Starting phenix.real_space_refine on Sat May 17 09:13:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3q_34473/05_2025/8h3q_34473.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3q_34473/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h3q_34473/05_2025/8h3q_34473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3q_34473/05_2025/8h3q_34473.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3q_34473/05_2025/8h3q_34473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3q_34473/05_2025/8h3q_34473.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.93, per 1000 atoms: 0.58 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: 3.72 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.53 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: 6.30 Time building geometry restraints manager: 4.36 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 40.290 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.120 ------------------------------------------------------------------------------- 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 : 18.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.049 0.003 TRP C 513 HIS 0.012 0.001 HIS C 84 PHE 0.045 0.002 PHE A 395 TYR 0.039 0.002 TYR A 270 ARG 0.014 0.001 ARG C 629 Details of bonding type rmsd hydrogen bonds : bond 0.13521 ( 984) hydrogen bonds : angle 6.32888 ( 2940) metal coordination : bond 0.00430 ( 11) metal coordination : angle 2.05106 ( 6) covalent geometry : bond 0.00699 (15761) covalent geometry : angle 1.13703 (21287) *********************** 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 : 2.444 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: 0.2996 time to fit residues: 267.9442 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 : 1.599 ------------------------------------------------------------------------------- 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 163 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 113 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.149261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.126709 restraints weight = 32280.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.130879 restraints weight = 17239.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.133676 restraints weight = 10760.267| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1790 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= 0.178 Angle : 0.783 9.371 21293 Z= 0.406 Chirality : 0.045 0.327 2490 Planarity : 0.006 0.118 2711 Dihedral : 10.882 69.026 2295 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.42 % Favored : 90.16 % Rotamer: Outliers : 7.99 % Allowed : 29.04 % Favored : 62.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 1942 helix: 0.52 (0.14), residues: 1340 sheet: -1.28 (1.65), residues: 13 loop : -3.46 (0.21), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 933 HIS 0.009 0.001 HIS C 84 PHE 0.025 0.002 PHE A 395 TYR 0.027 0.002 TYR A 270 ARG 0.012 0.001 ARG A 47 Details of bonding type rmsd hydrogen bonds : bond 0.05185 ( 984) hydrogen bonds : angle 5.03471 ( 2940) metal coordination : bond 0.00789 ( 11) metal coordination : angle 1.92883 ( 6) covalent geometry : bond 0.00384 (15761) covalent geometry : angle 0.78228 (21287) *********************** 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 637 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 497 time to evaluate : 1.731 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: 0.7619 (OUTLIER) cc_final: 0.7218 (m-80) REVERT: A 17 SER cc_start: 0.6663 (OUTLIER) cc_final: 0.6299 (p) REVERT: A 47 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6354 (mtm110) REVERT: A 48 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6912 (mtmm) REVERT: A 51 LYS cc_start: 0.8517 (tptp) cc_final: 0.8019 (ttpp) REVERT: A 65 GLN cc_start: 0.8101 (mt0) cc_final: 0.7841 (mt0) REVERT: A 129 ASN cc_start: 0.7576 (t0) cc_final: 0.7365 (t0) REVERT: A 158 MET cc_start: 0.8199 (tpt) cc_final: 0.7642 (tpt) REVERT: A 177 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8237 (mm) REVERT: A 209 ASP cc_start: 0.6699 (OUTLIER) cc_final: 0.6392 (t0) REVERT: A 215 LEU cc_start: 0.7939 (mt) cc_final: 0.7625 (mt) REVERT: A 218 LEU cc_start: 0.6175 (pp) cc_final: 0.5735 (pp) REVERT: A 261 ASN cc_start: 0.8162 (t0) cc_final: 0.7659 (m-40) REVERT: A 275 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6958 (p90) REVERT: A 445 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6076 (mp0) REVERT: A 446 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7782 (mmtm) REVERT: A 527 CYS cc_start: 0.8202 (m) cc_final: 0.7324 (t) REVERT: A 551 ARG cc_start: 0.7682 (tpt170) cc_final: 0.7398 (tpm170) REVERT: A 675 ASP cc_start: 0.7445 (t0) cc_final: 0.7213 (t0) REVERT: A 826 LYS cc_start: 0.8136 (tptp) cc_final: 0.7677 (tptt) REVERT: A 836 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8092 (mm) REVERT: A 938 LYS cc_start: 0.8062 (tppp) cc_final: 0.7752 (tppp) REVERT: A 967 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8030 (tt) REVERT: A 1023 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7661 (ttm110) REVERT: A 1037 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7869 (mmtp) REVERT: A 1083 LYS cc_start: 0.8461 (mmmm) cc_final: 0.8239 (mmmm) REVERT: A 1089 MET cc_start: 0.8123 (mmm) cc_final: 0.7368 (mmm) REVERT: A 1106 LEU cc_start: 0.8185 (mm) cc_final: 0.7932 (mt) REVERT: A 1120 LYS cc_start: 0.8430 (mmmm) cc_final: 0.7932 (mmtm) REVERT: A 1121 MET cc_start: 0.8450 (mtp) cc_final: 0.7955 (mmm) REVERT: A 1156 LYS cc_start: 0.8489 (tppt) cc_final: 0.7982 (mmmt) REVERT: A 1164 GLN cc_start: 0.7257 (mp10) cc_final: 0.6956 (mp10) REVERT: A 1165 GLU cc_start: 0.8000 (mp0) cc_final: 0.7638 (tp30) REVERT: C 176 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6360 (tm-30) REVERT: C 206 GLU cc_start: 0.5810 (OUTLIER) cc_final: 0.4769 (tt0) REVERT: C 209 PHE cc_start: 0.6415 (t80) cc_final: 0.5141 (t80) REVERT: C 213 SER cc_start: 0.8016 (p) cc_final: 0.7334 (p) REVERT: C 218 GLN cc_start: 0.7995 (tt0) cc_final: 0.7555 (mt0) REVERT: C 228 ASN cc_start: 0.5288 (OUTLIER) cc_final: 0.4876 (m-40) REVERT: C 244 GLU cc_start: 0.7476 (tp30) cc_final: 0.6788 (mm-30) REVERT: C 258 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: C 289 LYS cc_start: 0.8414 (tppt) cc_final: 0.8109 (tppt) REVERT: C 346 LEU cc_start: 0.8469 (mt) cc_final: 0.8053 (mm) REVERT: C 386 GLU cc_start: 0.7126 (tp30) cc_final: 0.6925 (tp30) REVERT: C 420 ARG cc_start: 0.7415 (tpp80) cc_final: 0.7035 (mtp85) REVERT: C 444 LYS cc_start: 0.6578 (tptp) cc_final: 0.6217 (tptp) REVERT: C 473 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6786 (ttm) REVERT: C 513 TRP cc_start: 0.7901 (m100) cc_final: 0.7408 (m100) REVERT: C 533 GLU cc_start: 0.7756 (tp30) cc_final: 0.7406 (tp30) REVERT: C 542 LYS cc_start: 0.7840 (mmmm) cc_final: 0.7638 (tptp) REVERT: C 632 GLN cc_start: 0.7374 (pp30) cc_final: 0.7085 (pp30) REVERT: C 673 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7347 (mmtm) REVERT: C 689 LYS cc_start: 0.7766 (ptpp) cc_final: 0.7466 (pttt) REVERT: C 690 GLU cc_start: 0.6874 (pp20) cc_final: 0.6474 (pp20) REVERT: C 693 GLN cc_start: 0.7783 (pp30) cc_final: 0.7305 (pp30) REVERT: C 697 ASP cc_start: 0.7596 (m-30) cc_final: 0.7289 (m-30) REVERT: C 698 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: C 700 LYS cc_start: 0.8372 (mttt) cc_final: 0.7650 (mttt) REVERT: C 707 ILE cc_start: 0.8622 (tp) cc_final: 0.7923 (tp) REVERT: C 711 MET cc_start: 0.5973 (mmt) cc_final: 0.5663 (mmt) REVERT: C 722 LEU cc_start: 0.7668 (pp) cc_final: 0.7430 (mt) REVERT: C 725 GLU cc_start: 0.7405 (tt0) cc_final: 0.6950 (tm-30) REVERT: C 744 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7836 (ttt180) REVERT: E 27 TRP cc_start: 0.8000 (t60) cc_final: 0.7788 (t60) outliers start: 140 outliers final: 69 residues processed: 577 average time/residue: 0.2934 time to fit residues: 241.8486 Evaluate side-chains 559 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 474 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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 77 SER 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 177 LEU 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 462 VAL 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 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 1013 LYS 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 64 MET 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 232 VAL 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 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 538 PHE 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 88 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 0.0970 chunk 143 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 786 GLN A 998 GLN C 87 ASN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4094 r_free = 0.4094 target = 0.148899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.126495 restraints weight = 31955.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.130617 restraints weight = 17081.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133334 restraints weight = 10639.547| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.2366 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= 0.156 Angle : 0.751 11.332 21293 Z= 0.382 Chirality : 0.044 0.193 2490 Planarity : 0.006 0.118 2711 Dihedral : 8.703 60.456 2193 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.37 % Favored : 90.27 % Rotamer: Outliers : 6.67 % Allowed : 29.55 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1942 helix: 0.84 (0.14), residues: 1336 sheet: -1.31 (1.59), residues: 13 loop : -3.45 (0.21), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 72 HIS 0.004 0.001 HIS A 514 PHE 0.026 0.002 PHE A 395 TYR 0.017 0.001 TYR A 980 ARG 0.006 0.000 ARG A 281 Details of bonding type rmsd hydrogen bonds : bond 0.04781 ( 984) hydrogen bonds : angle 4.83625 ( 2940) metal coordination : bond 0.00576 ( 11) metal coordination : angle 2.15216 ( 6) covalent geometry : bond 0.00337 (15761) covalent geometry : angle 0.75006 (21287) *********************** 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 617 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 500 time to evaluate : 1.673 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: 0.7607 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: A 47 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6251 (mpp-170) REVERT: A 51 LYS cc_start: 0.8506 (tptp) cc_final: 0.8182 (ptmm) REVERT: A 65 GLN cc_start: 0.8219 (mt0) cc_final: 0.7966 (mt0) REVERT: A 129 ASN cc_start: 0.7573 (t0) cc_final: 0.7354 (t0) REVERT: A 155 LEU cc_start: 0.8581 (mm) cc_final: 0.8310 (mm) REVERT: A 158 MET cc_start: 0.8236 (tpt) cc_final: 0.7849 (tpt) REVERT: A 209 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6282 (t0) REVERT: A 212 GLU cc_start: 0.7950 (mp0) cc_final: 0.7551 (pm20) REVERT: A 215 LEU cc_start: 0.7995 (mt) cc_final: 