Starting phenix.real_space_refine on Tue Dec 31 11:08:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h3q_34473/12_2024/8h3q_34473.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h3q_34473/12_2024/8h3q_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_34473/12_2024/8h3q_34473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h3q_34473/12_2024/8h3q_34473.map" model { file = "/net/cci-nas-00/data/ceres_data/8h3q_34473/12_2024/8h3q_34473.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h3q_34473/12_2024/8h3q_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.10, per 1000 atoms: 0.59 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: 4.33 Conformation dependent library (CDL) restraints added in 2.1 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: 1.80 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: 5.97 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3357 1.33 - 1.45: 3094 1.45 - 1.57: 9149 1.57 - 1.70: 0 1.70 - 1.82: 161 Bond restraints: 15761 Sorted by residual: bond pdb=" N VAL A1138 " pdb=" CA VAL A1138 " ideal model delta sigma weight residual 1.456 1.493 -0.036 9.50e-03 1.11e+04 1.47e+01 bond pdb=" N ARG A 364 " pdb=" CA ARG A 364 " ideal model delta sigma weight residual 1.462 1.517 -0.055 1.44e-02 4.82e+03 1.46e+01 bond pdb=" N GLU A1147 " pdb=" CA GLU A1147 " ideal model delta sigma weight residual 1.462 1.490 -0.028 7.70e-03 1.69e+04 1.29e+01 bond pdb=" C ILE A 296 " pdb=" O ILE A 296 " ideal model delta sigma weight residual 1.237 1.276 -0.039 1.13e-02 7.83e+03 1.21e+01 bond pdb=" N ASP A 222 " pdb=" CA ASP A 222 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.17e+01 ... (remaining 15756 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 20345 2.59 - 5.19: 843 5.19 - 7.78: 84 7.78 - 10.38: 13 10.38 - 12.97: 2 Bond angle restraints: 21287 Sorted by residual: angle pdb=" N VAL A1138 " pdb=" CA VAL A1138 " pdb=" C VAL A1138 " ideal model delta sigma weight residual 113.53 107.34 6.19 9.80e-01 1.04e+00 3.99e+01 angle pdb=" N GLN C 465 " pdb=" CA GLN C 465 " pdb=" C GLN C 465 " ideal model delta sigma weight residual 113.02 105.48 7.54 1.20e+00 6.94e-01 3.95e+01 angle pdb=" N ASN A 295 " pdb=" CA ASN A 295 " pdb=" C ASN A 295 " ideal model delta sigma weight residual 111.07 104.79 6.28 1.07e+00 8.73e-01 3.45e+01 angle pdb=" C SER A 488 " pdb=" CA SER A 488 " pdb=" CB SER A 488 " ideal model delta sigma weight residual 116.54 110.15 6.39 1.15e+00 7.56e-01 3.09e+01 angle pdb=" N THR A 405 " pdb=" CA THR A 405 " pdb=" C THR A 405 " ideal model delta sigma weight residual 112.93 106.73 6.20 1.12e+00 7.97e-01 3.07e+01 ... (remaining 21282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7979 17.97 - 35.95: 1183 35.95 - 53.92: 457 53.92 - 71.89: 119 71.89 - 89.87: 28 Dihedral angle restraints: 9766 sinusoidal: 4011 harmonic: 5755 Sorted by residual: dihedral pdb=" C ARG A 364 " pdb=" N ARG A 364 " pdb=" CA ARG A 364 " pdb=" CB ARG A 364 " ideal model delta harmonic sigma weight residual -122.60 -136.91 14.31 0 2.50e+00 1.60e-01 3.28e+01 dihedral pdb=" CA SER A1192 " pdb=" C SER A1192 " pdb=" N PRO A1193 " pdb=" CA PRO A1193 " ideal model delta harmonic sigma weight residual 180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP A 59 " pdb=" C ASP A 59 " pdb=" N LYS A 60 " pdb=" CA LYS A 60 " ideal model delta harmonic sigma weight residual 180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 9763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2131 0.090 - 0.181: 311 0.181 - 0.271: 38 0.271 - 0.362: 8 0.362 - 0.452: 2 Chirality restraints: 2490 Sorted by residual: chirality pdb=" CA ARG A 364 " pdb=" N ARG A 364 " pdb=" C ARG A 364 " pdb=" CB ARG A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CA TYR A 772 " pdb=" N TYR A 772 " pdb=" C TYR A 772 " pdb=" CB TYR A 772 " both_signs ideal model delta sigma weight residual False 2.51 2.95 -0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CA THR C 467 " pdb=" N THR C 467 " pdb=" C THR C 467 " pdb=" CB THR C 467 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 2487 not shown) Planarity restraints: 2711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 364 " 0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ARG A 364 " -0.086 2.00e-02 2.50e+03 pdb=" O ARG A 364 " 0.032 2.00e-02 2.50e+03 pdb=" N HIS A 365 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 551 " -0.078 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO A 552 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 552 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 552 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 771 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C GLY A 771 " 0.060 2.00e-02 2.50e+03 pdb=" O GLY A 771 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR A 772 " -0.021 2.00e-02 2.50e+03 ... (remaining 2708 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 149 2.59 - 3.17: 13941 3.17 - 3.75: 26472 3.75 - 4.32: 33340 4.32 - 4.90: 53564 Nonbonded interactions: 127466 Sorted by model distance: nonbonded pdb=" OD2 ASP E 97 " pdb="ZN ZN E4002 " model vdw 2.017 2.230 nonbonded pdb=" OE2 GLU A 915 " pdb=" OG SER A 919 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP A 160 " pdb=" NE ARG A 164 " model vdw 2.204 3.120 nonbonded pdb=" O MET C 477 " pdb=" OG SER C 480 " model vdw 2.205 3.040 nonbonded pdb=" O LEU A 102 " pdb=" OG SER A 106 " model vdw 2.214 3.040 ... (remaining 127461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 41.060 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- 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 15761 Z= 0.460 Angle : 1.137 12.970 21287 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 *********************** 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 : 1.854 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: 0.3292 time to fit residues: 295.3423 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 : 1.812 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 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 15761 Z= 0.253 Angle : 0.782 9.371 21287 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 *********************** 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 : 1.969 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: 0.7986 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: A 17 SER cc_start: 0.6386 (OUTLIER) cc_final: 0.6104 (p) REVERT: A 48 LYS cc_start: 0.6345 (OUTLIER) cc_final: 0.6085 (mtmm) REVERT: A 91 LEU cc_start: 0.7826 (mt) cc_final: 0.7611 (mt) REVERT: A 158 MET cc_start: 0.7609 (tpt) cc_final: 0.7323 (tpt) REVERT: A 177 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8290 (mm) REVERT: A 209 ASP cc_start: 0.6200 (OUTLIER) cc_final: 0.5917 (t0) REVERT: A 215 LEU cc_start: 0.7468 (mt) cc_final: 0.7212 (mt) REVERT: A 218 LEU cc_start: 0.6016 (pp) cc_final: 0.5192 (pp) REVERT: A 261 ASN cc_start: 0.8268 (t0) cc_final: 0.7757 (m-40) REVERT: A 429 GLN cc_start: 0.7988 (pp30) cc_final: 0.7780 (pp30) REVERT: A 445 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: A 527 CYS cc_start: 0.6960 (m) cc_final: 0.6534 (t) REVERT: A 675 ASP cc_start: 0.7250 (t0) cc_final: 0.6961 (t0) REVERT: A 826 LYS cc_start: 0.7565 (tptp) cc_final: 0.7150 (tptt) REVERT: A 842 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7863 (tp) REVERT: A 880 LEU cc_start: 0.8761 (tt) cc_final: 0.8503 (tt) REVERT: A 938 LYS cc_start: 0.8200 (tppp) cc_final: 0.7936 (tppp) REVERT: A 967 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7490 (tt) REVERT: A 1106 LEU cc_start: 0.7664 (mm) cc_final: 0.7370 (mt) REVERT: A 1121 MET cc_start: 0.7177 (mtp) cc_final: 0.6732 (mmm) REVERT: A 1156 LYS cc_start: 0.8064 (tppt) cc_final: 0.7836 (mmmt) REVERT: C 