc_final: 0.7258 (t0) REVERT: A 155 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8501 (mm) REVERT: A 158 MET cc_start: 0.8049 (tpt) cc_final: 0.7478 (tpt) REVERT: A 160 ASP cc_start: 0.8012 (m-30) cc_final: 0.7215 (m-30) REVERT: A 162 LEU cc_start: 0.8270 (mt) cc_final: 0.7984 (mt) REVERT: A 164 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6384 (mpp80) REVERT: A 215 LEU cc_start: 0.8184 (mt) cc_final: 0.7914 (mt) REVERT: A 218 LEU cc_start: 0.6661 (pp) cc_final: 0.6039 (pp) REVERT: A 233 CYS cc_start: 0.8115 (t) cc_final: 0.7847 (t) REVERT: A 261 ASN cc_start: 0.8206 (t0) cc_final: 0.7875 (t0) REVERT: A 268 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6798 (ptm-80) REVERT: A 275 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6851 (p90) REVERT: A 403 LYS cc_start: 0.8390 (mtmm) cc_final: 0.7900 (mmmt) REVERT: A 429 GLN cc_start: 0.7520 (pp30) cc_final: 0.7294 (pp30) REVERT: A 444 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8259 (mmmm) REVERT: A 446 LYS cc_start: 0.8381 (mmtt) cc_final: 0.8085 (mmtm) REVERT: A 471 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8437 (mp10) REVERT: A 482 PHE cc_start: 0.8090 (t80) cc_final: 0.7707 (t80) REVERT: A 500 CYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7596 (p) REVERT: A 527 CYS cc_start: 0.8173 (m) cc_final: 0.7210 (t) REVERT: A 566 LYS cc_start: 0.8913 (tppt) cc_final: 0.8583 (tptp) REVERT: A 633 THR cc_start: 0.8405 (m) cc_final: 0.8002 (p) REVERT: A 647 VAL cc_start: 0.8366 (m) cc_final: 0.8039 (p) REVERT: A 650 GLU cc_start: 0.6693 (mm-30) cc_final: 0.6324 (mm-30) REVERT: A 662 ASN cc_start: 0.7662 (p0) cc_final: 0.7245 (t0) REVERT: A 675 ASP cc_start: 0.7456 (t0) cc_final: 0.7255 (t0) REVERT: A 703 GLU cc_start: 0.7502 (tp30) cc_final: 0.7067 (tp30) REVERT: A 752 LEU cc_start: 0.8362 (tp) cc_final: 0.8159 (tp) REVERT: A 776 LEU cc_start: 0.6386 (mm) cc_final: 0.6163 (mm) REVERT: A 826 LYS cc_start: 0.8326 (tptp) cc_final: 0.7764 (tptt) REVERT: A 854 GLN cc_start: 0.7256 (pp30) cc_final: 0.6722 (pp30) REVERT: A 915 GLU cc_start: 0.7327 (tp30) cc_final: 0.6879 (tp30) REVERT: A 938 LYS cc_start: 0.8137 (tppp) cc_final: 0.7723 (tppp) REVERT: A 945 GLU cc_start: 0.6111 (tm-30) cc_final: 0.5727 (tm-30) REVERT: A 982 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7523 (mtm-85) REVERT: A 1023 ARG cc_start: 0.8013 (ttm110) cc_final: 0.7258 (ttm110) REVERT: A 1087 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7922 (tt0) REVERT: A 1108 HIS cc_start: 0.7885 (m90) cc_final: 0.7620 (m90) REVERT: A 1120 LYS cc_start: 0.8480 (mmmm) cc_final: 0.8070 (mmmt) REVERT: A 1126 MET cc_start: 0.7913 (tpp) cc_final: 0.7593 (mmm) REVERT: A 1144 ARG cc_start: 0.7054 (mtp85) cc_final: 0.6733 (mtm110) REVERT: A 1164 GLN cc_start: 0.7519 (mp10) cc_final: 0.7124 (mp10) REVERT: A 1165 GLU cc_start: 0.7952 (mp0) cc_final: 0.7511 (tp30) REVERT: A 1171 GLU cc_start: 0.7819 (tp30) cc_final: 0.7226 (tp30) REVERT: C 42 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8084 (tm-30) REVERT: C 79 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7350 (pp20) REVERT: C 83 GLU cc_start: 0.7846 (pp20) cc_final: 0.7514 (pp20) REVERT: C 88 LYS cc_start: 0.8188 (tptt) cc_final: 0.7630 (tppp) REVERT: C 91 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7277 (tm-30) REVERT: C 112 HIS cc_start: 0.7861 (t70) cc_final: 0.7603 (t70) REVERT: C 124 MET cc_start: 0.3492 (tmm) cc_final: 0.3166 (tmm) REVERT: C 153 ARG cc_start: 