0.7666 (mt) REVERT: A 218 LEU cc_start: 0.5998 (pp) cc_final: 0.5375 (pp) REVERT: A 261 ASN cc_start: 0.8179 (t0) cc_final: 0.7793 (m-40) REVERT: A 268 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6782 (ptm-80) REVERT: A 275 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6947 (p90) REVERT: A 403 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7899 (mmmt) REVERT: A 429 GLN cc_start: 0.7516 (pp30) cc_final: 0.7292 (pp30) REVERT: A 437 LYS cc_start: 0.8110 (mttt) cc_final: 0.7875 (mttt) REVERT: A 442 GLN cc_start: 0.7706 (mm-40) cc_final: 0.6651 (mm-40) REVERT: A 445 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6089 (mp0) REVERT: A 564 TYR cc_start: 0.8023 (m-80) cc_final: 0.7810 (m-80) REVERT: A 580 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5676 (t70) REVERT: A 662 ASN cc_start: 0.7297 (p0) cc_final: 0.6960 (t0) REVERT: A 675 ASP cc_start: 0.7449 (t0) cc_final: 0.7195 (t0) REVERT: A 685 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7135 (mp) REVERT: A 703 GLU cc_start: 0.7627 (tp30) cc_final: 0.7325 (tp30) REVERT: A 826 LYS cc_start: 0.8142 (tptp) cc_final: 0.7632 (tptt) REVERT: A 836 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8104 (mm) REVERT: A 854 GLN cc_start: 0.7210 (pp30) cc_final: 0.6793 (tm-30) REVERT: A 915 GLU cc_start: 0.7411 (tp30) cc_final: 0.7177 (tp30) REVERT: A 938 LYS cc_start: 0.8068 (tppp) cc_final: 0.7552 (tppp) REVERT: A 960 LEU cc_start: 0.7660 (mm) cc_final: 0.7157 (mt) REVERT: A 982 ARG cc_start: 0.8128 (mtt90) cc_final: 0.7887 (mtt90) REVERT: A 1023 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7385 (ttm110) REVERT: A 1037 LYS cc_start: 0.8018 (mmtp) cc_final: 0.7765 (mttt) REVERT: A 1089 MET cc_start: 0.8114 (mmm) cc_final: 0.7371 (mmm) REVERT: A 1108 HIS cc_start: 0.7927 (m90) cc_final: 0.7675 (m170) REVERT: A 1117 TYR cc_start: 0.8086 (t80) cc_final: 0.7799 (t80) REVERT: A 1120 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8056 (mmmt) REVERT: A 1121 MET cc_start: 0.8422 (mtp) cc_final: 0.8180 (mmm) REVERT: A 1156 LYS cc_start: 0.8498 (tppt) cc_final: 0.8017 (mmmt) REVERT: A 1164 GLN cc_start: 0.7288 (mp10) cc_final: 0.7004 (mp10) REVERT: A 1165 GLU cc_start: 0.7992 (mp0) cc_final: 0.7616 (tp30) REVERT: A 1169 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8004 (mm-40) REVERT: A 1170 ASP cc_start: 0.7853 (m-30) cc_final: 0.7565 (m-30) REVERT: C 59 ARG cc_start: 0.7353 (ttp-170) cc_final: 0.7042 (ttp-170) REVERT: C 109 TRP cc_start: 0.8195 (t-100) cc_final: 0.7954 (t-100) REVERT: C 112 HIS cc_start: 0.7653 (t70) cc_final: 0.7170 (t70) REVERT: C 126 MET cc_start: 0.7691 (ppp) cc_final: 0.7428 (ppp) REVERT: C 176 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6230 (tm-30) REVERT: C 184 ARG cc_start: 0.7238 (ttt180) cc_final: 0.6865 (ttm-80) REVERT: C 206 GLU cc_start: 0.5656 (OUTLIER) cc_final: 0.4519 (tt0) REVERT: C 211 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6108 (mt-10) REVERT: C 213 SER cc_start: 0.8060 (p) cc_final: 0.7829 (t) REVERT: C 228 ASN cc_start: 0.5275 (OUTLIER) cc_final: 0.4908 (m-40) REVERT: C 244 GLU cc_start: 0.7411 (tp30) cc_final: 0.6681 (mm-30) REVERT: C 247 ARG cc_start: 0.7302 (ttp80) cc_final: 0.7007 (ttp80) REVERT: C 258 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: C 266 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7435 (ttp80) REVERT: C 284 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8375 (tt) REVERT: C 286 HIS cc_start: 0.7631 (t70) cc_final: 0.7339 (t70) REVERT: C 288 LEU cc_start: 0.8773 (mt) cc_final: 0.8519 (mt) REVERT: C 289 LYS cc_start: 0.8394 (tppt) cc_final: 0.8074 (tppt) REVERT: C 313 MET cc_start: 0.7651 (ttm) cc_final: 0.7393 (ttm) REVERT: C 368 GLN cc_start: 0.7183 (tm-30) cc_final: 0.6904 (tm-30) REVERT: C 422 MET cc_start: 0.8563 (ttp) cc_final: 0.8300 (ttm) REVERT: C 459 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7888 (mmmt) REVERT: C 473 MET cc_start: 0.7456 (OUTLIER) cc_final: 0.5936 (ttm) REVERT: C 513 TRP cc_start: 0.7875 (m100) cc_final: 0.7410 (m100) REVERT: C 533 GLU cc_start: 0.7833 (tp30) cc_final: 0.7420 (tp30) REVERT: C 538 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7118 (t80) REVERT: C 673 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7224 (mmtm) REVERT: C 689 LYS cc_start: 0.7892 (ptpp) cc_final: 0.7546 (ptpt) REVERT: C 690 GLU cc_start: 0.6906 (pp20) cc_final: 0.6412 (pp20) REVERT: C 693 GLN cc_start: 0.7883 (pp30) cc_final: 0.7330 (pp30) REVERT: C 697 ASP cc_start: 0.7625 (m-30) cc_final: 0.7317 (m-30) REVERT: C 700 LYS cc_start: 0.8327 (mttt) cc_final: 0.7502 (mttt) REVERT: C 710 ILE cc_start: 0.7542 (tp) cc_final: 0.6959 (tt) REVERT: C 711 MET cc_start: 0.6114 (mmt) cc_final: 0.5731 (mmt) REVERT: C 744 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7674 (ttt180) REVERT: C 748 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.6163 (tt) outliers start: 117 outliers final: 65 residues processed: 569 average time/residue: 0.2936 time to fit residues: 237.7064 Evaluate side-chains 560 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 477 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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 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 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 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 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 268 ARG 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 580 ASP 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 685 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 857 LEU Chi-restraints excluded: chain A residue 900 THR 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 1081 ILE 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 254 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 404 THR 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 538 PHE 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 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 121 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 188 optimal weight: 30.0000 chunk 150 optimal weight: 0.0970 chunk 13 optimal weight: 4.9990 chunk 126 optimal weight: 0.0980 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.147794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.125111 restraints weight = 32075.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129270 restraints weight = 17161.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.132051 restraints weight = 10730.279| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15772 Z= 0.150 Angle : 0.722 9.755 21293 Z= 0.369 Chirality : 0.043 0.220 2490 Planarity : 0.006 0.118 2711 Dihedral : 7.640 59.842 2169 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.47 % Favored : 90.16 % Rotamer: Outliers : 7.13 % Allowed : 30.01 % Favored : 62.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.19), residues: 1942 helix: 0.95 (0.14), residues: 1336 sheet: -1.30 (1.45), residues: 13 loop : -3.47 (0.20), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 72 HIS 0.007 0.001 HIS A 939 PHE 0.019 0.001 PHE A 395 TYR 0.028 0.001 TYR C 154 ARG 0.006 0.001 ARG A1099 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 984) hydrogen bonds : angle 4.76567 ( 2940) metal coordination : bond 0.00586 ( 11) metal coordination : angle 2.08587 ( 6) covalent geometry : bond 0.00326 (15761) covalent geometry : angle 0.72113 (21287) *********************** 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 609 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 484 time to evaluate : 1.656 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: 0.7649 (OUTLIER) cc_final: 0.7315 (m-80) REVERT: A 47 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6193 (mpp-170) REVERT: A 51 LYS cc_start: 0.8473 (tptp) cc_final: 0.8165 (ptmm) REVERT: A 65 GLN cc_start: 0.8314 (mt0) cc_final: 0.8001 (mt0) REVERT: A 67 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7474 (mm) REVERT: A 129 ASN cc_start: 0.7617 (t0) cc_final: 0.7402 (t0) REVERT: A 155 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 158 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7842 (tpt) REVERT: A 160 ASP cc_start: 0.8124 (m-30) cc_final: 0.7558 (m-30) REVERT: A 164 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6186 (mpp80) REVERT: A 209 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6501 (t0) REVERT: A 215 LEU cc_start: 0.7985 (mt) cc_final: 0.7701 (mt) REVERT: A 218 LEU cc_start: 0.5974 (pp) cc_final: 0.5508 (pp) REVERT: A 233 CYS cc_start: 0.8250 (t) cc_final: 0.7928 (t) REVERT: A 261 ASN cc_start: 0.8194 (t0) cc_final: 0.7801 (m-40) REVERT: A 275 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6891 (p90) REVERT: A 358 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7222 (t0) REVERT: A 387 GLU cc_start: 0.4819 (OUTLIER) cc_final: 0.3973 (pm20) REVERT: A 403 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7939 (mmmt) REVERT: A 471 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8804 (mp10) REVERT: A 551 ARG cc_start: 0.7796 (tpt170) cc_final: 0.7446 (tpm170) REVERT: A 564 TYR cc_start: 0.8067 (m-80) cc_final: 0.7792 (m-80) REVERT: A 580 ASP cc_start: 0.6179 (OUTLIER) cc_final: 0.5738 (t70) REVERT: A 590 ILE cc_start: 0.8486 (mm) cc_final: 0.7958 (mm) REVERT: A 662 ASN cc_start: 0.7349 (p0) cc_final: 0.7041 (t0) REVERT: A 675 ASP cc_start: 0.7479 (t0) cc_final: 0.7205 (t0) REVERT: A 689 MET cc_start: 0.7066 (pmm) cc_final: 0.5813 (ptt) REVERT: A 762 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8604 (tp) REVERT: A 826 LYS cc_start: 0.8120 (tptp) cc_final: 0.7604 (tptt) REVERT: A 836 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8102 (mm) REVERT: A 854 GLN cc_start: 0.7223 (pp30) cc_final: 0.6700 (tm-30) REVERT: A 915 GLU cc_start: 0.7415 (tp30) cc_final: 0.7129 (tp30) REVERT: A 938 LYS cc_start: 0.8094 (tppp) cc_final: 0.7568 (tppp) REVERT: A 982 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7763 (mtm110) REVERT: A 1023 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7308 (ttm110) REVERT: A 1089 MET cc_start: 0.8156 (mmm) cc_final: 0.7326 (mmm) REVERT: A 1108 HIS cc_start: 0.7914 (m90) cc_final: 0.7694 (m90) REVERT: A 1120 LYS cc_start: 0.8368 (mmmm) cc_final: 0.7961 (mttm) REVERT: A 1121 MET cc_start: 0.8428 (mtp) cc_final: 0.8172 (mmm) REVERT: A 1144 ARG cc_start: 0.6902 (mtp85) cc_final: 0.6690 (mtp85) REVERT: A 1156 LYS cc_start: 0.8502 (tppt) cc_final: 0.8117 (mmmt) REVERT: A 1164 GLN cc_start: 0.7393 (mp10) cc_final: 0.7068 (mp10) REVERT: A 1165 GLU cc_start: 0.8009 (mp0) cc_final: 0.7626 (tp30) REVERT: A 1169 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8225 (mm-40) REVERT: A 1170 ASP cc_start: 0.7868 (m-30) cc_final: 0.7552 (m-30) REVERT: A 1171 GLU cc_start: 0.7881 (tp30) cc_final: 0.7461 (tp30) REVERT: C 59 ARG cc_start: 0.7380 (ttp-170) cc_final: 0.7038 (ttp-170) REVERT: C 126 MET cc_start: 0.7715 (ppp) cc_final: 0.7411 (ppp) REVERT: C 176 GLU