117 VAL cc_start: 0.7277 (m) cc_final: 0.7068 (t) REVERT: C 176 GLU cc_start: 0.6431 (tm-30) cc_final: 0.6216 (tm-30) REVERT: C 206 GLU cc_start: 0.5785 (OUTLIER) cc_final: 0.4730 (tt0) REVERT: C 209 PHE cc_start: 0.6484 (t80) cc_final: 0.5113 (t80) REVERT: C 213 SER cc_start: 0.7943 (p) cc_final: 0.7252 (p) REVERT: C 218 GLN cc_start: 0.7777 (tt0) cc_final: 0.7365 (mt0) REVERT: C 228 ASN cc_start: 0.5330 (OUTLIER) cc_final: 0.4910 (m-40) REVERT: C 244 GLU cc_start: 0.7508 (tp30) cc_final: 0.6842 (mm-30) REVERT: C 258 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: C 289 LYS cc_start: 0.8292 (tppt) cc_final: 0.7979 (tppt) REVERT: C 346 LEU cc_start: 0.8528 (mt) cc_final: 0.8105 (mm) REVERT: C 414 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7989 (mmmt) REVERT: C 420 ARG cc_start: 0.7515 (tpp80) cc_final: 0.6988 (mtp85) REVERT: C 444 LYS cc_start: 0.6598 (tptp) cc_final: 0.6191 (tptp) REVERT: C 473 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7295 (ttm) REVERT: C 513 TRP cc_start: 0.7365 (m100) cc_final: 0.6823 (m100) REVERT: C 533 GLU cc_start: 0.7875 (tp30) cc_final: 0.7506 (tp30) REVERT: C 542 LYS cc_start: 0.8008 (mmmm) cc_final: 0.7786 (tptp) REVERT: C 632 GLN cc_start: 0.7386 (pp30) cc_final: 0.7125 (pp30) REVERT: C 673 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7393 (mmtm) REVERT: C 689 LYS cc_start: 0.7687 (ptpp) cc_final: 0.7390 (pttt) REVERT: C 690 GLU cc_start: 0.6947 (pp20) cc_final: 0.6587 (pp20) REVERT: C 693 GLN cc_start: 0.7820 (pp30) cc_final: 0.7378 (pp30) REVERT: C 697 ASP cc_start: 0.7753 (m-30) cc_final: 0.7416 (m-30) REVERT: C 698 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: C 700 LYS cc_start: 0.8212 (mttt) cc_final: 0.7544 (mttt) REVERT: C 707 ILE cc_start: 0.8198 (tp) cc_final: 0.7501 (tp) REVERT: C 711 MET cc_start: 0.6173 (mmt) cc_final: 0.5714 (mmt) REVERT: C 725 GLU cc_start: 0.7363 (tt0) cc_final: 0.6819 (tm-30) REVERT: C 744 ARG cc_start: 0.8303 (ttm170) cc_final: 0.7981 (ttt180) outliers start: 140 outliers final: 69 residues processed: 577 average time/residue: 0.3215 time to fit residues: 264.6873 Evaluate side-chains 559 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 476 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 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 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 842 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 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 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 190 optimal weight: 50.0000 chunk 157 optimal weight: 0.8980 chunk 175 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15761 Z= 0.231 Angle : 0.743 10.114 21287 Z= 0.381 Chirality : 0.044 0.197 2490 Planarity : 0.006 0.119 2711 Dihedral : 8.795 61.816 2193 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.58 % Favored : 90.06 % Rotamer: Outliers : 6.50 % Allowed : 30.12 % Favored : 63.38 % 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: -0.68 (0.19), residues: 1942 helix: 0.79 (0.14), residues: 1343 sheet: -1.29 (1.59), residues: 13 loop : -3.50 (0.21), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 72 HIS 0.004 0.001 HIS A 847 PHE 0.022 0.002 PHE A 395 TYR 0.015 0.001 TYR A 980 ARG 0.011 0.000 ARG C 629 *********************** 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 610 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 496 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: A 67 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6723 (mm) REVERT: A 155 LEU cc_start: 0.7353 (mm) cc_final: 0.7142 (mm) REVERT: A 209 ASP cc_start: 0.6330 (OUTLIER) cc_final: 0.5905 (t0) REVERT: A 215 LEU cc_start: 0.7550 (mt) cc_final: 0.7318 (mt) REVERT: A 218 LEU cc_start: 0.5822 (pp) cc_final: 0.4786 (pp) REVERT: A 261 ASN cc_start: 0.8280 (t0) cc_final: 0.7873 (m-40) REVERT: A 268 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.6401 (ptm-80) REVERT: A 403 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8002 (mmmt) REVERT: A 445 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6660 (mp0) REVERT: A 580 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.6106 (t70) REVERT: A 662 ASN cc_start: 0.7727 (p0) cc_final: 0.7434 (t0) REVERT: A 675 ASP cc_start: 0.7169 (t0) cc_final: 0.6929 (t0) REVERT: A 685 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7212 (mp) REVERT: A 703 GLU cc_start: 0.7132 (tp30) cc_final: 0.6860 (tp30) REVERT: A 826 LYS cc_start: 0.7610 (tptp) cc_final: 0.7129 (tptt) REVERT: A 842 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7802 (tt) REVERT: A 854 GLN cc_start: 0.6902 (pp30) cc_final: 0.6585 (tm-30) REVERT: A 1117 TYR cc_start: 0.8243 (t80) cc_final: 0.7982 (t80) REVERT: A 1121 MET cc_start: 0.7192 (mtp) cc_final: 0.6956 (mmm) REVERT: A 1156 LYS cc_start: 0.8083 (tppt) cc_final: 0.7860 (mmmt) REVERT: C 59 ARG cc_start: 0.6919 (ttp-170) cc_final: 0.6645 (ttp-170) REVERT: C 112 HIS cc_start: 0.7726 (t70) cc_final: 0.7303 (t70) REVERT: C 184 ARG cc_start: 0.7072 (ttt180) cc_final: 0.6356 (ttm-80) REVERT: C 206 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.4504 (tt0) REVERT: C 209 PHE cc_start: 0.6581 (t80) cc_final: 0.5272 (t80) REVERT: C 211 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6018 (mt-10) REVERT: C 228 ASN cc_start: 0.5289 (OUTLIER) cc_final: 0.4914 (m-40) REVERT: C 244 GLU cc_start: 0.7449 (tp30) cc_final: 0.6738 (mm-30) REVERT: C 258 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.7014 (mm-30) REVERT: C 289 LYS cc_start: 0.8279 (tppt) cc_final: 0.7974 (tppt) REVERT: C 313 MET cc_start: 0.7612 (ttm) cc_final: 0.7350 (ttm) REVERT: C 386 GLU cc_start: 0.7140 (tp30) cc_final: 0.6504 (tp30) REVERT: C 422 MET cc_start: 0.8773 (ttp) cc_final: 0.8492 (ttm) REVERT: C 424 GLU cc_start: 0.7158 (mp0) cc_final: 0.6955 (mp0) REVERT: C 431 TYR cc_start: 0.7888 (m-10) cc_final: 0.7621 (m-80) REVERT: C 460 THR cc_start: 0.7552 (t) cc_final: 0.7218 (p) REVERT: C 473 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.6540 (ttm) REVERT: C 513 TRP cc_start: 0.7298 (m100) cc_final: 0.6869 (m100) REVERT: C 533 GLU cc_start: 0.7949 (tp30) cc_final: 0.7529 (tp30) REVERT: C 538 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7293 (t80) REVERT: C 603 MET cc_start: 0.7273 (mmm) cc_final: 0.7072 (mmm) REVERT: C 673 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7303 (mmtm) REVERT: C 689 LYS cc_start: 0.7807 (ptpp) cc_final: 0.7453 (ptpt) REVERT: C 690 GLU cc_start: 0.6958 (pp20) cc_final: 0.6504 (pp20) REVERT: C 693 GLN cc_start: 0.7905 (pp30) cc_final: 0.7386 (pp30) REVERT: C 697 ASP cc_start: 0.7722 (m-30) cc_final: 0.7386 (m-30) REVERT: C 698 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: C 700 LYS cc_start: 0.8172 (mttt) cc_final: 0.7424 (mttt) REVERT: C 707 ILE cc_start: 0.8154 (tp) cc_final: 0.7135 (tp) REVERT: C 711 MET cc_start: 0.6268 (mmt) cc_final: 0.5860 (mmt) REVERT: C 725 GLU cc_start: 0.7457 (tt0) cc_final: 0.6882 (tm-30) REVERT: C 744 ARG cc_start: 0.8250 (ttm170) cc_final: 0.7815 (ttt180) REVERT: C 748 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.6001 (tt) outliers start: 114 outliers final: 64 residues processed: 562 average time/residue: 0.3256 time to fit residues: 263.0519 Evaluate side-chains 548 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 467 time to evaluate : 2.048 ------------------------------------------------------------------------------- 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 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 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 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 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 842 LEU Chi-restraints excluded: chain A residue 855 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 1045 LEU 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 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 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 273 MET 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 695 VAL Chi-restraints excluded: chain C residue 698 ASP 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 174 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 GLN A 707 HIS ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15761 Z= 0.225 Angle : 0.731 9.973 21287 Z= 0.376 Chirality : 0.044 0.197 2490 Planarity : 0.006 0.118 2711 Dihedral : 7.977 59.692 2175 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.58 % Favored : 90.06 % Rotamer: Outliers : 7.53 % Allowed : 29.04 % Favored : 63.