0.7669 (mtt-85) cc_final: 0.7258 (mmm-85) REVERT: C 176 GLU cc_start: 0.6417 (tm-30) cc_final: 0.6101 (tm-30) REVERT: C 187 CYS cc_start: 0.8137 (m) cc_final: 0.7790 (m) REVERT: C 188 GLN cc_start: 0.7622 (mt0) cc_final: 0.7145 (mm-40) REVERT: C 211 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.6299 (mt-10) REVERT: C 213 SER cc_start: 0.8069 (p) cc_final: 0.7845 (p) REVERT: C 228 ASN cc_start: 0.5307 (OUTLIER) cc_final: 0.4941 (m-40) REVERT: C 236 LYS cc_start: 0.7736 (ttmt) cc_final: 0.7425 (ttpt) REVERT: C 246 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7043 (mm-30) REVERT: C 265 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6823 (mt-10) REVERT: C 288 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8624 (mt) REVERT: C 289 LYS cc_start: 0.8511 (tppt) cc_final: 0.8028 (tppt) REVERT: C 313 MET cc_start: 0.7973 (ttm) cc_final: 0.7612 (ttm) REVERT: C 320 TYR cc_start: 0.8274 (t80) cc_final: 0.7984 (t80) REVERT: C 326 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7598 (mmtm) REVERT: C 359 SER cc_start: 0.8177 (p) cc_final: 0.7781 (m) REVERT: C 368 GLN cc_start: 0.7325 (tm-30) cc_final: 0.7032 (tm-30) REVERT: C 369 THR cc_start: 0.7981 (t) cc_final: 0.7488 (t) REVERT: C 375 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6994 (tm-30) REVERT: C 386 GLU cc_start: 0.7443 (tp30) cc_final: 0.6078 (tp30) REVERT: C 387 TYR cc_start: 0.7829 (m-80) cc_final: 0.7437 (m-80) REVERT: C 416 MET cc_start: 0.7747 (mmm) cc_final: 0.7464 (mmp) REVERT: C 430 ARG cc_start: 0.8239 (tpp80) cc_final: 0.7965 (tpp80) REVERT: C 431 TYR cc_start: 0.8342 (m-10) cc_final: 0.8002 (m-80) REVERT: C 444 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.6306 (tptp) REVERT: C 454 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.6858 (tmm) REVERT: C 459 LYS cc_start: 0.8479 (mmmt) cc_final: 0.7914 (ttmm) REVERT: C 461 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6746 (tp30) REVERT: C 473 MET cc_start: 0.7802 (ttt) cc_final: 0.6581 (tpp) REVERT: C 513 TRP cc_start: 0.8194 (m100) cc_final: 0.7483 (m100) REVERT: C 533 GLU cc_start: 0.7815 (tp30) cc_final: 0.7300 (tp30) REVERT: C 689 LYS cc_start: 0.8097 (ptpp) cc_final: 0.7728 (pttt) REVERT: C 690 GLU cc_start: 0.6990 (pp20) cc_final: 0.6375 (pp20) REVERT: C 693 GLN cc_start: 0.8023 (pp30) cc_final: 0.7311 (pp30) REVERT: C 694 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8221 (ttmt) REVERT: C 697 ASP cc_start: 0.7561 (m-30) cc_final: 0.7218 (m-30) REVERT: C 701 HIS cc_start: 0.7743 (m170) cc_final: 0.7281 (m170) REVERT: C 707 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.7590 (mm) REVERT: C 711 MET cc_start: 0.6212 (mmt) cc_final: 0.5796 (mmt) REVERT: C 725 GLU cc_start: 0.7514 (tt0) cc_final: 0.7048 (tp30) REVERT: C 731 LYS cc_start: 0.8373 (ttmm) cc_final: 0.7874 (ttmm) REVERT: C 744 ARG cc_start: 0.8097 (ttm170) cc_final: 0.7757 (ttm170) REVERT: E 27 TRP cc_start: 0.8182 (t60) cc_final: 0.7974 (t60) REVERT: E 87 TRP cc_start: 0.7523 (t60) cc_final: 0.6822 (t60) outliers start: 89 outliers final: 54 residues processed: 574 average time/residue: 0.1262 time to fit residues: 103.6751 Evaluate side-chains 577 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 508 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain A residue 1157 VAL Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 729 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain E residue 35 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 114 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.140964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.117332 restraints weight = 32061.