cc_start: 0.6552 (tm-30) cc_final: 0.6291 (tm-30) REVERT: C 184 ARG cc_start: 0.7289 (ttt180) cc_final: 0.7036 (tpp80) REVERT: C 204 ASP cc_start: 0.2793 (OUTLIER) cc_final: 0.2468 (m-30) REVERT: C 213 SER cc_start: 0.8074 (p) cc_final: 0.7733 (t) REVERT: C 218 GLN cc_start: 0.8091 (tt0) cc_final: 0.7622 (mt0) REVERT: C 228 ASN cc_start: 0.5205 (OUTLIER) cc_final: 0.4851 (m-40) REVERT: C 235 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7093 (mmmt) REVERT: C 244 GLU cc_start: 0.7424 (tp30) cc_final: 0.6708 (mm-30) REVERT: C 258 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: C 266 ARG cc_start: 0.7852 (ttp80) cc_final: 0.7620 (ttp80) REVERT: C 286 HIS cc_start: 0.7696 (t70) cc_final: 0.7476 (t70) REVERT: C 289 LYS cc_start: 0.8472 (tppt) cc_final: 0.8186 (tppt) REVERT: C 313 MET cc_start: 0.7770 (ttm) cc_final: 0.7473 (ttm) REVERT: C 355 PHE cc_start: 0.7590 (m-80) cc_final: 0.7356 (m-80) REVERT: C 368 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6823 (tm-30) REVERT: C 383 ARG cc_start: 0.7454 (mtp85) cc_final: 0.7219 (mtp85) REVERT: C 386 GLU cc_start: 0.7241 (tp30) cc_final: 0.6064 (tp30) REVERT: C 416 MET cc_start: 0.7867 (mmm) cc_final: 0.7532 (mmm) REVERT: C 422 MET cc_start: 0.8513 (ttp) cc_final: 0.8220 (ttm) REVERT: C 431 TYR cc_start: 0.8039 (m-10) cc_final: 0.7415 (m-80) REVERT: C 454 MET cc_start: 0.7950 (mmm) cc_final: 0.7139 (tmm) REVERT: C 459 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7775 (mmmt) REVERT: C 506 ARG cc_start: 0.7372 (mmm-85) cc_final: 0.7110 (mtp85) REVERT: C 533 GLU cc_start: 0.7828 (tp30) cc_final: 0.7485 (tp30) REVERT: C 542 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7790 (mmtm) REVERT: C 603 MET cc_start: 0.7424 (mmp) cc_final: 0.7145 (mmp) REVERT: C 688 ARG cc_start: 0.6735 (ttm110) cc_final: 0.6099 (ttm110) REVERT: C 689 LYS cc_start: 0.7907 (ptpp) cc_final: 0.7645 (ptpt) REVERT: C 690 GLU cc_start: 0.7005 (pp20) cc_final: 0.6520 (pp20) REVERT: C 693 GLN cc_start: 0.7876 (pp30) cc_final: 0.7302 (pp30) REVERT: C 697 ASP cc_start: 0.7586 (m-30) cc_final: 0.7281 (m-30) REVERT: C 700 LYS cc_start: 0.8329 (mttt) cc_final: 0.7231 (mttt) REVERT: C 701 HIS cc_start: 0.7674 (m170) cc_final: 0.7158 (m170) REVERT: C 710 ILE cc_start: 0.7513 (tp) cc_final: 0.6847 (tt) REVERT: C 711 MET cc_start: 0.6170 (mmt) cc_final: 0.5854 (mmt) REVERT: C 731 LYS cc_start: 0.8376 (ttmm) cc_final: 0.7917 (ttmm) REVERT: C 744 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7431 (tpt-90) REVERT: C 748 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6286 (tt) REVERT: E 100 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7044 (tt0) outliers start: 125 outliers final: 64 residues processed: 559 average time/residue: 0.2927 time to fit residues: 230.8277 Evaluate side-chains 555 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 472 time to evaluate : 1.831 ------------------------------------------------------------------------------- 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 99 LYS 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 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 345 MET 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 471 GLN 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 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 723 TYR Chi-restraints excluded: chain A residue 762 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 857 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 974 LEU 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 1122 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 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 204 ASP 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 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 345 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 439 ARG 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 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 677 VAL 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 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 94 optimal weight: 0.6980 chunk 135 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 148 optimal weight: 0.9990 chunk 41 optimal weight: 0.0970 chunk 23 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 47 optimal weight: 0.0020 chunk 140 optimal weight: 0.4980 overall best weight: 0.2986 ------------------------------------------------------------------------------- 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 516 HIS A 707 HIS A1035 HIS C 188 GLN ** C 222 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.148929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.126338 restraints weight = 32362.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.130502 restraints weight = 17101.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.133229 restraints weight = 10669.721| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15772 Z= 0.142 Angle : 0.722 10.176 21293 Z= 0.365 Chirality : 0.043 0.201 2490 Planarity : 0.006 0.116 2711 Dihedral : 7.155 53.193 2157 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.42 % Favored : 90.32 % Rotamer: Outliers : 6.90 % Allowed : 30.92 % Favored : 62.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1942 helix: 1.03 (0.14), residues: 1338 sheet: -1.32 (1.43), residues: 13 loop : -3.41 (0.21), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 513 HIS 0.009 0.001 HIS A 847 PHE 0.020 0.001 PHE A 991 TYR 0.023 0.001 TYR C 154 ARG 0.008 0.000 ARG C 354 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 984) hydrogen bonds : angle 4.68005 ( 2940) metal coordination : bond 0.00483 ( 11) metal coordination : angle 1.94617 ( 6) covalent geometry : bond 0.00308 (15761) covalent geometry : angle 0.72146 (21287) *********************** 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 609 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 488 time to evaluate : 1.859 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: 0.6783 (OUTLIER) cc_final: 0.6197 (mpp-170) REVERT: A 51 LYS cc_start: 0.8459 (tptp) cc_final: 0.8143 (ptmm) REVERT: A 65 GLN cc_start: 0.8289 (mt0) cc_final: 0.7923 (mt0) REVERT: A 67 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7487 (mm) REVERT: A 129 ASN cc_start: 0.7617 (t0) cc_final: 0.7387 (t0) REVERT: A 155 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 158 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7794 (tpt) REVERT: A 164 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6245 (mpp80) REVERT: A 209 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6445 (t0) REVERT: A 215 LEU cc_start: 0.7954 (mt) cc_final: 0.7663 (mt) REVERT: A 218 LEU cc_start: 0.5922 (pp) cc_final: 0.5496 (pp) REVERT: A 233 CYS cc_start: 0.8287 (t) cc_final: 0.7912 (t) REVERT: A 261 ASN cc_start: 0.8207 (t0) cc_final: 0.7821 (m-40) REVERT: A 268 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6772 (ptm-80) REVERT: A 275 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6848 (p90) REVERT: A 358 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7164 (t0) REVERT: A 387 GLU cc_start: 0.3998 (OUTLIER) cc_final: 0.3650 (pm20) REVERT: A 391 LYS cc_start: 0.7920 (tmtt) cc_final: 0.7094 (tptp) REVERT: A 395 PHE cc_start: 0.8316 (m-10) cc_final: 0.7973 (m-10) REVERT: A 403 LYS cc_start: 0.8367 (mtmm) cc_final: 0.7944 (mmmt) REVERT: A 444 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8387 (mmmm) REVERT: A 456 ASN cc_start: 0.8127 (m-40) cc_final: 0.7532 (m-40) REVERT: A 551 ARG cc_start: 0.7708 (tpt170) cc_final: 0.7403 (tpm170) REVERT: A 564 TYR cc_start: 0.8016 (m-80) cc_final: 0.7645 (m-80) REVERT: A 580 ASP cc_start: 0.6193 (OUTLIER) cc_final: 0.5772 (t70) REVERT: A 590 ILE cc_start: 0.8465 (mm) cc_final: 0.7923 (mm) REVERT: A 647 VAL cc_start: 0.8446 (m) cc_final: 0.8071 (p) REVERT: A 675 ASP cc_start: 0.7461 (t0) cc_final: 0.7260 (t0) REVERT: A 689 MET cc_start: 0.7049 (pmm) cc_final: 0.5940 (ptt) REVERT: A 748 GLN cc_start: 0.6904 (pp30) cc_final: 0.6687 (pm20) REVERT: A 821 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6763 (m-10) REVERT: A 826 LYS cc_start: 0.8122 (tptp) cc_final: 0.7571 (tptt) REVERT: A 836 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8119 (mm) REVERT: A 854 GLN cc_start: 0.7210 (pp30) cc_final: 0.6381 (pp30) REVERT: A 915 GLU cc_start: 0.7351 (tp30) cc_final: 0.7078 (tp30) REVERT: A 938 LYS cc_start: 0.8065 (tppp) cc_final: 0.7486 (tppp) REVERT: A 953 GLU cc_start: 0.6547 (mm-30) cc_final: 0.5989 (mm-30) REVERT: A 982 ARG cc_start: 0.8119 (mtt90) cc_final: 0.7765 (mtm110) REVERT: A 1023 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7246 (ttm110) REVERT: A 1037 LYS cc_start: 0.8081 (mttm) cc_final: 0.7633 (mmtp) REVERT: A 1120 LYS cc_start: 0.8434 (mmmm) cc_final: 0.7920 (mttm) REVERT: A 1144 ARG cc_start: 0.6870 (mtp85) cc_final: 0.6669 (mtp85) REVERT: A 1156 LYS cc_start: 0.8450 (tppt) cc_final: 0.8115 (mmmt) REVERT: A 1164 GLN cc_start: 0.7414 (mp10) cc_final: 0.7049 (mp10) REVERT: A 1165 GLU cc_start: 0.8018 (mp0) cc_final: 0.7626 (tp30) REVERT: A 1169 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8202 (mm-40) REVERT: A 1170 ASP cc_start: 0.7821 (m-30) cc_final: 0.7511 (m-30) REVERT: A 1171 GLU cc_start: 0.7875 (tp30) cc_final: 0.7422 (tp30) REVERT: C 59 ARG cc_start: 0.7340 (ttp-170) cc_final: 0.6979 (ttp-170) REVERT: C 66 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8392 (pp) REVERT: C 126 MET cc_start: 0.7726 (ppp) cc_final: 0.7394 (ppp) REVERT: C 176 GLU cc_start: 0.6580 (tm-30) cc_final: 0.6302 (tm-30) REVERT: C 188 GLN cc_start: 0.7375 (mt0) cc_final: 0.6714 (mm-40) REVERT: C 204 ASP cc_start: 0.2847 (OUTLIER) cc_final: 0.2572 (m-30) REVERT: C 211 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6230 (mt-10) REVERT: C 213 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7752 (t) REVERT: C 218 GLN cc_start: 0.8036 (tt0) cc_final: 0.7604 (mt0) REVERT: C 228 ASN cc_start: 0.5129 (OUTLIER) cc_final: 0.4782 (m-40) REVERT: C 235 LYS cc_start: 0.7872 (mmmt) cc_final: 0.7007 (mmmt) REVERT: C 236 LYS cc_start: 0.7847 (ttmt) cc_final: 0.7433 (ttpt) REVERT: C 244 GLU cc_start: 0.7458 (tp30) cc_final: 0.6709 (mm-30) REVERT: C 266 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7288 (ttp80) REVERT: C 286 HIS cc_start: 0.7673 (t70) cc_final: 0.7366 (t70) REVERT: C 289 LYS cc_start: 0.8502 (tppt) cc_final: 0.8233 (tppt) REVERT: C 313 MET cc_start: 0.7720 (ttm) cc_final: 0.7404 (ttm) REVERT: C 368 GLN cc_start: 0.7220 (tm-30) cc_final: 0.6816 (tm-30) REVERT: C 416 MET cc_start: 0.7903 (mmm) cc_final: 0.7641 (mmm) REVERT: C 444 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.6096 (tptp) REVERT: C 454 MET cc_start: 0.7927 (mmm) cc_final: 0.7121 (tmm) REVERT: C 459 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7761 (mmmt) REVERT: C 506 ARG cc_start: 0.7345 (mmm-85) cc_final: 0.7045 (mtp85) REVERT: C 533 GLU cc_start: 0.7931 (tp30) cc_final: 0.7497 (tp30) REVERT: C 542 LYS cc_start: 0.8012 (mmtm) cc_final: 0.7803 (mmtm) REVERT: C 603 MET cc_start: 0.7367 (mmp) cc_final: 0.7153 (mmm) REVERT: C 688 ARG cc_start: 0.6747 (ttm110) cc_final: 0.6124 (ttm110) REVERT: C 689 LYS cc_start: 0.7873 (ptpp) cc_final: 0.7503 (ptpt) REVERT: C 690 GLU cc_start: 0.7043 (pp20) cc_final: 0.6485 (pp20) REVERT: C 693 GLN cc_start: 0.7934 (pp30) cc_final: 0.7292 (pp30) REVERT: C 697 ASP cc_start: 0.7574 (m-30) cc_final: 0.7265 (m-30) REVERT: C 700 LYS cc_start: 0.8313 (mttt) cc_final: 0.7172 (mttt) REVERT: C 701 HIS cc_start: 0.7620 (m170) cc_final: 0.7128 (m170) REVERT: C 710 ILE cc_start: 0.7516 (tp) cc_final: 0.6765 (tt) REVERT: C 711 MET cc_start: 0.6042 (mmt) cc_final: 0.5744 (mmt) REVERT: C 731 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7894 (ttmm) REVERT: C 744 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7416 (tpt-90) REVERT: C 748 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6251 (tt) REVERT: E 100 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6995 (tt0) outliers start: 121 outliers final: 67 residues processed: 557 average time/residue: 0.3089 time to fit residues: 243.7501 Evaluate side-chains 569 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 481 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 67 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 77 SER 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 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 268 ARG Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain A residue 358 ASP 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 453 CYS Chi-restraints excluded: chain A residue 580 ASP 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 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 806 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 904 LYS Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 974 LEU 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 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 66 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 187 CYS 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 319 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 390 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 469 LYS Chi-restraints excluded: chain C residue 503 LEU 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 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 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 2 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.146834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.124117 restraints weight = 32137.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.128260 restraints weight = 17049.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.131000 restraints weight = 10643.552| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.3268 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= 0.151 Angle : 0.727 9.776 21293 Z= 0.373 Chirality : 0.044 0.209 2490 Planarity : 0.006 0.116 2711 Dihedral : 6.678 54.741 2143 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.32 % Favored : 90.42 % Rotamer: Outliers : 6.62 % Allowed : 31.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.19), residues: 1942 helix: 1.05 (0.14), residues: 1342 sheet: -1.15 (1.45), residues: 13 loop : -3.36 (0.21), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 513 HIS 0.007 0.001 HIS A 847 PHE 0.024 0.002 PHE A 991 TYR 0.026 0.002 TYR C 300 ARG 0.030 0.001 ARG C 629 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 984) hydrogen bonds : angle 4.68769 ( 2940) metal coordination : bond 0.00582 ( 11) metal coordination : angle 1.86195 ( 6) covalent geometry : bond 0.00332 (15761) covalent geometry : angle 0.72642 (21287) *********************** 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 620 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 504 time to evaluate : 1.765 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: symmetry clash REVERT: A 47 ARG cc_start: 0.6804 (OUTLIER) cc_final: 0.6158 (mpp-170) REVERT: A 51 LYS cc_start: 0.8472 (tptp) cc_final: 0.8138 (ptmm) REVERT: A 65 GLN cc_start: 0.8323 (mt0) cc_final: 0.7915 (mt0) REVERT: A 67 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7475 (mm) REVERT: A 129 ASN cc_start: 0.7605 (t0) cc_final: 0.7381 (t0) REVERT: A 155 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8300 (mm) REVERT: A 158 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7802 (tpt) REVERT: A 160 ASP cc_start: 0.8114 (m-30) cc_final: 0.7508 (t0) REVERT: A 177 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 215 LEU cc_start: 0.7989 (mt) cc_final: 0.7698 (mt) REVERT: A 218 LEU cc_start: 0.5942 (pp) cc_final: 0.5511 (pp) REVERT: A 233 CYS cc_start: 0.8319 (t) cc_final: 0.7950 (t) REVERT: A 261 ASN cc_start: 0.8216 (t0) cc_final: 0.7827 (m-40) REVERT: A 268 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6845 (ptm-80) REVERT: A 275 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6845 (p90) REVERT: A 358 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7264 (t0) REVERT: A 387 GLU cc_start: 0.3777 (OUTLIER) cc_final: 0.3564 (pm20) REVERT: A 391 LYS cc_start: 0.8023 (tmtt) cc_final: 0.7475 (tmtt) REVERT: A 395 PHE cc_start: 0.8250 (m-10) cc_final: 0.7889 (m-10) REVERT: A 403 LYS cc_start: 0.8372 (mtmm) cc_final: 0.7960 (mmmt) REVERT: A 446 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7834 (mmtm) REVERT: A 456 ASN cc_start: 0.8247 (m-40) cc_final: 0.7563 (m-40) REVERT: A 471 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: A 500 CYS cc_start: 0.8130 (t) cc_final: 0.7787 (p) REVERT: A 551 ARG cc_start: 0.7758 (tpt170) cc_final: 0.7478 (tpm170) REVERT: A 580 ASP cc_start: 0.6234 (OUTLIER) cc_final: 0.5791 (t70) REVERT: A 590 ILE cc_start: 0.8449 (mm) cc_final: 0.7948 (mm) REVERT: A 593 MET cc_start: 0.7342 (tpp) cc_final: 0.6515 (tpp) REVERT: A 647 VAL cc_start: 0.8395 (m) cc_final: 0.8024 (p) REVERT: A 662 ASN cc_start: 0.7576 (t0) cc_final: 0.7334 (t0) REVERT: A 675 ASP cc_start: 0.7481 (t0) cc_final: 0.7245 (t0) REVERT: A 689 MET cc_start: 0.7005 (pmm) cc_final: 0.6050 (ptt) REVERT: A 703 GLU cc_start: 0.7591 (tp30) cc_final: 0.7141 (tp30) REVERT: A 748 GLN cc_start: 0.6991 (pp30) cc_final: 0.6729 (pm20) REVERT: A 762 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8663 (tp) REVERT: A 821 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6739 (m-10) REVERT: A 826 LYS cc_start: 0.8205 (tptp) cc_final: 0.7625 (tptt) REVERT: A 836 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8123 (mm) REVERT: A 854 GLN cc_start: 0.7252 (pp30) cc_final: 0.6334 (pp30) REVERT: A 915 GLU cc_start: 0.7376 (tp30) cc_final: 0.7064 (tp30) REVERT: A 918 SER cc_start: 0.6923 (p) cc_final: 0.6696 (p) REVERT: A 938 LYS cc_start: 0.8086 (tppp) cc_final: 0.7592 (tppp) REVERT: A 945 GLU cc_start: 0.6168 (tm-30) cc_final: 0.5899 (tm-30) REVERT: A 953 GLU cc_start: 0.6603 (mm-30) cc_final: 0.6083 (mm-30) REVERT: A 982 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7795 (mtm110) REVERT: A 1023 ARG cc_start: 0.7942 (ttm110) cc_final: 0.7399 (ttm110) REVERT: A 1109 VAL cc_start: 0.8535 (m) cc_final: 0.8307 (p) REVERT: A 1120 LYS cc_start: 0.8438 (mmmm) cc_final: 0.7960 (mttm) REVERT: A 1126 MET cc_start: 0.7947 (tpp) cc_final: 0.7635 (mmm) REVERT: A 1144 ARG cc_start: 0.6947 (mtp85) cc_final: 0.6739 (mtp85) REVERT: A 1156 LYS cc_start: 0.8428 (tppt) cc_final: 0.8196 (mmtt) REVERT: A 1164 GLN cc_start: 0.7509 (mp10) cc_final: 0.7137 (mp10) REVERT: A 1165 GLU cc_start: 0.8019 (mp0) cc_final: 0.7667 (tp30) REVERT: A 1169 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8217 (mm-40) REVERT: A 1170 ASP cc_start: 0.7829 (m-30) cc_final: 0.7498 (m-30) REVERT: A 1171 GLU cc_start: 0.7900 (tp30) cc_final: 0.7401 (tp30) REVERT: C 59 ARG cc_start: 0.7361 (ttp-170) cc_final: 0.6977 (ttp-170) REVERT: C 66 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8383 (pp) REVERT: C 79 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7306 (pp20) REVERT: C 94 LEU cc_start: 0.8544 (mt) cc_final: 0.8299 (mt) REVERT: C 126 MET cc_start: 0.7771 (ppp) cc_final: 0.7503 (ppp) REVERT: C 176 GLU cc_start: 0.6671 (tm-30) cc_final: 0.6352 (tm-30) REVERT: C 204 ASP cc_start: 0.2936 (OUTLIER) cc_final: 0.2666 (m-30) REVERT: C 206 GLU cc_start: 0.5967 (OUTLIER) cc_final: 0.5055 (tt0) REVERT: C 213 SER cc_start: 0.8113 (p) cc_final: 0.7804 (t) REVERT: C 218 GLN cc_start: 0.8080 (tt0) cc_final: 0.7580 (mt0) REVERT: C 228 ASN cc_start: 0.5249 (OUTLIER) cc_final: 0.4898 (m-40) REVERT: C 235 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7106 (mmmt) REVERT: C 236 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7505 (ttpt) REVERT: C 244 GLU cc_start: 0.7373 (tp30) cc_final: 0.6522 (mm-30) REVERT: C 266 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7511 (ttp80) REVERT: C 286 HIS cc_start: 0.7725 (t70) cc_final: 0.7387 (t70) REVERT: C 289 LYS cc_start: 0.8491 (tppt) cc_final: 0.8286 (tppt) REVERT: C 300 TYR cc_start: 0.7905 (t80) cc_final: 0.7686 (t80) REVERT: C 313 MET cc_start: 0.7811 (ttm) cc_final: 0.7475 (ttm) REVERT: C 368 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6880 (tm-30) REVERT: C 383 ARG cc_start: 0.7558 (mtp85) cc_final: 0.7356 (mtp85) REVERT: C 416 MET cc_start: 0.7924 (mmm) cc_final: 0.7660 (mmm) REVERT: C 429 GLU cc_start: 0.7423 (tt0) cc_final: 0.7162 (tt0) REVERT: C 444 LYS cc_start: 0.6558 (OUTLIER) cc_final: 0.6138 (tptp) REVERT: C 454 MET cc_start: 0.7942 (mmm) cc_final: 0.7114 (tmm) REVERT: C 459 LYS cc_start: 0.8124 (mmmt) cc_final: 0.7788 (mmmt) REVERT: C 466 PHE cc_start: 0.5969 (p90) cc_final: 0.5628 (p90) REVERT: C 473 MET cc_start: 0.7740 (tpt) cc_final: 0.6777 (tpt) REVERT: C 506 ARG cc_start: 0.7367 (mmm-85) cc_final: 0.7045 (mtp85) REVERT: C 513 TRP cc_start: 0.8131 (m100) cc_final: 0.7415 (m100) REVERT: C 533 GLU cc_start: 0.7954 (tp30) cc_final: 0.7495 (tp30) REVERT: C 688 ARG cc_start: 0.6744 (ttm110) cc_final: 0.6143 (ttm110) REVERT: C 689 LYS cc_start: 0.7934 (ptpp) cc_final: 0.7573 (ptpt) REVERT: C 690 GLU cc_start: 0.7077 (pp20) cc_final: 0.6504 (pp20) REVERT: C 693 GLN cc_start: 0.7956 (pp30) cc_final: 0.7297 (pp30) REVERT: C 697 ASP cc_start: 0.7596 (m-30) cc_final: 0.7284 (m-30) REVERT: C 700 LYS cc_start: 0.8358 (mttt) cc_final: 0.7213 (mttt) REVERT: C 701 HIS cc_start: 0.7644 (m170) cc_final: 0.7142 (m170) REVERT: C 710 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.6857 (tt) REVERT: C 711 MET cc_start: 0.6128 (mmt) cc_final: 0.5827 (mmt) REVERT: C 728 GLN cc_start: 0.8130 (tp40) cc_final: 0.7721 (tp40) REVERT: C 731 LYS cc_start: 0.8366 (ttmm) cc_final: 0.7832 (ttmm) REVERT: C 744 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7469 (tpt-90) REVERT: C 748 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6297 (tt) REVERT: E 100 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6914 (tt0) outliers start: 116 outliers final: 78 residues processed: 569 average time/residue: 0.3027 time to fit residues: 243.7601 Evaluate