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.56 (0.19), residues: 1942 helix: 0.90 (0.14), residues: 1334 sheet: -1.01 (1.59), residues: 13 loop : -3.45 (0.20), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 72 HIS 0.006 0.001 HIS A 939 PHE 0.023 0.002 PHE A 395 TYR 0.029 0.002 TYR C 154 ARG 0.008 0.001 ARG A1099 *********************** 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 620 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 488 time to evaluate : 1.862 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 6 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: A 67 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6775 (mm) REVERT: A 155 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7099 (mm) REVERT: A 164 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6797 (mpp80) REVERT: A 209 ASP cc_start: 0.6361 (OUTLIER) cc_final: 0.6004 (t0) REVERT: A 218 LEU cc_start: 0.5630 (pp) cc_final: 0.4764 (pp) REVERT: A 233 CYS cc_start: 0.6894 (t) cc_final: 0.6632 (t) REVERT: A 261 ASN cc_start: 0.8291 (t0) cc_final: 0.7908 (m-40) REVERT: A 358 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6813 (t0) REVERT: A 387 GLU cc_start: 0.4735 (OUTLIER) cc_final: 0.3806 (pm20) REVERT: A 403 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8100 (mmmt) REVERT: A 580 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6189 (t70) REVERT: A 590 ILE cc_start: 0.8493 (mm) cc_final: 0.7981 (mm) REVERT: A 662 ASN cc_start: 0.7811 (p0) cc_final: 0.7571 (t0) REVERT: A 675 ASP cc_start: 0.7192 (t0) cc_final: 0.6940 (t0) REVERT: A 685 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7288 (mp) REVERT: A 762 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7826 (tp) REVERT: A 821 PHE cc_start: 0.5916 (m-10) cc_final: 0.5623 (m-10) REVERT: A 826 LYS cc_start: 0.7625 (tptp) cc_final: 0.7137 (tptt) REVERT: A 842 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7728 (tp) REVERT: A 854 GLN cc_start: 0.6923 (pp30) cc_final: 0.5935 (tm-30) REVERT: A 916 ILE cc_start: 0.8471 (mt) cc_final: 0.8266 (mt) REVERT: A 938 LYS cc_start: 0.8258 (tppp) cc_final: 0.7784 (tppp) REVERT: A 1003 LEU cc_start: 0.7126 (tp) cc_final: 0.6916 (tp) REVERT: A 1004 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5681 (tt) REVERT: A 1109 VAL cc_start: 0.7605 (p) cc_final: 0.7307 (p) REVERT: A 1165 GLU cc_start: 0.7657 (mp0) cc_final: 0.7442 (tp30) REVERT: C 59 ARG cc_start: 0.6926 (ttp-170) cc_final: 0.6654 (ttp-170) REVERT: C 109 TRP cc_start: 0.7982 (t-100) cc_final: 0.7727 (t-100) REVERT: C 184 ARG cc_start: 0.7101 (ttt180) cc_final: 0.6767 (tpp80) REVERT: C 204 ASP cc_start: 0.1886 (OUTLIER) cc_final: 0.1632 (m-30) REVERT: C 206 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.4886 (tt0) REVERT: C 211 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6134 (mt-10) REVERT: C 218 GLN cc_start: 0.7865 (tt0) cc_final: 0.7415 (mt0) REVERT: C 228 ASN cc_start: 0.5339 (OUTLIER) cc_final: 0.4964 (m-40) REVERT: C 235 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7122 (mmmt) REVERT: C 244 GLU cc_start: 0.7561 (tp30) cc_final: 0.6745 (mm-30) REVERT: C 258 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.7022 (mm-30) REVERT: C 266 ARG cc_start: 0.7789 (ttp80) cc_final: 0.7547 (ttp80) REVERT: C 289 LYS cc_start: 0.8352 (tppt) cc_final: 0.8048 (tppt) REVERT: C 313 MET cc_start: 0.7762 (ttm) cc_final: 0.7428 (ttm) REVERT: C 355 PHE cc_start: 0.7617 (m-80) cc_final: 0.7404 (m-80) REVERT: C 383 ARG cc_start: 0.7472 (mtp85) cc_final: 0.7265 (mtp85) REVERT: C 386 GLU cc_start: 0.7241 (tp30) cc_final: 0.6088 (tp30) REVERT: C 414 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7956 (mmmt) REVERT: C 416 MET cc_start: 0.8064 (mmm) cc_final: 0.7688 (mmm) REVERT: C 422 MET cc_start: 0.8723 (ttp) cc_final: 0.8444 (ttm) REVERT: C 431 TYR cc_start: 0.7881 (m-10) cc_final: 0.7303 (m-80) REVERT: C 444 LYS cc_start: 0.6550 (OUTLIER) cc_final: 0.6076 (tptp) REVERT: C 454 MET cc_start: 0.8257 (mmm) cc_final: 0.7318 (tmm) REVERT: C 460 THR cc_start: 0.7581 (t) cc_final: 0.7305 (p) REVERT: C 533 GLU cc_start: 0.7973 (tp30) cc_final: 0.7605 (tp30) REVERT: C 542 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7845 (mmtm) REVERT: C 688 ARG cc_start: 0.6785 (ttm110) cc_final: 0.6192 (ttm110) REVERT: C 689 LYS cc_start: 0.7883 (ptpp) cc_final: 0.7552 (ptpt) REVERT: C 690 GLU cc_start: 0.7049 (pp20) cc_final: 0.6617 (pp20) REVERT: C 693 GLN cc_start: 0.7916 (pp30) cc_final: 0.7361 (pp30) REVERT: C 697 ASP cc_start: 0.7701 (m-30) cc_final: 0.7366 (m-30) REVERT: C 698 ASP cc_start: 0.7760 (t0) cc_final: 0.7559 (m-30) REVERT: C 700 LYS cc_start: 0.8183 (mttt) cc_final: 0.7105 (mttt) REVERT: C 701 HIS cc_start: 0.7849 (m170) cc_final: 0.7300 (m170) REVERT: C 710 ILE cc_start: 0.7270 (OUTLIER) cc_final: 0.6702 (tt) REVERT: C 711 MET cc_start: 0.6213 (mmt) cc_final: 0.5773 (mmt) REVERT: C 731 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7590 (ttmm) REVERT: C 744 ARG cc_start: 0.8300 (ttm170) cc_final: 0.7422 (tpt-90) REVERT: C 748 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.6087 (tt) REVERT: E 100 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6842 (tt0) outliers start: 132 outliers final: 72 residues processed: 565 average time/residue: 0.3475 time to fit residues: 278.6435 Evaluate side-chains 565 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 472 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 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 85 GLU 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 155 LEU Chi-restraints excluded: chain A residue 164 ARG 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 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 453 CYS 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 684 SER 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 723 TYR 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 786 GLN Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 842 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 1004 LEU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1068 MET 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 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 258 GLU 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 296 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 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 677 VAL Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 710 ILE 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 156 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN ** A 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 HIS ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 361 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15761 Z= 0.237 Angle : 0.738 8.731 21287 Z= 0.381 Chirality : 0.045 0.188 2490 Planarity : 0.006 0.118 2711 Dihedral : 7.434 55.922 2162 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.63 % Favored : 90.11 % Rotamer: Outliers : 7.36 % Allowed : 30.41 % Favored : 62.24 % 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: 0.91 (0.14), residues: 1340 sheet: -0.84 (1.58), residues: 13 loop : -3.40 (0.21), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 513 HIS 0.010 0.001 HIS A 847 PHE 0.022 0.002 PHE C 538 TYR 0.025 0.002 TYR C 154 ARG 0.009 0.001 ARG A1023 *********************** 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 625 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 496 time to evaluate : 1.886 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 15 MET cc_start: 0.7670 (mtt) cc_final: 0.7349 (mtt) REVERT: A 67 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6943 (mm) REVERT: A 155 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7251 (mm) REVERT: A 160 ASP cc_start: 0.7596 (m-30) cc_final: 0.7163 (t70) REVERT: A 218 LEU cc_start: 0.5857 (pp) cc_final: 0.5196 (pp) REVERT: A 233 CYS cc_start: 0.6960 (t) cc_final: 0.6733 (t) REVERT: A 261 ASN cc_start: 0.8294 (t0) cc_final: 0.7877 (m-40) REVERT: A 358 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6851 (t0) REVERT: A 387 GLU cc_start: 0.3775 (OUTLIER) cc_final: 0.3349 (pm20) REVERT: A 391 LYS cc_start: 0.7469 (tmtt) cc_final: 0.6920 (tptp) REVERT: A 403 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8102 (mmmt) REVERT: A 514 HIS cc_start: 0.6809 (m90) cc_final: 0.6556 (m90) REVERT: A 527 CYS cc_start: 0.7002 (m) cc_final: 0.6527 (t) REVERT: A 564 TYR cc_start: 0.5948 (m-80) cc_final: 0.5689 (m-80) REVERT: A 590 ILE cc_start: 0.8503 (mm) cc_final: 0.8017 (mm) REVERT: A 647 VAL cc_start: 0.7581 (m) cc_final: 0.7350 (p) REVERT: A 650 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7182 (mm-30) REVERT: A 675 ASP cc_start: 0.7208 (t0) cc_final: 0.6943 (t0) REVERT: A 689 MET cc_start: 0.7031 (pmm) cc_final: 0.6068 (ptt) REVERT: A 703 GLU cc_start: 0.7100 (tp30) cc_final: 0.6615 (tp30) REVERT: A 821 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5655 (m-10) REVERT: A 826 LYS cc_start: 0.7672 (tptp) cc_final: 0.7159 (tptt) REVERT: A 842 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7709 (tt) REVERT: A 845 VAL cc_start: 0.8123 (m) cc_final: 0.7854 (p) REVERT: A 854 GLN cc_start: 0.6898 (pp30) cc_final: 0.5994 (pp30) REVERT: A 967 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7563 (tt) REVERT: A 1156 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7467 (mmmt) REVERT: A 1165 GLU cc_start: 0.7659 (mp0) cc_final: 0.7444 (tp30) REVERT: A 1169 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7820 (mm-40) REVERT: A 1171 GLU cc_start: 0.7624 (tp30) cc_final: 0.7328 (tp30) REVERT: C 59 ARG cc_start: 0.6976 (ttp-170) cc_final: 0.6674 (ttp-170) REVERT: C 176 GLU cc_start: 0.6210 (tm-30) cc_final: 0.5945 (tm-30) REVERT: C 184 ARG cc_start: 0.7088 (ttt180) cc_final: 0.6718 (tpp80) REVERT: C 204 ASP cc_start: 0.2192 (OUTLIER) cc_final: 0.1952 (m-30) REVERT: C 218 GLN cc_start: 0.7827 (tt0) cc_final: 0.7368 (mt0) REVERT: C 220 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6888 (tp30) REVERT: C 228 ASN cc_start: 0.5389 (OUTLIER) cc_final: 0.5013 (m-40) REVERT: C 235 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7102 (mmmt) REVERT: C 236 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7550 (ttpt) REVERT: C 266 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7452 (ttp80) REVERT: C 288 LEU cc_start: 0.8995 (mm) cc_final: 0.8711 (mt) REVERT: C 289 LYS cc_start: 0.8341 (tppt) cc_final: 0.8093 (tppt) REVERT: C 300 TYR cc_start: 0.7988 (t80) cc_final: 0.7699 (t80) REVERT: C 313 MET cc_start: 0.7781 (ttm) cc_final: 0.7459 (ttm) REVERT: C 361 ASN cc_start: 0.8508 (OUTLIER) cc_final: 0.8119 (p0) REVERT: C 386 GLU cc_start: 0.7231 (tp30) cc_final: 0.6825 (tp30) REVERT: C 414 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7994 (mmmt) REVERT: C 416 MET cc_start: 0.8087 (mmm) cc_final: 0.7810 (mmm) REVERT: C 422 MET cc_start: 0.8713 (ttp) cc_final: 0.8456 (ttm) REVERT: C 424 GLU cc_start: 0.7484 (mp0) cc_final: 0.7056 (mp0) REVERT: C 444 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6131 (tptp) REVERT: C 454 MET cc_start: 0.8221 (mmm) cc_final: 0.7291 (tmm) REVERT: C 460 THR cc_start: 0.7679 (t) cc_final: 0.7341 (p) REVERT: C 473 MET cc_start: 0.8108 (ttt) cc_final: 0.7755 (tpt) REVERT: C 533 GLU cc_start: 0.8000 (tp30) cc_final: 0.7608 (tp30) REVERT: C 542 LYS cc_start: 0.8151 (mmtm) cc_final: 0.7827 (mmtp) REVERT: C 603 MET cc_start: 0.7217 (mmm) cc_final: 0.6963 (mmm) REVERT: C 673 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.7271 (mmtm) REVERT: C 689 LYS cc_start: 0.7932 (ptpp) cc_final: 0.7547 (ptpt) REVERT: C 690 GLU cc_start: 0.7100 (pp20) cc_final: 0.6634 (pp20) REVERT: C 693 GLN cc_start: 0.7948 (pp30) cc_final: 0.7401 (pp30) REVERT: C 697 ASP cc_start: 0.7731 (m-30) cc_final: 0.7409 (m-30) REVERT: C 698 ASP cc_start: 0.7774 (t0) cc_final: 0.7545 (m-30) REVERT: C 700 LYS cc_start: 0.8184 (mttt) cc_final: 0.7231 (mttt) REVERT: C 701 HIS cc_start: 0.7820 (m170) cc_final: 0.7258 (m170) REVERT: C 710 ILE cc_start: 0.7263 (tp) cc_final: 0.6587 (tt) REVERT: C 711 MET cc_start: 0.6276 (mmt) cc_final: 0.5813 (mmt) REVERT: C 731 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7561 (ttmm) REVERT: C 744 ARG cc_start: 0.8317 (ttm170) cc_final: 0.7424 (tpt-90) REVERT: C 748 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6163 (tt) REVERT: E 100 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6640 (tt0) outliers start: 129 outliers final: 77 residues processed: 572 average time/residue: 0.3249 time to fit residues: 261.4452 Evaluate side-chains 578 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 487 time to evaluate : 1.914 ------------------------------------------------------------------------------- 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 42 ASP Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 151 GLN Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 398 TYR 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 453 CYS 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 684 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 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 842 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 967 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 1060 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 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 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 361 ASN Chi-restraints excluded: chain C residue 390 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 459 LYS Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 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 729 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 745 ILE 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 63 optimal weight: 0.0970 chunk 168 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 46 optimal weight: 0.0170 chunk 187 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 HIS ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1035 HIS C 188 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15761 Z= 0.221 Angle : 0.754 11.428 21287 Z= 0.384 Chirality : 0.044 0.194 2490 Planarity : 0.006 0.117 2711 Dihedral : 6.989 54.550 2146 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.06 % Favored : 90.68 % Rotamer: Outliers : 6.33 % Allowed : 31.72 % Favored : 61.95 % 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: -0.41 (0.19), residues: 1942 helix: 0.97 (0.14), residues: 1341 sheet: -0.87 (1.55), residues: 13 loop : -3.31 (0.21), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 72 HIS 0.007 0.001 HIS A 847 PHE 0.050 0.002 PHE A 395 TYR 0.023 0.002 TYR C 62 ARG 