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.121429 restraints weight = 17233.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.124062 restraints weight = 10899.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.125937 restraints weight = 7745.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127091 restraints weight = 5985.384| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15772 Z= 0.190 Angle : 0.833 13.411 21293 Z= 0.422 Chirality : 0.047 0.237 2490 Planarity : 0.006 0.117 2711 Dihedral : 5.825 57.525 2119 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.91 % Favored : 90.89 % Rotamer: Outliers : 4.22 % Allowed : 36.11 % Favored : 59.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.43 (0.19), residues: 1942 helix: 0.94 (0.14), residues: 1341 sheet: -0.39 (1.55), residues: 13 loop : -3.30 (0.21), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 506 TYR 0.027 0.002 TYR C 341 PHE 0.032 0.002 PHE A 991 TRP 0.025 0.002 TRP A 933 HIS 0.013 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00414 (15761) covalent geometry : angle 0.83261 (21287) hydrogen bonds : bond 0.04961 ( 984) hydrogen bonds : angle 4.87905 ( 2940) metal coordination : bond 0.00707 ( 11) metal coordination : angle 2.20202 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 511 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6413 (mpp-170) REVERT: A 51 LYS cc_start: 0.8475 (tptp) cc_final: 0.8121 (ptmm) REVERT: A 55 LYS cc_start: 0.8152 (tppt) cc_final: 0.7762 (tppt) REVERT: A 63 GLU cc_start: 0.7566 (mp0) cc_final: 0.7040 (pm20) REVERT: A 65 GLN cc_start: 0.8420 (mt0) cc_final: 0.7874 (mm-40) REVERT: A 67 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7706 (mm) REVERT: A 78 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8091 (tppt) REVERT: A 111 LYS cc_start: 0.8794 (tppp) cc_final: 0.8570 (tppp) REVERT: A 129 ASN cc_start: 0.7556 (t0) cc_final: 0.7320 (t0) REVERT: A 153 GLU cc_start: 0.7643 (mp0) cc_final: 0.7195 (mp0) REVERT: A 155 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8548 (mm) REVERT: A 158 MET cc_start: 0.8077 (tpt) cc_final: 0.7531 (tpt) REVERT: A 160 ASP cc_start: 0.8058 (m-30) cc_final: 0.7270 (m-30) REVERT: A 162 LEU cc_start: 0.8306 (mt) cc_final: 0.8015 (mt) REVERT: A 164 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6448 (mpp80) REVERT: A 215 LEU cc_start: 0.8245 (mt) cc_final: 0.7961 (mt) REVERT: A 218 LEU cc_start: 0.6796 (pp) cc_final: 0.6479 (pp) REVERT: A 233 CYS cc_start: 0.8133 (t) cc_final: 0.7889 (t) REVERT: A 261 ASN cc_start: 0.8218 (t0) cc_final: 0.7895 (m-40) REVERT: A 268 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7080 (ptm-80) REVERT: A 275 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6933 (p90) REVERT: A 391 LYS cc_start: 0.8042 (tmtt) cc_final: 0.7416 (tptp) REVERT: A 395 PHE cc_start: 0.8592 (m-80) cc_final: 0.8055 (m-80) REVERT: A 403 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8030 (mmmt) REVERT: A 429 GLN cc_start: 0.7590 (pp30) cc_final: 0.7269 (pp30) REVERT: A 444 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8352 (mmmm) REVERT: A 446 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8224 (mmtm) REVERT: A 452 GLN cc_start: 0.7388 (mt0) cc_final: 0.6434 (tm-30) REVERT: A 457 MET cc_start: 0.8094 (tpp) cc_final: 0.7778 (ttm) REVERT: A 476 LEU cc_start: 0.8747 (mt) cc_final: 0.8446 (mt) REVERT: A 500 CYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7606 (p) REVERT: A 527 CYS cc_start: 0.8242 (m) cc_final: 0.7303 (t) REVERT: A 566 LYS cc_start: 0.8933 (tppt) cc_final: 0.8555 (tptp) REVERT: A 592 CYS cc_start: 0.7982 (t) cc_final: 0.7769 (t) REVERT: A 633 THR cc_start: 0.8474 (m) cc_final: 0.8076 (p) REVERT: A 647 VAL cc_start: 0.8453 (m) cc_final: 0.8126 (p) REVERT: A 650 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6436 (mm-30) REVERT: A 662 ASN cc_start: 0.7669 (p0) cc_final: 0.7262 (t0) REVERT: A 695 ASP cc_start: 0.7781 (t70) cc_final: 0.7531 (p0) REVERT: A 703 GLU cc_start: 0.7550 (tp30) cc_final: 0.7136 (tp30) REVERT: A 776 LEU cc_start: 0.6599 (mm) cc_final: 0.6385 (mm) REVERT: A 836 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8224 (mm) REVERT: A 854 GLN cc_start: 0.7304 (pp30) cc_final: 0.6751 (pp30) REVERT: A 915 GLU cc_start: 0.7301 (tp30) cc_final: 0.6857 (tp30) REVERT: A 935 LEU cc_start: 0.8029 (tp) cc_final: 0.7791 (tt) REVERT: A 938 LYS cc_start: 0.8199 (tppp) cc_final: 0.7769 (tppp) REVERT: A 945 GLU cc_start: 0.6226 (tm-30) cc_final: 0.5810 (tm-30) REVERT: A 982 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7661 (mtm-85) REVERT: A 1023 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7512 (ttm110) REVERT: A 1079 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8567 (tt) REVERT: A 1086 PHE cc_start: 0.8384 (m-80) cc_final: 0.8031 (m-80) REVERT: A 1087 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7987 (tt0) REVERT: A 1120 LYS cc_start: 0.8530 (mmmm) cc_final: 0.8104 (mmmt) REVERT: A 1144 ARG cc_start: 0.7148 (mtp85) cc_final: 0.6844 (mtm110) REVERT: A 1164 GLN cc_start: 0.7539 (mp10) cc_final: 0.7158 (mp10) REVERT: A 1165 GLU cc_start: 0.7969 (mp0) cc_final: 0.7546 (tp30) REVERT: A 1171 GLU cc_start: 0.7793 (tp30) cc_final: 0.7167 (tp30) REVERT: C 42 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8150 (tm-30) REVERT: C 59 ARG cc_start: 0.7419 (ttp-170) cc_final: 0.6978 (ttp-170) REVERT: C 79 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7398 (pp20) REVERT: C 83 GLU cc_start: 0.7920 (pp20) cc_final: 0.7585 (pp20) REVERT: C 88 LYS cc_start: 0.8190 (tptt) cc_final: 0.7873 (tptt) REVERT: C 90 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7697 (mmm-85) REVERT: C 91 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7275 (tm-30) REVERT: C 124 MET cc_start: 0.3873 (tmm) cc_final: 0.3486 (tmm) REVERT: C 153 ARG cc_start: 0.7696 (mtt-85) cc_final: 0.7260 (mmm-85) REVERT: C 176 GLU cc_start: 0.6473 (tm-30) cc_final: 0.6164 (tm-30) REVERT: C 187 CYS cc_start: 0.8148 (m) cc_final: 0.7886 (m) REVERT: C 188 GLN cc_start: 0.7563 (mt0) cc_final: 0.7251 (mm-40) REVERT: C 213 SER cc_start: 0.8126 (p) cc_final: 0.7785 (t) REVERT: C 222 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7687 (tp-100) REVERT: C 228 ASN cc_start: 0.5653 (OUTLIER) cc_final: 0.5208 (m-40) REVERT: C 246 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7066 (mm-30) REVERT: C 288 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8705 (mt) REVERT: C 289 LYS cc_start: 0.8520 (tppt) cc_final: 0.7996 (tppt) REVERT: C 296 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8356 (tp) REVERT: C 313 MET cc_start: 0.8015 (ttm) cc_final: 0.7654 (ttm) REVERT: C 326 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7771 (mmtm) REVERT: C 340 ASP cc_start: 0.7399 (m-30) cc_final: 0.7018 (m-30) REVERT: C 359 SER cc_start: 0.8208 (p) cc_final: 0.7978 (m) REVERT: C 366 PHE cc_start: 0.8105 (m-80) cc_final: 0.7465 (m-10) REVERT: C 368 GLN cc_start: 0.7318 (tm-30) cc_final: 0.7031 (tm-30) REVERT: C 369 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7577 (t) REVERT: C 375 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7055 (tm-30) REVERT: C 386 GLU cc_start: 0.7486 (tp30) cc_final: 0.6883 (tp30) REVERT: C 387 TYR cc_start: 0.7791 (m-80) cc_final: 0.7555 (m-80) REVERT: C 416 MET cc_start: 0.7764 (mmm) cc_final: 0.7492 (mmp) REVERT: C 430 ARG cc_start: 0.8307 (tpp80) cc_final: 0.8034 (tpp80) REVERT: C 444 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6411 (tptp) REVERT: C 454 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.6934 (tmm) REVERT: C 459 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8010 (ttmm) REVERT: C 460 THR cc_start: 0.8242 (t) cc_final: 0.7970 (p) REVERT: C 461 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6799 (tp30) REVERT: C 473 MET cc_start: 0.7860 (ttt) cc_final: 0.6624 (tpp) REVERT: C 513 TRP cc_start: 0.8245 (m100) cc_final: 0.7556 (m100) REVERT: C 533 GLU cc_start: 0.7798 (tp30) cc_final: 0.7291 (tp30) REVERT: C 690 GLU cc_start: 0.7060 (pp20) cc_final: 0.6465 (pp20) REVERT: C 693 GLN cc_start: 0.8074 (pp30) cc_final: 0.7448 (pp30) REVERT: C 694 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8192 (ttmm) REVERT: C 697 ASP cc_start: 0.7644 (m-30) cc_final: 0.7294 (m-30) REVERT: C 707 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.7611 (mm) REVERT: C 711 MET cc_start: 0.6375 (mmt) cc_final: 0.6069 (mmt) REVERT: C 725 GLU cc_start: 0.7581 (tt0) cc_final: 0.7278 (tm-30) REVERT: C 731 LYS cc_start: 0.8380 (ttmm) cc_final: 0.7867 (ttmm) REVERT: C 744 ARG cc_start: 0.8131 (ttm170) cc_final: 0.7851 (ttm170) REVERT: C 761 ARG cc_start: 0.8010 (mmt-90) cc_final: 0.7781 (mmt-90) REVERT: E 101 TRP cc_start: 0.6838 (t-100) cc_final: 0.6267 (t-100) outliers start: 74 outliers final: 46 residues processed: 553 average time/residue: 0.1207 time to fit residues: 95.0209 Evaluate side-chains 570 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 506 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 613 PHE Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 729 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain E residue 35 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 31 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 175 optimal weight: 0.0040 chunk 52 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN ** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.141631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.118836 restraints weight = 31963.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.122830 restraints weight = 17042.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.125503 restraints weight = 10731.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127180 restraints weight = 7565.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.128449 restraints weight = 5856.385| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15772 Z= 0.169 Angle : 0.836 12.607 21293 Z= 0.420 Chirality : 0.047 0.334 2490 Planarity : 0.006 0.117 2711 Dihedral : 5.642 57.860 2114 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.86 % Favored : 90.94 % Rotamer: Outliers : 4.34 % Allowed : 36.57 % Favored : 59.