side-chains 591 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 491 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 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 75 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 175 SER Chi-restraints excluded: chain A residue 177 LEU 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 358 ASP 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 453 CYS Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 581 ILE 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 680 ASN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 762 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 806 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 821 PHE 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 935 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 984 SER 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 1100 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 66 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 187 CYS 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 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 345 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 439 ARG 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 508 LEU 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 672 VAL Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 710 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 154 optimal weight: 0.8980 chunk 3 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 132 optimal weight: 0.0370 chunk 145 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 GLN A 911 HIS ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** 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 = 0.4077 r_free = 0.4077 target = 0.147606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.124542 restraints weight = 31788.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.128712 restraints weight = 16748.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.131476 restraints weight = 10457.198| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15772 Z= 0.149 Angle : 0.733 10.565 21293 Z= 0.373 Chirality : 0.044 0.236 2490 Planarity : 0.006 0.116 2711 Dihedral : 6.361 53.706 2137 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.22 % Favored : 90.53 % Rotamer: Outliers : 6.73 % Allowed : 32.00 % Favored : 61.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1942 helix: 1.06 (0.15), residues: 1343 sheet: -0.94 (1.48), residues: 13 loop : -3.32 (0.21), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 933 HIS 0.008 0.001 HIS C 84 PHE 0.021 0.001 PHE A 991 TYR 0.020 0.001 TYR C 300 ARG 0.011 0.000 ARG C 629 Details of bonding type rmsd hydrogen bonds : bond 0.04412 ( 984) hydrogen bonds : angle 4.68075 ( 2940) metal coordination : bond 0.00541 ( 11) metal coordination : angle 1.84834 ( 6) covalent geometry : bond 0.00328 (15761) covalent geometry : angle 0.73260 (21287) *********************** 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 625 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 507 time to evaluate : 1.793 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6299 (mpp-170) REVERT: A 51 LYS cc_start: 0.8488 (tptp) cc_final: 0.8126 (ptmm) REVERT: A 65 GLN cc_start: 0.8299 (mt0) cc_final: 0.7677 (mm-40) REVERT: A 67 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7511 (mm) REVERT: A 70 LYS cc_start: 0.7187 (mmtt) cc_final: 0.6664 (mmtp) REVERT: A 78 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8110 (mmmt) REVERT: A 129 ASN cc_start: 0.7640 (t0) cc_final: 0.7419 (t0) REVERT: A 137 ARG cc_start: 0.7970 (mmm-85) cc_final: 0.7580 (mmm160) REVERT: A 155 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8313 (mm) REVERT: A 158 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7750 (tpt) REVERT: A 160 ASP cc_start: 0.8139 (m-30) cc_final: 0.7587 (t70) REVERT: A 177 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 215 LEU cc_start: 0.8048 (mt) cc_final: 0.7778 (mt) REVERT: A 218 LEU cc_start: 0.5949 (pp) cc_final: 0.5547 (pp) REVERT: A 233 CYS cc_start: 0.8308 (t) cc_final: 0.7973 (t) REVERT: A 261 ASN cc_start: 0.8207 (t0) cc_final: 0.7894 (t0) REVERT: A 268 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6747 (ptm-80) REVERT: A 275 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6861 (p90) REVERT: A 358 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7178 (t0) REVERT: A 391 LYS cc_start: 0.8067 (tmtt) cc_final: 0.7499 (tmtt) REVERT: A 395 PHE cc_start: 0.8310 (m-10) cc_final: 0.7884 (m-10) REVERT: A 403 LYS cc_start: 0.8392 (mtmm) cc_final: 0.7968 (mmmt) REVERT: A 446 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7849 (mmtm) REVERT: A 456 ASN cc_start: 0.8260 (m-40) cc_final: 0.7496 (m-40) REVERT: A 476 LEU cc_start: 0.8801 (mt) cc_final: 0.8594 (mt) REVERT: A 482 PHE cc_start: 0.8198 (t80) cc_final: 0.7846 (t80) REVERT: A 500 CYS cc_start: 0.8138 (t) cc_final: 0.7774 (p) REVERT: A 527 CYS cc_start: 0.8257 (m) cc_final: 0.7327 (t) REVERT: A 551 ARG cc_start: 0.7753 (tpt170) cc_final: 0.7474 (tpm170) REVERT: A 580 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5735 (t70) REVERT: A 590 ILE cc_start: 0.8425 (mm) cc_final: 0.7893 (mm) REVERT: A 593 MET cc_start: 0.7389 (tpp) cc_final: 0.6513 (tpp) REVERT: A 647 VAL cc_start: 0.8505 (m) cc_final: 0.8135 (p) REVERT: A 650 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6345 (mm-30) REVERT: A 662 ASN cc_start: 0.7629 (t0) cc_final: 0.7298 (t0) REVERT: A 675 ASP cc_start: 0.7486 (t0) cc_final: 0.7259 (t0) REVERT: A 689 MET cc_start: 0.7122 (pmm) cc_final: 0.6193 (ptt) REVERT: A 703 GLU cc_start: 0.7548 (tp30) cc_final: 0.7004 (tp30) REVERT: A 748 GLN cc_start: 0.7010 (pp30) cc_final: 0.6730 (pm20) REVERT: A 826 LYS cc_start: 0.8235 (tptp) cc_final: 0.7779 (tptp) REVERT: A 836 LEU cc_start: 0.8397 (mt) cc_final: 0.8111 (mm) REVERT: A 915 GLU cc_start: 0.7402 (tp30) cc_final: 0.7025 (tp30) REVERT: A 918 SER cc_start: 0.6875 (p) cc_final: 0.6620 (p) REVERT: A 938 LYS cc_start: 0.8106 (tppp) cc_final: 0.7603 (tppp) REVERT: A 945 GLU cc_start: 0.6073 (tm-30) cc_final: 0.5783 (tm-30) REVERT: A 982 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7754 (mtm110) REVERT: A 1016 GLU cc_start: 0.8196 (tp30) cc_final: 0.7077 (tp30) REVERT: A 1023 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7401 (ttm110) REVERT: A 1109 VAL cc_start: 0.8511 (m) cc_final: 0.8309 (p) REVERT: A 1121 MET cc_start: 0.8463 (mmm) cc_final: 0.8195 (mmm) REVERT: A 1126 MET cc_start: 0.7904 (tpp) cc_final: 0.7615 (mmm) REVERT: A 1144 ARG cc_start: 0.6999 (mtp85) cc_final: 0.6788 (mtp85) REVERT: A 1164 GLN cc_start: 0.7525 (mp10) cc_final: 0.7166 (mp10) REVERT: A 1165 GLU cc_start: 0.8005 (mp0) cc_final: 0.7669 (tp30) REVERT: A 1169 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8212 (mm-40) REVERT: A 1170 ASP cc_start: 0.7846 (m-30) cc_final: 0.7520 (m-30) REVERT: A 1171 GLU cc_start: 0.7958 (tp30) cc_final: 0.7369 (tp30) REVERT: C 45 GLN cc_start: 0.7990 (tt0) cc_final: 0.7540 (tm-30) REVERT: C 59 ARG cc_start: 0.7379 (ttp-170) cc_final: 0.6964 (ttp-170) REVERT: C 66 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8391 (pp) REVERT: C 79 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7292 (pp20) REVERT: C 90 ARG cc_start: 0.7644 (mtp-110) cc_final: 0.7293 (mmm-85) REVERT: C 94 LEU cc_start: 0.8563 (mt) cc_final: 0.8310 (mt) REVERT: C 204 ASP cc_start: 0.3083 (OUTLIER) cc_final: 0.2860 (m-30) REVERT: C 213 SER cc_start: 0.8102 (OUTLIER) cc_final: 0.7823 (t) REVERT: C 218 GLN cc_start: 0.8080 (tt0) cc_final: 0.7766 (tt0) REVERT: C 228 ASN cc_start: 0.5226 (OUTLIER) cc_final: 0.4875 (m-40) REVERT: C 235 LYS cc_start: 0.7947 (mmmt) cc_final: 0.7104 (mmmt) REVERT: C 236 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7602 (ttpt) REVERT: C 238 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 244 GLU cc_start: 0.7338 (tp30) cc_final: 0.6663 (mm-30) REVERT: C 249 MET cc_start: 0.7372 (mmm) cc_final: 0.7024 (tpp) REVERT: C 265 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6954 (mt-10) REVERT: C 266 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7416 (ttp80) REVERT: C 286 HIS cc_start: 0.7734 (t70) cc_final: 0.7438 (t-170) REVERT: C 288 LEU cc_start: 0.8997 (mm) cc_final: 0.8673 (mt) REVERT: C 289 LYS cc_start: 0.8466 (tppt) cc_final: 0.8208 (tppt) REVERT: C 300 TYR cc_start: 0.7902 (t80) cc_final: 0.7619 (t80) REVERT: C 313 MET cc_start: 0.7823 (ttm) cc_final: 0.7490 (ttm) REVERT: C 326 LYS cc_start: 0.7072 (mmmt) cc_final: 0.6715 (mptt) REVERT: C 345 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7792 (tt) REVERT: C 359 SER cc_start: 0.8187 (p) cc_final: 0.7742 (m) REVERT: C 368 GLN cc_start: 0.7286 (tm-30) cc_final: 0.6871 (tm-30) REVERT: C 386 GLU cc_start: 0.7472 (tp30) cc_final: 0.6817 (tp30) REVERT: C 393 ASP cc_start: 0.7319 (t0) cc_final: 0.6967 (t70) REVERT: C 416 MET cc_start: 0.7950 (mmm) cc_final: 0.7688 (mmm) REVERT: C 429 GLU cc_start: 0.7398 (tt0) cc_final: 0.7000 (tt0) REVERT: C 444 LYS cc_start: 0.6592 (OUTLIER) cc_final: 0.6187 (tptp) REVERT: C 454 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7268 (tmm) REVERT: C 466 PHE cc_start: 0.6070 (p90) cc_final: 0.5592 (p90) REVERT: C 506 ARG cc_start: 0.7314 (mmm-85) cc_final: 0.6967 (mtp85) REVERT: C 533 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7411 (tp30) REVERT: C 688 ARG cc_start: 0.6748 (ttm110) cc_final: 0.6115 (ttm110) REVERT: C 689 LYS cc_start: 0.7986 (ptpp) cc_final: 0.7615 (ptpt) REVERT: C 690 GLU cc_start: 0.7087 (pp20) cc_final: 0.6486 (pp20) REVERT: C 693 GLN cc_start: 0.7969 (pp30) cc_final: 0.7286 (pp30) REVERT: C 697 ASP cc_start: 0.7579 (m-30) cc_final: 0.7280 (m-30) REVERT: C 700 LYS cc_start: 0.8350 (mttt) cc_final: 0.7155 (mttt) REVERT: C 701 HIS cc_start: 0.7646 (m170) cc_final: 0.7134 (m170) REVERT: C 707 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.7448 (mm) REVERT: C 710 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.6802 (tt) REVERT: C 711 MET cc_start: 0.6178 (mmt) cc_final: 0.5798 (mmt) REVERT: C 731 LYS cc_start: 0.8371 (ttmm) cc_final: 0.7878 (ttmm) REVERT: C 744 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7432 (tpt-90) REVERT: C 748 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6309 (tt) REVERT: E 100 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6869 (tt0) outliers start: 118 outliers final: 73 residues processed: 573 average time/residue: 0.3066 time to fit residues: 248.3269 Evaluate side-chains 592 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 498 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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 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 75 LEU 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 177 LEU 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 358 ASP Chi-restraints excluded: chain A residue 386 ARG 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 580 ASP Chi-restraints excluded: chain A residue 581 ILE 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 680 ASN 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 792 HIS Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1100 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 66 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 187 CYS 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 345 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 MET 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 469 LYS Chi-restraints excluded: chain C residue 503 LEU 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 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 677 VAL Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain C residue 710 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 30 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 146 optimal weight: 0.0470 chunk 169 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 154 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 158 optimal weight: 0.2980 chunk 126 optimal weight: 0.0000 chunk 134 optimal weight: 3.9990 chunk 27 optimal weight: 0.0030 overall best weight: 0.1892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 GLN C 222 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.148672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.125567 restraints weight = 31439.