0.016 0.001 ARG C 629 *********************** 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 600 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 489 time to evaluate : 1.831 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 15 MET cc_start: 0.7671 (mtt) cc_final: 0.7298 (mtt) REVERT: A 55 LYS cc_start: 0.7436 (pttp) cc_final: 0.7208 (ttpp) REVERT: A 67 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6835 (mm) REVERT: A 155 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7219 (mm) REVERT: A 160 ASP cc_start: 0.7619 (m-30) cc_final: 0.7130 (t70) REVERT: A 218 LEU cc_start: 0.5993 (pp) cc_final: 0.5430 (pp) REVERT: A 261 ASN cc_start: 0.8299 (t0) cc_final: 0.7885 (m-40) REVERT: A 403 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8111 (mmmt) REVERT: A 446 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8424 (mmtm) REVERT: A 527 CYS cc_start: 0.6959 (m) cc_final: 0.6504 (t) REVERT: A 580 ASP cc_start: 0.6602 (OUTLIER) cc_final: 0.6274 (t70) REVERT: A 590 ILE cc_start: 0.8472 (mm) cc_final: 0.8007 (mm) REVERT: A 647 VAL cc_start: 0.7639 (m) cc_final: 0.7374 (p) REVERT: A 689 MET cc_start: 0.6974 (pmm) cc_final: 0.6089 (ptt) REVERT: A 821 PHE cc_start: 0.5988 (OUTLIER) cc_final: 0.5611 (m-10) REVERT: A 826 LYS cc_start: 0.7677 (tptp) cc_final: 0.7160 (tptt) REVERT: A 842 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7592 (tt) REVERT: A 854 GLN cc_start: 0.6919 (pp30) cc_final: 0.6023 (pp30) REVERT: A 938 LYS cc_start: 0.8267 (tppp) cc_final: 0.7810 (tppp) REVERT: A 967 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7571 (tt) REVERT: A 1004 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5654 (tt) REVERT: A 1156 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7531 (tppt) REVERT: A 1165 GLU cc_start: 0.7649 (mp0) cc_final: 0.7448 (tp30) REVERT: A 1169 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7849 (mm-40) REVERT: C 59 ARG cc_start: 0.6945 (ttp-170) cc_final: 0.6609 (ttp-170) REVERT: C 176 GLU cc_start: 0.6176 (tm-30) cc_final: 0.5868 (tm-30) REVERT: C 211 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6087 (mt-10) REVERT: C 218 GLN cc_start: 0.7829 (tt0) cc_final: 0.7462 (mt0) REVERT: C 228 ASN cc_start: 0.5335 (OUTLIER) cc_final: 0.4965 (m-40) REVERT: C 235 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7084 (mmmt) REVERT: C 236 LYS cc_start: 0.7887 (ttmt) cc_final: 0.7564 (ttpt) REVERT: C 265 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6836 (mt-10) REVERT: C 267 GLU cc_start: 0.7455 (tp30) cc_final: 0.6872 (tp30) REVERT: C 284 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8415 (tt) REVERT: C 288 LEU cc_start: 0.8973 (mm) cc_final: 0.8537 (mt) REVERT: C 289 LYS cc_start: 0.8311 (tppt) cc_final: 0.7563 (tppt) REVERT: C 300 TYR cc_start: 0.8036 (t80) cc_final: 0.7820 (t80) REVERT: C 313 MET cc_start: 0.7766 (ttm) cc_final: 0.7439 (ttm) REVERT: C 320 TYR cc_start: 0.8183 (t80) cc_final: 0.7587 (t80) REVERT: C 326 LYS cc_start: 0.6962 (mmmt) cc_final: 0.6583 (mptt) REVERT: C 386 GLU cc_start: 0.7107 (tp30) cc_final: 0.6783 (tp30) REVERT: C 414 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7958 (mmmt) REVERT: C 416 MET cc_start: 0.8107 (mmm) cc_final: 0.7786 (mmm) REVERT: C 422 MET cc_start: 0.8701 (ttp) cc_final: 0.8434 (ttm) REVERT: C 424 GLU cc_start: 0.7485 (mp0) cc_final: 0.7081 (mp0) REVERT: C 444 LYS cc_start: 0.6629 (OUTLIER) cc_final: 0.6111 (tptp) REVERT: C 454 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7337 (tmm) REVERT: C 460 THR cc_start: 0.7614 (t) cc_final: 0.7308 (p) REVERT: C 466 PHE cc_start: 0.6458 (p90) cc_final: 0.6055 (p90) REVERT: C 473 MET cc_start: 0.8135 (ttt) cc_final: 0.7749 (tpt) REVERT: C 533 GLU cc_start: 0.8052 (tp30) cc_final: 0.7631 (tp30) REVERT: C 542 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7903 (mmtm) REVERT: C 603 MET cc_start: 0.7276 (mmm) cc_final: 0.6928 (mmm) REVERT: C 673 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7247 (mmtm) REVERT: C 689 LYS cc_start: 0.7902 (ptpp) cc_final: 0.7507 (ptpt) REVERT: C 690 GLU cc_start: 0.7088 (pp20) cc_final: 0.6569 (pp20) REVERT: C 693 GLN cc_start: 0.7973 (pp30) cc_final: 0.7355 (pp30) REVERT: C 697 ASP cc_start: 0.7725 (m-30) cc_final: 0.7408 (m-30) REVERT: C 700 LYS cc_start: 0.8189 (mttt) cc_final: 0.7146 (mttt) REVERT: C 701 HIS cc_start: 0.7776 (m170) cc_final: 0.7238 (m170) REVERT: C 710 ILE cc_start: 0.7266 (tp) cc_final: 0.6610 (tt) REVERT: C 711 MET cc_start: 0.6228 (mmt) cc_final: 0.5786 (mmt) REVERT: C 731 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7525 (ttmm) REVERT: C 744 ARG cc_start: 0.8337 (ttm170) cc_final: 0.7578 (tpt-90) REVERT: C 748 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6099 (tt) outliers start: 111 outliers final: 75 residues processed: 546 average time/residue: 0.3235 time to fit residues: 250.2079 Evaluate side-chains 575 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 486 time to evaluate : 1.949 ------------------------------------------------------------------------------- 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 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 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 211 ILE Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 398 TYR 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 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 684 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 772 TYR Chi-restraints excluded: chain A residue 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 842 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 967 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 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 284 LEU 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 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 444 LYS Chi-restraints excluded: chain C residue 454 MET Chi-restraints excluded: chain C residue 459 LYS Chi-restraints excluded: chain C residue 469 LYS Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 0.9980 chunk 21 optimal weight: 0.0980 chunk 106 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 186 optimal weight: 0.0770 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 115 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 456 ASN ** 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 222 GLN ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 423 GLN ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15761 Z= 0.222 Angle : 0.765 10.473 21287 Z= 0.390 Chirality : 0.044 0.206 2490 Planarity : 0.006 0.117 2711 Dihedral : 6.522 54.787 2136 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.22 % Favored : 90.53 % Rotamer: Outliers : 6.67 % Allowed : 32.57 % 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: -0.38 (0.19), residues: 1942 helix: 1.00 (0.14), residues: 1343 sheet: -0.78 (1.50), residues: 13 loop : -3.34 (0.21), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 27 HIS 0.008 0.001 HIS C 84 PHE 0.040 0.002 PHE A 395 TYR 0.021 0.001 TYR C 62 ARG 0.011 0.001 ARG A1023 *********************** 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 614 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 497 time to evaluate : 1.957 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 67 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6869 (mm) REVERT: A 155 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7246 (mm) REVERT: A 164 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6947 (mpp80) REVERT: A 177 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8139 (mm) REVERT: A 218 LEU cc_start: 0.5843 (pp) cc_final: 0.5170 (pp) REVERT: A 261 ASN cc_start: 0.8293 (t0) cc_final: 0.7895 (m-40) REVERT: A 403 