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.42 (0.19), residues: 1942 helix: 0.94 (0.14), residues: 1339 sheet: -0.38 (1.57), residues: 13 loop : -3.24 (0.21), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 629 TYR 0.027 0.002 TYR C 341 PHE 0.021 0.002 PHE C 538 TRP 0.029 0.002 TRP E 27 HIS 0.010 0.001 HIS A 939 Details of bonding type rmsd covalent geometry : bond 0.00372 (15761) covalent geometry : angle 0.83540 (21287) hydrogen bonds : bond 0.04843 ( 984) hydrogen bonds : angle 4.87632 ( 2940) metal coordination : bond 0.00592 ( 11) metal coordination : angle 2.03148 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3884 Ramachandran restraints generated. 1942 Oldfield, 0 Emsley, 1942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 509 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6396 (mpp-170) REVERT: A 51 LYS cc_start: 0.8471 (tptp) cc_final: 0.8171 (ptmm) REVERT: A 55 LYS cc_start: 0.8151 (tppt) cc_final: 0.7759 (tppt) REVERT: A 63 GLU cc_start: 0.7619 (mp0) cc_final: 0.7126 (pm20) REVERT: A 65 GLN cc_start: 0.8427 (mt0) cc_final: 0.7876 (mm-40) REVERT: A 67 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7679 (mm) REVERT: A 78 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8119 (tppt) REVERT: A 99 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6880 (tmmt) REVERT: A 111 LYS cc_start: 0.8789 (tppp) cc_final: 0.8560 (tppp) REVERT: A 129 ASN cc_start: 0.7512 (t0) cc_final: 0.7275 (t0) REVERT: A 153 GLU cc_start: 0.7614 (mp0) cc_final: 0.7161 (mp0) REVERT: A 155 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8544 (mm) REVERT: A 158 MET cc_start: 0.8061 (tpt) cc_final: 0.7516 (tpt) REVERT: A 160 ASP cc_start: 0.8032 (m-30) cc_final: 0.7279 (m-30) REVERT: A 162 LEU cc_start: 0.8292 (mt) cc_final: 0.7991 (mt) REVERT: A 164 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6434 (mpp80) REVERT: A 215 LEU cc_start: 0.8218 (mt) cc_final: 0.7945 (mt) REVERT: A 218 LEU cc_start: 0.6796 (pp) cc_final: 0.6466 (pp) REVERT: A 233 CYS cc_start: 0.8133 (t) cc_final: 0.7869 (t) REVERT: A 256 VAL cc_start: 0.8811 (m) cc_final: 0.8586 (p) REVERT: A 261 ASN cc_start: 0.8221 (t0) cc_final: 0.7884 (t0) REVERT: A 268 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6912 (ptm-80) REVERT: A 275 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6909 (p90) REVERT: A 387 GLU cc_start: 0.3959 (OUTLIER) cc_final: 0.3493 (pm20) REVERT: A 391 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7563 (tptp) REVERT: A 395 PHE cc_start: 0.8580 (m-80) cc_final: 0.8242 (m-10) REVERT: A 403 LYS cc_start: 0.8400 (mtmm) cc_final: 0.8018 (mmmt) REVERT: A 429 GLN cc_start: 0.7571 (pp30) cc_final: 0.7351 (pp30) REVERT: A 444 LYS cc_start: 0.8699 (mmmm) cc_final: 0.8344 (mmmm) REVERT: A 446 LYS cc_start: 0.8478 (mmtt) cc_final: 0.8189 (mmtm) REVERT: A 452 GLN cc_start: 0.7377 (mt0) cc_final: 0.6427 (tm-30) REVERT: A 500 CYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7588 (p) REVERT: A 527 CYS cc_start: 0.8242 (m) cc_final: 0.7270 (t) REVERT: A 566 LYS cc_start: 0.8926 (tppt) cc_final: 0.8545 (tptp) REVERT: A 587 GLU cc_start: 0.7357 (pp20) cc_final: 0.6994 (pp20) REVERT: A 592 CYS cc_start: 0.7989 (t) cc_final: 0.7780 (t) REVERT: A 633 THR cc_start: 0.8431 (m) cc_final: 0.8034 (p) REVERT: A 647 VAL cc_start: 0.8437 (m) cc_final: 0.8118 (p) REVERT: A 650 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6408 (mm-30) REVERT: A 662 ASN cc_start: 0.7612 (p0) cc_final: 0.7266 (t0) REVERT: A 703 GLU cc_start: 0.7551 (tp30) cc_final: 