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.129774 restraints weight = 16639.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132564 restraints weight = 10362.545| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15772 Z= 0.142 Angle : 0.744 10.319 21293 Z= 0.375 Chirality : 0.044 0.209 2490 Planarity : 0.006 0.114 2711 Dihedral : 6.279 56.866 2135 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.91 % Favored : 90.83 % Rotamer: Outliers : 5.53 % Allowed : 32.92 % Favored : 61.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1942 helix: 1.11 (0.15), residues: 1344 sheet: -1.15 (1.45), residues: 13 loop : -3.28 (0.21), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 933 HIS 0.010 0.001 HIS C 84 PHE 0.018 0.001 PHE A 991 TYR 0.018 0.001 TYR C 300 ARG 0.012 0.001 ARG C 629 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 984) hydrogen bonds : angle 4.63687 ( 2940) metal coordination : bond 0.00436 ( 11) metal coordination : angle 1.80683 ( 6) covalent geometry : bond 0.00309 (15761) covalent geometry : angle 0.74397 (21287) *********************** 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 598 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 501 time to evaluate : 1.635 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 47 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6300 (mpp-170) REVERT: A 51 LYS cc_start: 0.8478 (tptp) cc_final: 0.8104 (ptmm) REVERT: A 65 GLN cc_start: 0.8288 (mt0) cc_final: 0.7696 (mt0) REVERT: A 67 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7450 (mm) REVERT: A 78 LYS cc_start: 0.8365 (mmmt) cc_final: 0.8045 (tppt) REVERT: A 129 ASN cc_start: 0.7608 (t0) cc_final: 0.7372 (t0) REVERT: A 137 ARG cc_start: 0.7938 (mmm-85) cc_final: 0.7579 (mmm160) REVERT: A 155 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8322 (mm) REVERT: A 158 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7730 (tpt) REVERT: A 160 ASP cc_start: 0.8129 (m-30) cc_final: 0.7163 (t0) REVERT: A 164 ARG cc_start: 0.7014 (OUTLIER) cc_final: 0.5971 (mpp80) REVERT: A 177 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8135 (mm) REVERT: A 215 LEU cc_start: 0.8002 (mt) cc_final: 0.7720 (mt) REVERT: A 218 LEU cc_start: 0.5879 (pp) cc_final: 0.5435 (pp) REVERT: A 233 CYS cc_start: 0.8224 (t) cc_final: 0.7911 (t) REVERT: A 256 VAL cc_start: 0.8847 (m) cc_final: 0.8642 (p) REVERT: A 261 ASN cc_start: 0.8192 (t0) cc_final: 0.7871 (t0) REVERT: A 268 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6717 (ptm-80) REVERT: A 275 PHE cc_start: 0.7270 (OUTLIER) cc_final: 0.6796 (p90) REVERT: A 358 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7135 (t0) REVERT: A 380 ILE cc_start: 0.8373 (mm) cc_final: 0.7961 (mt) REVERT: A 391 LYS cc_start: 0.7967 (tmtt) cc_final: 0.7364 (tmtt) REVERT: A 395 PHE cc_start: 0.8229 (m-10) cc_final: 0.7820 (m-10) REVERT: A 403 LYS cc_start: 0.8382 (mtmm) cc_final: 0.7941 (mmmt) REVERT: A 446 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7840 (mmtm) REVERT: A 456 ASN cc_start: 0.8261 (m-40) cc_final: 0.7521 (m-40) REVERT: A 482 PHE cc_start: 0.8219 (t80) cc_final: 0.7815 (t80) REVERT: A 500 CYS cc_start: 0.8157 (t) cc_final: 0.7766 (p) REVERT: A 527 CYS cc_start: 0.8194 (m) cc_final: 0.7305 (t) REVERT: A 580 ASP cc_start: 0.6186 (OUTLIER) cc_final: 0.5740 (t70) REVERT: A 590 ILE cc_start: 0.8346 (mm) cc_final: 0.7808 (mm) REVERT: A 593 MET cc_start: 0.7398 (tpp) cc_final: 0.6496 (tpp) REVERT: A 647 VAL cc_start: 0.8510 (m) cc_final: 0.8135 (p) REVERT: A 650 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6370 (mm-30) REVERT: A 662 ASN cc_start: 0.7515 (t0) cc_final: 0.7212 (t0) REVERT: A 689 MET cc_start: 0.7150 (pmm) cc_final: 0.6242 (ptt) REVERT: A 703 GLU cc_start: 0.7559 (tp30) cc_final: 0.7057 (tp30) REVERT: A 748 GLN cc_start: 0.6913 (pp30) cc_final: 0.6677 (pm20) REVERT: A 775 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7096 (mp) REVERT: A 826 LYS cc_start: 0.8175 (tptp) cc_final: 0.7647 (tptp) REVERT: A 836 LEU cc_start: 0.8343 (mt) cc_final: 0.8064 (mm) REVERT: A 854 GLN cc_start: 0.7513 (pp30) cc_final: 0.6873 (pp30) REVERT: A 915 GLU cc_start: 0.7329 (tp30) cc_final: 0.6928 (tp30) REVERT: A 918 SER cc_start: 0.6738 (p) cc_final: 0.6495 (p) REVERT: A 938 LYS cc_start: 0.8068 (tppp) cc_final: 0.7598 (tppp) REVERT: A 982 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7652 (mtm-85) REVERT: A 1023 ARG cc_start: 0.7937 (ttm110) cc_final: 0.7365 (ttm110) REVERT: A 1083 LYS cc_start: 0.8513 (mmmm) cc_final: 0.7837 (mmmm) REVERT: A 1109 VAL cc_start: 0.8499 (m) cc_final: 0.8294 (p) REVERT: A 1120 LYS cc_start: 0.8398 (mmmm) cc_final: 0.7883 (mmtm) REVERT: A 1126 MET cc_start: 0.7900 (tpp) cc_final: 0.7589 (mmm) REVERT: A 1156 LYS cc_start: 0.8290 (mmmt) cc_final: 0.7982 (mmmt) REVERT: A 1164 GLN cc_start: 0.7493 (mp10) cc_final: 0.7145 (mp10) REVERT: A 1165 GLU cc_start: 0.8053 (mp0) cc_final: 0.7667 (tp30) REVERT: A 1169 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8206 (mm-40) REVERT: A 1170 ASP cc_start: 0.7828 (m-30) cc_final: 0.7405 (m-30) REVERT: A 1171 GLU cc_start: 0.7941 (tp30) cc_final: 0.7388 (tp30) REVERT: A 1174 ARG cc_start: 0.8329 (ttm110) cc_final: 0.8065 (ttm110) REVERT: C 59 ARG cc_start: 0.7380 (ttp-170) cc_final: 0.6960 (ttp-170) REVERT: C 66 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8385 (pp) REVERT: C 79 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7260 (pp20) REVERT: C 94 LEU cc_start: 0.8558 (mt) cc_final: 0.8307 (mt) REVERT: C 109 TRP cc_start: 0.8248 (t-100) cc_final: 0.7808 (t-100) REVERT: C 179 ASP cc_start: 0.7714 (t0) cc_final: 0.7235 (t0) REVERT: C 211 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6151 (mt-10) REVERT: C 213 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7606 (t) REVERT: C 218 GLN cc_start: 0.8053 (tt0) cc_final: 0.7607 (tt0) REVERT: C 228 ASN cc_start: 0.5106 (OUTLIER) cc_final: 0.4784 (m-40) REVERT: C 235 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7082 (mmmt) REVERT: C 236 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7572 (ttpt) REVERT: C 238 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7536 (mt-10) REVERT: C 244 GLU cc_start: 0.7390 (tp30) cc_final: 0.6749 (mm-30) REVERT: C 249 MET cc_start: 0.7265 (mmm) cc_final: 0.6950 (tpp) REVERT: C 265 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6990 (mt-10) REVERT: C 267 GLU cc_start: 0.7567 (tp30) cc_final: 0.6968 (tp30) REVERT: C 286 HIS cc_start: 0.7680 (t70) cc_final: 0.7399 (t-170) REVERT: C 288 LEU cc_start: 0.8953 (mm) cc_final: 0.8732 (mt) REVERT: C 300 TYR cc_start: 0.7855 (t80) cc_final: 0.7651 (t80) REVERT: C 313 MET cc_start: 0.7777 (ttm) cc_final: 0.7438 (ttm) REVERT: C 359 SER cc_start: 0.8207 (p) cc_final: 0.7751 (m) REVERT: C 368 GLN cc_start: 0.7228 (tm-30) cc_final: 0.6998 (tm-30) REVERT: C 386 GLU cc_start: 0.7395 (tp30) cc_final: 0.6914 (tp30) REVERT: C 393 ASP cc_start: 0.7334 (t0) cc_final: 0.6963 (t0) REVERT: C 416 MET cc_start: 0.7913 (mmm) cc_final: 0.7638 (mmm) REVERT: C 429 GLU cc_start: 0.7403 (tt0) cc_final: 0.6975 (tt0) REVERT: C 454 MET cc_start: 0.7870 (mmm) cc_final: 0.7084 (tmm) REVERT: C 459 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7764 (mmmt) REVERT: C 466 PHE cc_start: 0.6108 (p90) cc_final: 0.5611 (p90) REVERT: C 506 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6904 (mtp85) REVERT: C 533 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7386 (tp30) REVERT: C 688 ARG cc_start: 0.6819 (ttm110) cc_final: 0.6319 (ttm110) REVERT: C 689 LYS cc_start: 0.7915 (ptpp) cc_final: 0.7597 (ptpt) REVERT: C 690 GLU cc_start: 0.7050 (pp20) cc_final: 0.6403 (pp20) REVERT: C 693 GLN cc_start: 0.7962 (pp30) cc_final: 0.7241 (pp30) REVERT: C 697 ASP cc_start: 0.7563 (m-30) cc_final: 0.7257 (m-30) REVERT: C 700 LYS cc_start: 0.8363 (mttt) cc_final: 0.7118 (mttt) REVERT: C 701 HIS cc_start: 0.7643 (m170) cc_final: 0.7299 (m170) REVERT: C 707 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.7460 (mm) REVERT: C 711 MET cc_start: 0.6083 (mmt) cc_final: 0.5807 (mmt) REVERT: C 725 GLU cc_start: 0.7625 (tt0) cc_final: 0.7187 (tp30) REVERT: C 731 LYS cc_start: 0.8371 (ttmm) cc_final: 0.7831 (ttmm) REVERT: C 744 ARG cc_start: 0.8137 (ttm170) cc_final: 0.7420 (tpt-90) REVERT: E 81 PHE cc_start: 0.7935 (t80) cc_final: 0.7440 (t80) REVERT: E 100 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6805 (tt0) outliers start: 97 outliers final: 61 residues processed: 556 average time/residue: 0.3103 time to fit residues: 243.8689 Evaluate side-chains 571 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 491 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 75 LEU 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 175 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 191 VAL 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 358 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 581 ILE 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 686 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 775 LEU 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 857 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1178 ARG Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 187 CYS 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 236 LYS 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 392 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 439 ARG 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 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 677 VAL Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 707 ILE Chi-restraints excluded: chain E residue 100 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 79 optimal weight: 0.0040 chunk 80 optimal weight: 6.9990 chunk 46 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 68 optimal weight: 0.0010 chunk 190 optimal weight: 20.0000 chunk 187 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.147412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124233 restraints weight = 31647.