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8126 (mmmt) REVERT: A 439 LEU cc_start: 0.7368 (mm) cc_final: 0.7099 (mt) REVERT: A 446 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8429 (mmtm) REVERT: A 482 PHE cc_start: 0.7603 (t80) cc_final: 0.7357 (t80) REVERT: A 527 CYS cc_start: 0.6926 (m) cc_final: 0.6493 (t) REVERT: A 580 ASP cc_start: 0.6602 (OUTLIER) cc_final: 0.6291 (t70) REVERT: A 590 ILE cc_start: 0.8473 (mm) cc_final: 0.7962 (mm) REVERT: A 593 MET cc_start: 0.6854 (tpp) cc_final: 0.6310 (tpp) REVERT: A 647 VAL cc_start: 0.7743 (m) cc_final: 0.7480 (p) REVERT: A 650 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6924 (mm-30) REVERT: A 689 MET cc_start: 0.6913 (pmm) cc_final: 0.5982 (ptt) REVERT: A 703 GLU cc_start: 0.7089 (tp30) cc_final: 0.6698 (tp30) REVERT: A 762 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7866 (tp) REVERT: A 775 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6960 (mp) REVERT: A 826 LYS cc_start: 0.7740 (tptp) cc_final: 0.7358 (tptp) REVERT: A 842 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7608 (tt) REVERT: A 938 LYS cc_start: 0.8270 (tppp) cc_final: 0.7838 (tppp) REVERT: A 1004 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5574 (tt) REVERT: A 1109 VAL cc_start: 0.7755 (m) cc_final: 0.7347 (p) REVERT: A 1120 LYS cc_start: 0.7434 (mmtm) cc_final: 0.6947 (mmmm) REVERT: A 1165 GLU cc_start: 0.7706 (mp0) cc_final: 0.7444 (tp30) REVERT: A 1169 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7814 (mm-40) REVERT: C 59 ARG cc_start: 0.6954 (ttp-170) cc_final: 0.6621 (ttp-170) REVERT: C 91 GLU cc_start: 0.7362 (tm-30) cc_final: 0.7155 (tm-30) REVERT: C 176 GLU cc_start: 0.6168 (tm-30) cc_final: 0.5868 (tm-30) REVERT: C 184 ARG cc_start: 0.7096 (ttt180) cc_final: 0.6896 (tpp80) REVERT: C 211 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6086 (mt-10) REVERT: C 218 GLN cc_start: 0.7860 (tt0) cc_final: 0.7560 (tt0) REVERT: C 228 ASN cc_start: 0.5343 (OUTLIER) cc_final: 0.5011 (m-40) REVERT: C 236 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7547 (ttpt) REVERT: C 266 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7277 (ttp80) REVERT: C 288 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8605 (mt) REVERT: C 289 LYS cc_start: 0.8241 (tppt) cc_final: 0.7850 (tppt) REVERT: C 300 TYR cc_start: 0.8086 (t80) cc_final: 0.7789 (t80) REVERT: C 313 MET cc_start: 0.7808 (ttm) cc_final: 0.7449 (ttm) REVERT: C 320 TYR cc_start: 0.8195 (t80) cc_final: 0.7983 (t80) REVERT: C 326 LYS cc_start: 0.7017 (mmmt) cc_final: 0.6693 (mptt) REVERT: C 354 ARG cc_start: 0.7458 (ttp80) cc_final: 0.7184 (ttp80) REVERT: C 361 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8152 (p0) REVERT: C 386 GLU cc_start: 0.7115 (tp30) cc_final: 0.6771 (tp30) REVERT: C 393 ASP cc_start: 0.7325 (t0) cc_final: 0.7035 (t70) REVERT: C 410 THR cc_start: 0.8187 (t) cc_final: 0.7959 (p) REVERT: C 416 MET cc_start: 0.8105 (mmm) cc_final: 0.7800 (mmm) REVERT: C 422 MET cc_start: 0.8700 (ttp) cc_final: 0.8463 (ttm) REVERT: C 424 GLU cc_start: 0.7519 (mp0) cc_final: 0.7097 (mp0) REVERT: C 429 GLU cc_start: 0.7633 (tt0) cc_final: 0.7400 (tt0) REVERT: C 444 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6089 (tptp) REVERT: C 454 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7363 (tmm) REVERT: C 466 PHE cc_start: 0.6478 (p90) cc_final: 0.6069 (p90) REVERT: C 473 MET cc_start: 0.8150 (ttt) cc_final: 0.7031 (tpp) REVERT: C 513 TRP cc_start: 0.7798 (m100) cc_final: 0.6982 (m100) REVERT: C 533 GLU cc_start: 0.8033 (tp30) cc_final: 0.7448 (tp30) REVERT: C 603 MET cc_start: 0.7299 (mmm) cc_final: 0.6921 (mmm) REVERT: C 673 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7132 (mmtt) REVERT: C 689 LYS cc_start: 0.7871 (ptpp) cc_final: 0.7513 (ptpt) REVERT: C 690 GLU cc_start: 0.7116 (pp20) cc_final: 0.6549 (pp20) REVERT: C 693 GLN cc_start: 0.7985 (pp30) cc_final: 0.7360 (pp30) REVERT: C 697 ASP cc_start: 0.7719 (m-30) cc_final: 0.7380 (m-30) REVERT: C 700 LYS cc_start: 0.8192 (mttt) cc_final: 0.7139 (mttt) REVERT: C 701 HIS cc_start: 0.7755 (m170) cc_final: 0.7259 (m170) REVERT: C 707 ILE cc_start: 0.8285 (tp) cc_final: 0.7026 (tp) REVERT: C 711 MET cc_start: 0.6216 (mmt) cc_final: 0.5720 (mmt) REVERT: C 725 GLU cc_start: 0.7578 (tt0) cc_final: 0.7093 (tm-30) REVERT: C 731 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7493 (ttmm) REVERT: C 744 ARG cc_start: 0.8340 (ttm170) cc_final: 0.7585 (tpt-90) outliers start: 117 outliers final: 75 residues processed: 560 average time/residue: 0.3238 time to fit residues: 256.7193 Evaluate side-chains 575 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 483 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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 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 155 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 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 231 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 386 ARG 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 500 CYS 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 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 762 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 842 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1177 MET Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 436 LEU 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 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 729 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain E residue 35 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 170 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 ASN C 188 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15761 Z= 0.242 Angle : 0.788 12.961 21287 Z= 0.400 Chirality : 0.046 0.315 2490 Planarity : 0.006 0.117 2711 Dihedral : 6.526 55.515 2135 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.01 % Favored : 90.73 % Rotamer: Outliers : 6.10 % Allowed : 32.86 % 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: -0.33 (0.19), residues: 1942 helix: 0.99 (0.14), residues: 1343 sheet: -0.42 (1.50), residues: 13 loop : -3.20 (0.22), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 933 HIS 0.011 0.001 HIS C 84 PHE 0.036 0.002 PHE A 395 TYR 0.021 0.001 TYR C 62 ARG 0.026 0.001 ARG C 629 *********************** 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 608 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 501 time to evaluate : 1.760 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 15 MET cc_start: 0.7412 (mtt) cc_final: 0.6781 (mtt) REVERT: A 52 MET cc_start: 0.5990 (tpt) cc_final: 0.5779 (tpt) REVERT: A 67 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6917 (mm) REVERT: A 155 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7328 (mm) REVERT: A 164 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6994 (mpp80) REVERT: A 218 LEU cc_start: 0.5983 (pp) cc_final: 0.5345 (pp) REVERT: A 261 ASN cc_start: 0.8315 (t0) cc_final: 0.7922 (t0) REVERT: A 284 LYS cc_start: 0.6813 (mmtm) cc_final: 0.6424 (tppt) REVERT: A 380 ILE cc_start: 0.8425 (mm) cc_final: 0.8058 (mt) REVERT: A 403 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8158 (mmmt) REVERT: A 439 LEU cc_start: 0.7456 (mm) cc_final: 0.7188 (mt) REVERT: A 482 PHE cc_start: 0.7622 (t80) cc_final: 0.7388 (t80) REVERT: A 527 CYS cc_start: 0.6986 (m) cc_final: 0.6545 (t) REVERT: A 580 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6307 (t70) REVERT: A 590 ILE cc_start: 0.8446 (mm) cc_final: 0.7940 (mm) REVERT: A 593 MET cc_start: 0.6866 (tpp) cc_final: 0.6287 (tpp) REVERT: A 633 THR cc_start: 0.7379 (m) cc_final: 0.7052 (p) REVERT: A 647 VAL cc_start: 0.7841 (m) cc_final: 0.7569 (p) REVERT: A 650 