0.7148 (tp30) REVERT: A 776 LEU cc_start: 0.6636 (mm) cc_final: 0.6363 (mm) REVERT: A 854 GLN cc_start: 0.7277 (pp30) cc_final: 0.6722 (pp30) REVERT: A 915 GLU cc_start: 0.7308 (tp30) cc_final: 0.6855 (tp30) REVERT: A 938 LYS cc_start: 0.8144 (tppp) cc_final: 0.7735 (tppp) REVERT: A 945 GLU cc_start: 0.6178 (tm-30) cc_final: 0.5776 (tm-30) REVERT: A 982 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7485 (mtm-85) REVERT: A 1023 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7453 (ttm110) REVERT: A 1079 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8539 (tt) REVERT: A 1086 PHE cc_start: 0.8368 (m-80) cc_final: 0.8102 (m-80) REVERT: A 1087 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7953 (tt0) REVERT: A 1108 HIS cc_start: 0.7890 (m90) cc_final: 0.7564 (m90) REVERT: A 1120 LYS cc_start: 0.8507 (mmmm) cc_final: 0.8077 (mmmt) REVERT: A 1144 ARG cc_start: 0.7091 (mtp85) cc_final: 0.6812 (mtm110) REVERT: A 1164 GLN cc_start: 0.7500 (mp10) cc_final: 0.7132 (mp10) REVERT: A 1165 GLU cc_start: 0.7934 (mp0) cc_final: 0.7520 (tp30) REVERT: A 1170 ASP cc_start: 0.7844 (m-30) cc_final: 0.7486 (m-30) REVERT: A 1171 GLU cc_start: 0.7809 (tp30) cc_final: 0.7153 (tp30) REVERT: C 42 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8140 (tm-30) REVERT: C 59 ARG cc_start: 0.7437 (ttp-170) cc_final: 0.6998 (ttp-170) REVERT: C 79 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7367 (pp20) REVERT: C 83 GLU cc_start: 0.7894 (pp20) cc_final: 0.7558 (pp20) REVERT: C 88 LYS cc_start: 0.8171 (tptt) cc_final: 0.7833 (tptt) REVERT: C 90 ARG cc_start: 0.7925 (mtp-110) cc_final: 0.7620 (mmm-85) REVERT: C 91 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7266 (tm-30) REVERT: C 153 ARG cc_start: 0.7673 (mtt-85) cc_final: 0.7278 (mmm-85) REVERT: C 158 ARG cc_start: 0.8097 (mtp-110) cc_final: 0.7872 (mmm-85) REVERT: C 168 MET cc_start: 0.8289 (ttp) cc_final: 0.7921 (ttm) REVERT: C 176 GLU cc_start: 0.6453 (tm-30) cc_final: 0.6159 (tm-30) REVERT: C 188 GLN cc_start: 0.7627 (mt0) cc_final: 0.7256 (mm-40) REVERT: C 213 SER cc_start: 0.8139 (p) cc_final: 0.7735 (t) REVERT: C 228 ASN cc_start: 0.5254 (OUTLIER) cc_final: 0.4878 (m-40) REVERT: C 246 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7063 (mm-30) REVERT: C 266 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7390 (ttp80) REVERT: C 288 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8652 (mt) REVERT: C 289 LYS cc_start: 0.8482 (tppt) cc_final: 0.8205 (tppt) REVERT: C 296 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8374 (tp) REVERT: C 313 MET cc_start: 0.8015 (ttm) cc_final: 0.7640 (ttm) REVERT: C 326 LYS cc_start: 0.8084 (mmmt) cc_final: 0.7744 (mmtm) REVERT: C 340 ASP cc_start: 0.7316 (m-30) cc_final: 0.6968 (m-30) REVERT: C 366 PHE cc_start: 0.8036 (m-80) cc_final: 0.7466 (m-80) REVERT: C 368 GLN cc_start: 0.7327 (tm-30) cc_final: 0.7037 (tm-30) REVERT: C 369 THR cc_start: 0.8020 (OUTLIER) cc_final: 0.7532 (t) REVERT: C 375 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7057 (tm-30) REVERT: C 386 GLU cc_start: 0.7497 (tp30) cc_final: 0.6640 (tp30) REVERT: C 387 TYR cc_start: 0.7843 (m-80) cc_final: 0.7575 (m-80) REVERT: C 416 MET cc_start: 0.7780 (mmm) cc_final: 0.7501 (mmp) REVERT: C 430 ARG cc_start: 0.8263 (tpp80) cc_final: 0.8004 (tpp80) REVERT: C 431 TYR cc_start: 0.8342 (m-10) cc_final: 0.8089 (m-80) REVERT: C 444 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6387 (tptp) REVERT: C 454 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.6915 (tmm) REVERT: C 459 LYS cc_start: 0.8547 (mmmt) cc_final: 0.7950 (ttmm) REVERT: C 461 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6822 (tp30) REVERT: C 473 MET cc_start: 0.7895 (ttt) cc_final: 0.6649 (tpp) REVERT: C 513 TRP cc_start: 0.8222 (m100) cc_final: 0.7503 (m100) REVERT: C 533 GLU cc_start: 0.7818 (tp30) cc_final: 0.7244 (tp30) REVERT: C 690 GLU cc_start: 0.7078 (pp20) cc_final: 0.6447 (pp20) REVERT: C 693 GLN cc_start: 0.8034 (pp30) cc_final: 0.7375 (pp30) REVERT: C 694 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8175 (ttmm) REVERT: C 697 ASP cc_start: 0.7631 (m-30) cc_final: 0.7314 (m-30) REVERT: C 701 HIS cc_start: 0.7771 (m170) cc_final: 0.7333 (m170) REVERT: C 707 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.7568 (mm) REVERT: C 711 MET cc_start: 0.6322 (mmt) cc_final: 0.5949 (mmt) REVERT: C 725 GLU cc_start: 0.7589 (tt0) cc_final: 0.7278 (tm-30) REVERT: C 731 LYS cc_start: 0.8377 (ttmm) cc_final: 0.7869 (ttmm) REVERT: C 744 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7842 (ttm170) REVERT: E 81 PHE cc_start: 0.8275 (t80) cc_final: 0.7541 (t80) outliers start: 76 outliers final: 51 residues processed: 551 average time/residue: 0.1241 time to fit residues: 96.7484 Evaluate side-chains 570 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 502 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 615 PHE Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1079 LEU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 729 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain E residue 35 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 103 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 177 optimal weight: 20.0000 chunk 128 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 190 optimal weight: 40.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** C 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.140282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.117453 restraints weight = 31702.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121457 restraints weight = 16972.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124098 restraints weight = 10679.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125900 restraints weight = 7533.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.127038 restraints weight = 5773.543| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15772 Z= 0.176 Angle : 0.839 11.999 21293 Z= 0.422 Chirality : 0.047 0.338 2490 Planarity : 0.006 0.117 2711 Dihedral : 5.650 58.415 2114 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.17 % Favored : 90.63 % Rotamer: Outliers : 4.28 % Allowed : 36.51 % Favored : 59.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -0.36 (0.19), residues: 1942 helix: 0.94 (0.14), residues: 1338 sheet: -0.14 (1.62), residues: 13 loop : -3.11 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 629 TYR 0.026 0.002 TYR C 341 PHE 0.021 0.002 PHE C 538 TRP 0.020 0.002 TRP A 933 HIS 0.009 0.001 HIS A 847 Details of bonding type rmsd covalent geometry : bond 0.00386 (15761) covalent geometry : angle 0.83798 (21287) hydrogen bonds : bond 0.04917 ( 984) hydrogen bonds : angle 4.88942 ( 2940) metal coordination : bond 0.00640 ( 11) metal coordination : angle 2.12884 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2731.91 seconds wall clock time: 48 minutes 5.95 seconds (2885.95 seconds total)