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.128450 restraints weight = 16670.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.131219 restraints weight = 10402.618| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3781 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= 0.147 Angle : 0.771 11.424 21293 Z= 0.388 Chirality : 0.044 0.270 2490 Planarity : 0.006 0.115 2711 Dihedral : 6.129 56.933 2133 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.22 % Favored : 90.58 % Rotamer: Outliers : 5.19 % Allowed : 33.77 % Favored : 61.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.19), residues: 1942 helix: 1.10 (0.15), residues: 1344 sheet: -0.78 (1.48), residues: 13 loop : -3.22 (0.21), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 933 HIS 0.010 0.001 HIS C 84 PHE 0.019 0.001 PHE A 991 TYR 0.020 0.001 TYR C 300 ARG 0.031 0.001 ARG C 629 Details of bonding type rmsd hydrogen bonds : bond 0.04334 ( 984) hydrogen bonds : angle 4.65068 ( 2940) metal coordination : bond 0.00505 ( 11) metal coordination : angle 1.92125 ( 6) covalent geometry : bond 0.00324 (15761) covalent geometry : angle 0.77091 (21287) *********************** 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 586 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 495 time to evaluate : 1.635 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 47 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6325 (mpp-170) REVERT: A 51 LYS cc_start: 0.8471 (tptp) cc_final: 0.8135 (ptmm) REVERT: A 63 GLU cc_start: 0.7932 (mp0) cc_final: 0.7603 (pm20) REVERT: A 65 GLN cc_start: 0.8288 (mt0) cc_final: 0.7705 (mt0) REVERT: A 67 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7438 (mm) REVERT: A 78 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7896 (tppt) REVERT: A 129 ASN cc_start: 0.7591 (t0) cc_final: 0.7356 (t0) REVERT: A 155 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8307 (mm) REVERT: A 158 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7807 (tpt) REVERT: A 160 ASP cc_start: 0.8107 (m-30) cc_final: 0.7089 (t0) REVERT: A 164 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.5841 (mpp80) REVERT: A 177 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8163 (mm) REVERT: A 215 LEU cc_start: 0.8025 (mt) cc_final: 0.7742 (mt) REVERT: A 218 LEU cc_start: 0.5979 (pp) cc_final: 0.5723 (pp) REVERT: A 233 CYS cc_start: 0.8213 (t) cc_final: 0.7903 (t) REVERT: A 261 ASN cc_start: 0.8211 (t0) cc_final: 0.7866 (t0) REVERT: A 268 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6767 (ptm-80) REVERT: A 275 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6838 (p90) REVERT: A 284 LYS cc_start: 0.7154 (mmtm) cc_final: 0.6544 (tppt) REVERT: A 358 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7149 (t0) REVERT: A 380 ILE cc_start: 0.8414 (mm) cc_final: 0.7995 (mt) REVERT: A 391 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7334 (tmtt) REVERT: A 395 PHE cc_start: 0.8246 (m-10) cc_final: 0.7828 (m-10) REVERT: A 403 LYS cc_start: 0.8373 (mtmm) cc_final: 0.7947 (mmmt) REVERT: A 448 VAL cc_start: 0.7835 (p) cc_final: 0.6917 (p) REVERT: A 456 ASN cc_start: 0.8260 (m-40) cc_final: 0.7516 (m-40) REVERT: A 482 PHE cc_start: 0.8210 (t80) cc_final: 0.7806 (t80) REVERT: A 500 CYS cc_start: 0.8131 (t) cc_final: 0.7760 (p) REVERT: A 527 CYS cc_start: 0.8189 (m) cc_final: 0.7331 (t) REVERT: A 551 ARG cc_start: 0.7699 (tpt170) cc_final: 0.7451 (tpm170) REVERT: A 566 LYS cc_start: 0.8851 (tptp) cc_final: 0.8500 (tppt) REVERT: A 580 ASP cc_start: 0.6182 (OUTLIER) cc_final: 0.5718 (t70) REVERT: A 590 ILE cc_start: 0.8348 (mm) cc_final: 0.7806 (mm) REVERT: A 593 MET cc_start: 0.7421 (tpp) cc_final: 0.6506 (tpp) REVERT: A 647 VAL cc_start: 0.8495 (m) cc_final: 0.8144 (p) REVERT: A 650 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6379 (mm-30) REVERT: A 661 LYS cc_start: 0.7904 (mmtp) cc_final: 0.7702 (mmmm) REVERT: A 662 ASN cc_start: 0.7556 (t0) cc_final: 0.7203 (t0) REVERT: A 689 MET cc_start: 0.7160 (pmm) cc_final: 0.6277 (ptt) REVERT: A 703 GLU cc_start: 0.7558 (tp30) cc_final: 0.7050 (tp30) REVERT: A 748 GLN cc_start: 0.6913 (pp30) cc_final: 0.6697 (pm20) REVERT: A 775 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7046 (mp) REVERT: A 778 MET cc_start: 0.7803 (tmm) cc_final: 0.7274 (tmm) REVERT: A 826 LYS cc_start: 0.8201 (tptp) cc_final: 0.7648 (tptt) REVERT: A 836 LEU cc_start: 0.8360 (mt) cc_final: 0.8094 (mm) REVERT: A 854 GLN cc_start: 0.7485 (pp30) cc_final: 0.6842 (pp30) REVERT: A 915 GLU cc_start: 0.7303 (tp30) cc_final: 0.6865 (tp30) REVERT: A 918 SER cc_start: 0.6806 (p) cc_final: 0.6496 (p) REVERT: A 938 LYS cc_start: 0.8037 (tppp) cc_final: 0.7554 (tppp) REVERT: A 953 GLU cc_start: 0.6623 (mm-30) cc_final: 0.6414 (mm-30) REVERT: A 982 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7643 (mtm-85) REVERT: A 1023 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7258 (ttm110) REVERT: A 1056 THR cc_start: 0.7980 (m) cc_final: 0.7777 (p) REVERT: A 1083 LYS cc_start: 0.8567 (mmmm) cc_final: 0.7870 (mmmm) REVERT: A 1109 VAL cc_start: 0.8490 (m) cc_final: 0.8289 (p) REVERT: A 1120 LYS cc_start: 0.8419 (mmmm) cc_final: 0.8174 (mtpp) REVERT: A 1126 MET cc_start: 0.7894 (tpp) cc_final: 0.7582 (mmm) REVERT: A 1156 LYS cc_start: 0.8249 (mmmt) cc_final: 0.7920 (mmtt) REVERT: A 1164 GLN cc_start: 0.7521 (mp10) cc_final: 0.7147 (mp10) REVERT: A 1165 GLU cc_start: 0.8021 (mp0) cc_final: 0.7680 (tp30) REVERT: A 1169 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8209 (mm-40) REVERT: A 1170 ASP cc_start: 0.7826 (m-30) cc_final: 0.7379 (m-30) REVERT: A 1171 GLU cc_start: 0.7974 (tp30) cc_final: 0.7364 (tp30) REVERT: A 1174 ARG cc_start: 0.8323 (ttm110) cc_final: 0.8078 (ttm110) REVERT: C 59 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7025 (ttp-170) REVERT: C 66 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8408 (pp) REVERT: C 79 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7327 (pp20) REVERT: C 94 LEU cc_start: 0.8522 (mt) cc_final: 0.8292 (mt) REVERT: C 179 ASP cc_start: 0.7584 (t0) cc_final: 0.7064 (t0) REVERT: C 211 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6188 (mt-10) REVERT: C 213 SER cc_start: 0.8055 (p) cc_final: 0.7722 (t) REVERT: C 218 GLN cc_start: 0.8066 (tt0) cc_final: 0.7570 (mt0) REVERT: C 228 ASN cc_start: 0.5160 (OUTLIER) cc_final: 0.4801 (m-40) REVERT: C 235 LYS cc_start: 0.7937 (mmmt) cc_final: 0.7091 (mmmt) REVERT: C 244 GLU cc_start: 0.7389 (tp30) cc_final: 0.6610 (mm-30) REVERT: C 249 MET cc_start: 0.7460 (mmm) cc_final: 0.7022 (tpp) REVERT: C 265 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6955 (mt-10) REVERT: C 266 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7426 (ttp80) REVERT: C 286 HIS cc_start: 0.7712 (t70) cc_final: 0.7396 (t-170) REVERT: C 288 LEU cc_start: 0.8971 (mm) cc_final: 0.8587 (mt) REVERT: C 289 LYS cc_start: 0.8606 (tppt) cc_final: 0.8176 (tppt) REVERT: C 300 TYR cc_start: 0.7853 (t80) cc_final: 0.7598 (t80) REVERT: C 313 MET cc_start: 0.7787 (ttm) cc_final: 0.7441 (ttm) REVERT: C 359 SER cc_start: 0.8220 (p) cc_final: 0.7764 (m) REVERT: C 368 GLN cc_start: 0.7254 (tm-30) cc_final: 0.6855 (tm-30) REVERT: C 386 GLU cc_start: 0.7364 (tp30) cc_final: 0.6918 (tp30) REVERT: C 416 MET cc_start: 0.7912 (mmm) cc_final: 0.7630 (mmm) REVERT: C 422 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8230 (tmm) REVERT: C 429 GLU cc_start: 0.7431 (tt0) cc_final: 0.7071 (tt0) REVERT: C 454 MET cc_start: 0.7869 (mmm) cc_final: 0.7082 (tmm) REVERT: C 459 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7776 (mmmt) REVERT: C 466 PHE cc_start: 0.6247 (p90) cc_final: 0.5687 (p90) REVERT: C 506 ARG cc_start: 0.7326 (mmm-85) cc_final: 0.6898 (mtp85) REVERT: C 533 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7346 (tp30) REVERT: C 688 ARG cc_start: 0.6825 (ttm110) cc_final: 0.6303 (mtt90) REVERT: C 689 LYS cc_start: 0.7939 (ptpp) cc_final: 0.7585 (ptpt) REVERT: C 690 GLU cc_start: 0.7069 (pp20) cc_final: 0.6430 (pp20) REVERT: C 693 GLN cc_start: 0.7980 (pp30) cc_final: 0.7252 (pp30) REVERT: C 697 ASP cc_start: 0.7584 (m-30) cc_final: 0.7273 (m-30) REVERT: C 700 LYS cc_start: 0.8398 (mttt) cc_final: 0.7107 (mttt) REVERT: C 701 HIS cc_start: 0.7675 (m170) cc_final: 0.7164 (m170) REVERT: C 707 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.7466 (mm) REVERT: C 711 MET cc_start: 0.6109 (mmt) cc_final: 0.5770 (mmt) REVERT: C 725 GLU cc_start: 0.7651 (tt0) cc_final: 0.7222 (tp30) REVERT: C 728 GLN cc_start: 0.8141 (tp40) cc_final: 0.7729 (tp40) REVERT: C 731 LYS cc_start: 0.8384 (ttmm) cc_final: 0.7791 (ttmm) REVERT: C 744 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7471 (tpt-90) REVERT: E 100 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6754 (tt0) outliers start: 91 outliers final: 57 residues processed: 550 average time/residue: 0.2960 time to fit residues: 229.8047 Evaluate side-chains 563 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 488 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 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 175 SER Chi-restraints excluded: chain A residue 177 LEU 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 221 ASN Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 581 ILE 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 686 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 775 LEU 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 857 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 187 CYS 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 254 LYS Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 MET 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 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 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 100 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 119 optimal weight: 0.9980 chunk 190 optimal weight: 40.0000 chunk 155 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 137 optimal weight: 0.0000 chunk 130 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 181 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 HIS ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN C 84 HIS ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** 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 = 0.4075 r_free = 0.4075 target = 0.147098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.124070 restraints weight = 31827.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.128266 restraints weight = 16676.