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6957 (mm-30) REVERT: A 689 MET cc_start: 0.6926 (pmm) cc_final: 0.6038 (ptt) REVERT: A 703 GLU cc_start: 0.7095 (tp30) cc_final: 0.6605 (tp30) REVERT: A 778 MET cc_start: 0.7532 (tmm) cc_final: 0.7059 (tmm) REVERT: A 826 LYS cc_start: 0.7749 (tptp) cc_final: 0.7368 (tptp) REVERT: A 842 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7590 (tp) REVERT: A 854 GLN cc_start: 0.7143 (pp30) cc_final: 0.6681 (pp30) REVERT: A 938 LYS cc_start: 0.8294 (tppp) cc_final: 0.7864 (tppp) REVERT: A 982 ARG cc_start: 0.7342 (mtt90) cc_final: 0.7091 (mtm-85) REVERT: A 1004 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5647 (tt) REVERT: A 1109 VAL cc_start: 0.7737 (m) cc_final: 0.7332 (p) REVERT: A 1120 LYS cc_start: 0.7359 (mmtm) cc_final: 0.6943 (mmmm) REVERT: A 1165 GLU cc_start: 0.7715 (mp0) cc_final: 0.7497 (tp30) REVERT: A 1171 GLU cc_start: 0.7598 (tp30) cc_final: 0.7211 (tp30) REVERT: C 59 ARG cc_start: 0.6970 (ttp-170) cc_final: 0.6633 (ttp-170) REVERT: C 91 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7225 (tm-30) REVERT: C 163 GLN cc_start: 0.7498 (tp40) cc_final: 0.7297 (tp-100) REVERT: C 176 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5810 (tm-30) REVERT: C 184 ARG cc_start: 0.7061 (ttt180) cc_final: 0.6744 (ttm-80) REVERT: C 211 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: C 218 GLN cc_start: 0.7870 (tt0) cc_final: 0.7546 (tt0) REVERT: C 228 ASN cc_start: 0.5426 (OUTLIER) cc_final: 0.5084 (m-40) REVERT: C 236 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7581 (ttpt) REVERT: C 265 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6889 (mt-10) REVERT: C 288 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8663 (mt) REVERT: C 289 LYS cc_start: 0.8338 (tppt) cc_final: 0.7972 (tppt) REVERT: C 313 MET cc_start: 0.7849 (ttm) cc_final: 0.7500 (ttm) REVERT: C 326 LYS cc_start: 0.7138 (mmmt) cc_final: 0.6913 (mmtt) REVERT: C 354 ARG cc_start: 0.7473 (ttp80) cc_final: 0.7140 (ttp80) REVERT: C 386 GLU cc_start: 0.7231 (tp30) cc_final: 0.6831 (tp30) REVERT: C 393 ASP cc_start: 0.7313 (t0) cc_final: 0.7107 (t70) REVERT: C 410 THR cc_start: 0.8228 (t) cc_final: 0.7990 (p) REVERT: C 416 MET cc_start: 0.8127 (mmm) cc_final: 0.7798 (mmm) REVERT: C 422 MET cc_start: 0.8777 (ttp) cc_final: 0.8569 (ttm) REVERT: C 424 GLU cc_start: 0.7576 (mp0) cc_final: 0.7207 (mp0) REVERT: C 429 GLU cc_start: 0.7639 (tt0) cc_final: 0.7334 (tt0) REVERT: C 444 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6122 (tptp) REVERT: C 454 MET cc_start: 0.8178 (mmm) cc_final: 0.7280 (tmm) REVERT: C 466 PHE cc_start: 0.6654 (p90) cc_final: 0.6221 (p90) REVERT: C 473 MET cc_start: 0.8266 (ttt) cc_final: 0.7125 (tpp) REVERT: C 513 TRP cc_start: 0.7827 (m100) cc_final: 0.7050 (m100) REVERT: C 533 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: C 673 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7115 (mmtt) REVERT: C 689 LYS cc_start: 0.7917 (ptpp) cc_final: 0.7540 (ptpt) REVERT: C 690 GLU cc_start: 0.7150 (pp20) cc_final: 0.6565 (pp20) REVERT: C 693 GLN cc_start: 0.8004 (pp30) cc_final: 0.7375 (pp30) REVERT: C 697 ASP cc_start: 0.7737 (m-30) cc_final: 0.7399 (m-30) REVERT: C 700 LYS cc_start: 0.8238 (mttt) cc_final: 0.7136 (mttt) REVERT: C 701 HIS cc_start: 0.7824 (m170) cc_final: 0.7291 (m170) REVERT: C 710 ILE cc_start: 0.7255 (tp) cc_final: 0.6539 (tt) REVERT: C 711 MET cc_start: 0.6242 (mmt) cc_final: 0.5793 (mmt) REVERT: C 731 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7529 (ttmm) REVERT: C 744 ARG cc_start: 0.8364 (ttm170) cc_final: 0.7568 (tpt-90) outliers start: 107 outliers final: 77 residues processed: 559 average time/residue: 0.3271 time to fit residues: 257.6517 Evaluate side-chains 583 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 493 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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 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 155 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 275 PHE 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 453 CYS Chi-restraints excluded: chain A residue 500 CYS 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 773 MET 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 842 LEU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1177 MET 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 77 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ASP 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 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 288 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 436 LEU 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 533 GLU Chi-restraints excluded: chain C residue 597 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 613 PHE Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 673 LYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 695 VAL Chi-restraints excluded: chain C residue 729 GLN Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain E residue 35 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 0.0270 chunk 136 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 chunk 164 optimal weight: 0.0970 chunk 173 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN ** 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 48 ASN C 188 GLN ** C 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN E 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15761 Z= 0.230 Angle : 0.817 11.615 21287 Z= 0.411 Chirality : 0.046 0.294 2490 Planarity : 0.006 0.116 2711 Dihedral : 6.609 58.228 2135 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.47 % Favored : 90.32 % Rotamer: Outliers : 5.53 % Allowed : 34.11 % Favored : 60.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1942 helix: 1.02 (0.15), residues: 1339 sheet: -0.61 (1.43), residues: 13 loop : -3.13 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 933 HIS 0.010 0.001 HIS C 84 PHE 0.037 0.002 PHE A 395 TYR 0.024 0.002 TYR C 300 ARG 0.025 0.001 ARG C 629 *********************** 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 591 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 494 time to evaluate : 1.771 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 15 MET cc_start: 0.7444 (mtt) cc_final: 0.6807 (mtt) REVERT: A 52 MET cc_start: 0.6009 (tpt) cc_final: 0.5805 (tpt) REVERT: A 59 ASP cc_start: 0.4151 (p0) cc_final: 0.3773 (p0) REVERT: A 67 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6873 (mm) REVERT: A 78 LYS cc_start: 0.7790 (mmmt) cc_final: 0.7430 (tppt) REVERT: A 155 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7336 (mm) REVERT: A 261 ASN cc_start: 0.8330 (t0) cc_final: 0.7903 (t0) REVERT: A 284 LYS cc_start: 0.6831 (mmtm) cc_final: 0.6356 (tppt) REVERT: A 380 ILE cc_start: 0.8428 (mm) cc_final: 0.8047 (mt) REVERT: A 403 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8162 (mmmt) REVERT: A 439 LEU cc_start: 0.7437 (mm) cc_final: 0.7081 (mt) REVERT: A 482 PHE cc_start: 0.7586 (t80) cc_final: 0.7343 (t80) REVERT: A 505 LEU cc_start: 0.8261 (mm) cc_final: 0.7934 (mt) REVERT: A 527 CYS cc_start: 0.6887 (m) cc_final: 0.6473 (t) REVERT: A 580 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6312 (t70) REVERT: A 590 ILE cc_start: 0.8451 (mm) cc_final: 0.7947 (mm) REVERT: A 593 MET cc_start: 0.6855 (tpp) cc_final: 0.6308 (tpp) REVERT: A 647 VAL cc_start: 0.7739 (m) cc_final: 0.7494 (p) REVERT: A 650 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6967 (mm-30) REVERT: A 661 LYS cc_start: 0.7747 (mmtp) cc_final: 0.7542 (mmmm) REVERT: A 689 MET cc_start: 0.6920 (pmm) cc_final: 0.6027 (ptt) REVERT: A 778 MET cc_start: 0.7500 (tmm) cc_final: 0.7033 (tmm) REVERT: A 826 LYS cc_start: 0.7749 (tptp) cc_final: 