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.131022 restraints weight = 10332.106| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3900 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= 0.150 Angle : 0.789 12.199 21293 Z= 0.396 Chirality : 0.045 0.326 2490 Planarity : 0.006 0.114 2711 Dihedral : 6.110 59.472 2133 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.22 % Favored : 90.58 % Rotamer: Outliers : 4.45 % Allowed : 34.80 % Favored : 60.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 1942 helix: 1.10 (0.15), residues: 1341 sheet: -0.61 (1.49), residues: 13 loop : -3.20 (0.21), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 933 HIS 0.012 0.001 HIS A 847 PHE 0.026 0.001 PHE C 224 TYR 0.017 0.001 TYR C 300 ARG 0.025 0.001 ARG C 629 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 984) hydrogen bonds : angle 4.68805 ( 2940) metal coordination : bond 0.00518 ( 11) metal coordination : angle 1.90462 ( 6) covalent geometry : bond 0.00335 (15761) covalent geometry : angle 0.78839 (21287) ********************** 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 568 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 490 time to evaluate : 1.730 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: 0.6861 (OUTLIER) cc_final: 0.6303 (mpp-170) REVERT: A 51 LYS cc_start: 0.8469 (tptp) cc_final: 0.8165 (ptmm) REVERT: A 55 LYS cc_start: 0.8173 (tppt) cc_final: 0.7818 (ttpp) REVERT: A 63 GLU cc_start: 0.7937 (mp0) cc_final: 0.7689 (pm20) REVERT: A 65 GLN cc_start: 0.8291 (mt0) cc_final: 0.7730 (mt0) REVERT: A 67 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7462 (mm) REVERT: A 78 LYS cc_start: 0.8233 (mmmt) cc_final: 0.7971 (tppt) REVERT: A 129 ASN cc_start: 0.7576 (t0) cc_final: 0.7342 (t0) REVERT: A 155 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8317 (mm) REVERT: A 158 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7836 (tpt) REVERT: A 160 ASP cc_start: 0.8114 (m-30) cc_final: 0.7375 (t0) REVERT: A 215 LEU cc_start: 0.8045 (mt) cc_final: 0.7756 (mt) REVERT: A 218 LEU cc_start: 0.5882 (pp) cc_final: 0.5621 (pp) REVERT: A 233 CYS cc_start: 0.8230 (t) cc_final: 0.7890 (t) REVERT: A 261 ASN cc_start: 0.8217 (t0) cc_final: 0.7873 (t0) REVERT: A 268 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6815 (ptm-80) REVERT: A 275 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.6955 (p90) REVERT: A 284 LYS cc_start: 0.7237 (mmtm) cc_final: 0.6590 (tppt) REVERT: A 358 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7218 (t0) REVERT: A 380 ILE cc_start: 0.8463 (mm) cc_final: 0.8045 (mt) REVERT: A 391 LYS cc_start: 0.8063 (tmtt) cc_final: 0.7399 (tmtt) REVERT: A 395 PHE cc_start: 0.8246 (m-10) cc_final: 0.7824 (m-10) REVERT: A 403 LYS cc_start: 0.8387 (mtmm) cc_final: 0.7949 (mmmt) REVERT: A 456 ASN cc_start: 0.8264 (m-40) cc_final: 0.7483 (m-40) REVERT: A 482 PHE cc_start: 0.8211 (t80) cc_final: 0.7800 (t80) REVERT: A 500 CYS cc_start: 0.8117 (t) cc_final: 0.7751 (p) REVERT: A 527 CYS cc_start: 0.8190 (m) cc_final: 0.7322 (t) REVERT: A 551 ARG cc_start: 0.7710 (tpt170) cc_final: 0.7395 (tpm170) REVERT: A 580 ASP cc_start: 0.6188 (OUTLIER) cc_final: 0.5725 (t70) REVERT: A 590 ILE cc_start: 0.8351 (mm) cc_final: 0.7806 (mm) REVERT: A 593 MET cc_start: 0.7414 (tpp) cc_final: 0.6518 (tpp) REVERT: A 647 VAL cc_start: 0.8401 (m) cc_final: 0.8062 (p) REVERT: A 650 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6426 (mm-30) REVERT: A 661 LYS cc_start: 0.7909 (mmtp) cc_final: 0.7498 (mmmm) REVERT: A 662 ASN cc_start: 0.7575 (t0) cc_final: 0.7207 (t0) REVERT: A 689 MET cc_start: 0.7212 (pmm) cc_final: 0.6298 (ptt) REVERT: A 703 GLU cc_start: 0.7550 (tp30) cc_final: 0.7054 (tp30) REVERT: A 775 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7098 (mp) REVERT: A 778 MET cc_start: 0.7816 (tmm) cc_final: 0.7322 (tmm) REVERT: A 826 LYS cc_start: 0.8253 (tptp) cc_final: 0.7664 (tptt) REVERT: A 836 LEU cc_start: 0.8357 (mt) cc_final: 0.8089 (mm) REVERT: A 854 GLN cc_start: 0.7437 (pp30) cc_final: 0.6793 (pp30) REVERT: A 915 GLU cc_start: 0.7262 (tp30) cc_final: 0.6843 (tp30) REVERT: A 918 SER cc_start: 0.6845 (p) cc_final: 0.6600 (p) REVERT: A 938 LYS cc_start: 0.8021 (tppp) cc_final: 0.7508 (tppp) REVERT: A 953 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6512 (mm-30) REVERT: A 982 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7659 (mtm-85) REVERT: A 1023 ARG cc_start: 0.7923 (ttm110) cc_final: 0.7361 (ttm110) REVERT: A 1083 LYS cc_start: 0.8518 (mmmm) cc_final: 0.7866 (mmmm) REVERT: A 1109 VAL cc_start: 0.8489 (m) cc_final: 0.8282 (p) REVERT: A 1120 LYS cc_start: 0.8403 (mmmm) cc_final: 0.8143 (mtpp) REVERT: A 1126 MET cc_start: 0.7916 (tpp) cc_final: 0.7603 (mmm) REVERT: A 1156 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7986 (mmtt) REVERT: A 1164 GLN cc_start: 0.7507 (mp10) cc_final: 0.7115 (mp10) REVERT: A 1165 GLU cc_start: 0.8029 (mp0) cc_final: 0.7688 (tp30) REVERT: A 1169 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8228 (mm-40) REVERT: A 1170 ASP cc_start: 0.7824 (m-30) cc_final: 0.7391 (m-30) REVERT: A 1171 GLU cc_start: 0.7980 (tp30) cc_final: 0.7380 (tp30) REVERT: A 1174 ARG cc_start: 0.8324 (ttm110) cc_final: 0.8076 (ttm110) REVERT: C 45 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: C 59 ARG cc_start: 0.7445 (ttp-170) cc_final: 0.7033 (ttp-170) REVERT: C 66 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8395 (pp) REVERT: C 79 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7339 (pp20) REVERT: C 94 LEU cc_start: 0.8515 (mt) cc_final: 0.8272 (mt) REVERT: C 179 ASP cc_start: 0.7578 (t0) cc_final: 0.7033 (t0) REVERT: C 211 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6234 (mt-10) REVERT: C 213 SER cc_start: 0.8061 (p) cc_final: 0.7722 (t) REVERT: C 218 GLN cc_start: 0.8081 (tt0) cc_final: 0.7577 (mt0) REVERT: C 228 ASN cc_start: 0.5251 (OUTLIER) cc_final: 0.4911 (m-40) REVERT: C 244 GLU cc_start: 0.7398 (tp30) cc_final: 0.6619 (mm-30) REVERT: C 249 MET cc_start: 0.7407 (mmm) cc_final: 0.6982 (tpp) REVERT: C 265 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6955 (mt-10) REVERT: C 266 ARG cc_start: 0.7685 (ttp80) cc_final: 0.7326 (ttp80) REVERT: C 286 HIS cc_start: 0.7719 (t70) cc_final: 0.7433 (t-170) REVERT: C 288 LEU cc_start: 0.8970 (mm) cc_final: 0.8621 (mt) REVERT: C 289 LYS cc_start: 0.8607 (tppt) cc_final: 0.8047 (tppt) REVERT: C 300 TYR cc_start: 0.7842 (t80) cc_final: 0.7594 (t80) REVERT: C 313 MET cc_start: 0.7816 (ttm) cc_final: 0.7489 (ttm) REVERT: C 359 SER cc_start: 0.8223 (p) cc_final: 0.7769 (m) REVERT: C 368 GLN cc_start: 0.7275 (tm-30) cc_final: 0.6897 (tm-30) REVERT: C 386 GLU cc_start: 0.7341 (tp30) cc_final: 0.6867 (tp30) REVERT: C 412 LEU cc_start: 0.8482 (mm) cc_final: 0.8239 (mm) REVERT: C 416 MET cc_start: 0.7928 (mmm) cc_final: 0.7517 (mmm) REVERT: C 422 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8223 (tmm) REVERT: C 429 GLU cc_start: 0.7478 (tt0) cc_final: 0.7164 (tt0) REVERT: C 454 MET cc_start: 0.7863 (mmm) cc_final: 0.7660 (tpt) REVERT: C 459 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7775 (mmmt) REVERT: C 476 ASP cc_start: 0.8234 (t0) cc_final: 0.8009 (t0) REVERT: C 506 ARG cc_start: 0.7307 (mmm-85) cc_final: 0.6886 (mtp85) REVERT: C 533 GLU cc_start: 0.7918 (tp30) cc_final: 0.7429 (tp30) REVERT: C 688 ARG cc_start: 0.6813 (ttm110) cc_final: 0.6301 (mtm-85) REVERT: C 689 LYS cc_start: 0.7953 (ptpp) cc_final: 0.7565 (ptpt) REVERT: C 690 GLU cc_start: 0.7051 (pp20) cc_final: 0.6394 (pp20) REVERT: C 693 GLN cc_start: 0.7975 (pp30) cc_final: 0.7274 (pp30) REVERT: C 697 ASP cc_start: 0.7597 (m-30) cc_final: 0.7276 (m-30) REVERT: C 700 LYS cc_start: 0.8405 (mttt) cc_final: 0.7113 (mttt) REVERT: C 701 HIS cc_start: 0.7697 (m170) cc_final: 0.7179 (m170) REVERT: C 707 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.7493 (mm) REVERT: C 711 MET cc_start: 0.6116 (mmt) cc_final: 0.5774 (mmt) REVERT: C 725 GLU cc_start: 0.7670 (tt0) cc_final: 0.7202 (tp30) REVERT: C 728 GLN cc_start: 0.8143 (tp40) cc_final: 0.7729 (tp40) REVERT: C 731 LYS cc_start: 0.8374 (ttmm) cc_final: 0.7770 (ttmm) REVERT: C 744 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7446 (tpt-90) REVERT: E 100 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6711 (tt0) outliers start: 78 outliers final: 54 residues processed: 535 average time/residue: 0.3185 time to fit residues: 240.8962 Evaluate side-chains 549 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 479 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 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 175 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 ARG 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 358 ASP Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 580 ASP Chi-restraints excluded: chain A residue 581 ILE 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 686 THR Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 850 ASP Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 984 SER Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 45 GLN Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 187 CYS 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 254 LYS Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 503 LEU 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 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 100 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 153 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 189 optimal weight: 20.0000 chunk 188 optimal weight: 50.0000 chunk 80 optimal weight: 0.0040 chunk 47 optimal weight: 0.7980 chunk 95 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.147551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124494 restraints weight = 31600.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.128681 restraints weight = 16662.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.131483 restraints weight = 10352.634| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 15772 Z= 0.216 Angle : 0.959 59.192 21293 Z= 0.521 Chirality : 0.051 1.032 2490 Planarity : 0.006 0.114 2711 Dihedral : 5.865 59.511 2123 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.22 % Favored : 90.53 % Rotamer: Outliers : 4.22 % Allowed : 35.54 % Favored : 60.24 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.19), residues: 1942 helix: 1.08 (0.15), residues: 1344 sheet: -0.62 (1.48), residues: 13 loop : -3.20 (0.21), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 933 HIS 0.010 0.001 HIS A 847 PHE 0.025 0.002 PHE A 658 TYR 0.016 0.001 TYR A 772 ARG 0.027 0.001 ARG C 629 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 984) hydrogen bonds : angle 4.69950 ( 2940) metal coordination : bond 0.00511 ( 11) metal coordination : angle 1.90221 ( 6) covalent geometry : bond 0.00519 (15761) covalent geometry : angle 0.95843 (21287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5969.90 seconds wall clock time: 105 minutes 15.29 seconds (6315.29 seconds total)