0.7252 (tptt) REVERT: A 854 GLN cc_start: 0.7101 (pp30) cc_final: 0.6523 (pp30) REVERT: A 938 LYS cc_start: 0.8271 (tppp) cc_final: 0.7866 (tppp) REVERT: A 1004 LEU cc_start: 0.5834 (OUTLIER) cc_final: 0.5591 (tt) REVERT: A 1109 VAL cc_start: 0.7709 (m) cc_final: 0.7294 (p) REVERT: A 1120 LYS cc_start: 0.7333 (mmtm) cc_final: 0.6901 (mmmm) REVERT: C 42 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7521 (tm-30) REVERT: C 59 ARG cc_start: 0.6982 (ttp-170) cc_final: 0.6630 (ttp-170) REVERT: C 91 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7222 (tm-30) REVERT: C 176 GLU cc_start: 0.6210 (tm-30) cc_final: 0.5842 (tm-30) REVERT: C 184 ARG cc_start: 0.7086 (ttt180) cc_final: 0.6722 (ttm-80) REVERT: C 218 GLN cc_start: 0.7810 (tt0) cc_final: 0.7421 (tt0) REVERT: C 228 ASN cc_start: 0.5365 (OUTLIER) cc_final: 0.5028 (m-40) REVERT: C 236 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7529 (ttpt) REVERT: C 238 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7650 (mt-10) REVERT: C 267 GLU cc_start: 0.7442 (tp30) cc_final: 0.7054 (tp30) REVERT: C 288 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8604 (mt) REVERT: C 313 MET cc_start: 0.7765 (ttm) cc_final: 0.7403 (ttm) REVERT: C 326 LYS cc_start: 0.7198 (mmmt) cc_final: 0.6981 (mmtt) REVERT: C 354 ARG cc_start: 0.7481 (ttp80) cc_final: 0.7033 (ttp80) REVERT: C 386 GLU cc_start: 0.7328 (tp30) cc_final: 0.6623 (tp30) REVERT: C 393 ASP cc_start: 0.7277 (t0) cc_final: 0.7058 (t70) REVERT: C 410 THR cc_start: 0.8228 (t) cc_final: 0.7995 (p) REVERT: C 416 MET cc_start: 0.8133 (mmm) cc_final: 0.7787 (mmm) REVERT: C 422 MET cc_start: 0.8757 (ttp) cc_final: 0.8552 (ttm) REVERT: C 424 GLU cc_start: 0.7579 (mp0) cc_final: 0.7183 (mp0) REVERT: C 429 GLU cc_start: 0.7728 (tt0) cc_final: 0.7464 (tt0) REVERT: C 444 LYS cc_start: 0.6555 (OUTLIER) cc_final: 0.6334 (tptp) REVERT: C 454 MET cc_start: 0.8117 (mmm) cc_final: 0.7806 (tpt) REVERT: C 469 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8294 (mmtp) REVERT: C 473 MET cc_start: 0.8256 (ttt) cc_final: 0.7159 (tpp) REVERT: C 513 TRP cc_start: 0.7846 (m100) cc_final: 0.7039 (m100) REVERT: C 533 GLU cc_start: 0.8008 (tp30) cc_final: 0.7419 (tp30) REVERT: C 673 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7101 (mmtt) REVERT: C 689 LYS cc_start: 0.7924 (ptpp) cc_final: 0.7519 (ptpt) REVERT: C 690 GLU cc_start: 0.7128 (pp20) cc_final: 0.6521 (pp20) REVERT: C 693 GLN cc_start: 0.7980 (pp30) cc_final: 0.7375 (pp30) REVERT: C 697 ASP cc_start: 0.7722 (m-30) cc_final: 0.7381 (m-30) REVERT: C 700 LYS cc_start: 0.8219 (mttt) cc_final: 0.7244 (mttt) REVERT: C 701 HIS cc_start: 0.7826 (m170) cc_final: 0.7330 (m170) REVERT: C 711 MET cc_start: 0.6228 (mmt) cc_final: 0.5860 (mmt) REVERT: C 725 GLU cc_start: 0.7574 (tt0) cc_final: 0.7038 (tp30) REVERT: C 731 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7513 (ttmm) REVERT: C 744 ARG cc_start: 0.8374 (ttm170) cc_final: 0.7527 (tpt-90) outliers start: 97 outliers final: 69 residues processed: 548 average time/residue: 0.3289 time to fit residues: 254.1096 Evaluate side-chains 569 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 490 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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 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 175 SER 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 231 ILE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 500 CYS 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 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 974 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 187 CYS 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 288 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 436 LEU 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 613 PHE 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 729 GLN Chi-restraints excluded: chain C residue 735 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 184 optimal weight: 0.0010 chunk 112 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 chunk 177 optimal weight: 0.0170 chunk 153 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.4624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 15761 Z= 0.287 Angle : 0.973 59.199 21287 Z= 0.527 Chirality : 0.047 0.522 2490 Planarity : 0.006 0.116 2711 Dihedral : 6.242 58.392 2130 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.37 % Favored : 90.37 % Rotamer: Outliers : 4.91 % Allowed : 34.80 % Favored : 60.30 % 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: -0.28 (0.19), residues: 1942 helix: 1.02 (0.14), residues: 1338 sheet: -0.60 (1.43), residues: 13 loop : -3.13 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 933 HIS 0.010 0.001 HIS A 847 PHE 0.032 0.002 PHE A 395 TYR 0.029 0.002 TYR C 431 ARG 0.033 0.001 ARG C 629 ********************** 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 570 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 484 time to evaluate : 1.893 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 15 MET cc_start: 0.7443 (mtt) cc_final: 0.6807 (mtt) REVERT: A 59 ASP cc_start: 0.4124 (p0) cc_final: 0.3786 (p0) REVERT: A 67 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6871 (mm) REVERT: A 78 LYS cc_start: 0.7817 (mmmt) cc_final: 0.7445 (tppt) REVERT: A 155 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7336 (mm) REVERT: A 164 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6994 (mpp80) REVERT: A 261 ASN cc_start: 0.8327 (t0) cc_final: 0.7903 (t0) REVERT: A 284 LYS cc_start: 0.6829 (mmtm) cc_final: 0.6361 (tppt) REVERT: A 380 ILE cc_start: 0.8421 (mm) cc_final: 0.8047 (mt) REVERT: A 403 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8157 (mmmt) REVERT: A 439 LEU cc_start: 0.7387 (mm) cc_final: 0.7087 (mt) REVERT: A 482 PHE cc_start: 0.7592 (t80) cc_final: 0.7345 (t80) REVERT: A 527 CYS cc_start: 0.6891 (m) cc_final: 0.6465 (t) REVERT: A 580 ASP cc_start: 0.6645 (OUTLIER) cc_final: 0.6305 (t70) REVERT: A 590 ILE cc_start: 0.8448 (mm) cc_final: 0.7952 (mm) REVERT: A 593 MET cc_start: 0.6847 (tpp) cc_final: 0.6292 (tpp) REVERT: A 633 THR cc_start: 0.7332 (m) cc_final: 0.7026 (p) REVERT: A 647 VAL cc_start: 0.7745 (m) cc_final: 0.7488 (p) REVERT: A 650 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 689 MET cc_start: 0.6912 (pmm) cc_final: 0.6065 (ptt) REVERT: A 703 GLU cc_start: 0.7155 (tp30) cc_final: 0.6766 (tp30) REVERT: A 778 MET cc_start: 0.7484 (tmm) cc_final: 0.7045 (tmm) REVERT: A 826 LYS cc_start: 0.7750 (tptp) cc_final: 0.7352 (tptp) REVERT: A 842 LEU cc_start: 0.7849 (tp) cc_final: 0.7527 (tp) REVERT: A 854 GLN cc_start: 0.7091 (pp30) cc_final: 0.6524 (pp30) REVERT: A 938 LYS cc_start: 0.8256 (tppp) cc_final: 0.7866 (tppp) REVERT: A 953 GLU cc_start: 0.5414 (mm-30) cc_final: 0.5017 (mm-30) REVERT: A 1004 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5586 (tt) REVERT: A 1109 VAL cc_start: 0.7705 (m) cc_final: 0.7298 (p) REVERT: A 1120 LYS cc_start: 0.7324 (mmtm) cc_final: 0.6892 (mmmm) REVERT: A 1156 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7692 (mmpt) REVERT: A 1165 GLU cc_start: 0.6912 (tp30) cc_final: 0.6242 (tp30) REVERT: A 1169 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7612 (mm-40) REVERT: A 1171 GLU cc_start: 0.7642 (tp30) cc_final: 0.7167 (tp30) REVERT: C 42 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7527 (tm-30) REVERT: C 45 GLN cc_start: 0.7633 (tt0) cc_final: 0.7301 (tm-30) REVERT: C 59 ARG cc_start: 0.6977 (ttp-170) cc_final: 0.6613 (ttp-170) REVERT: C 91 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7218 (tm-30) REVERT: C 176 GLU cc_start: 0.6169 (tm-30) cc_final: 0.5820 (tm-30) REVERT: C 184 ARG cc_start: 0.7078 (ttt180) cc_final: 0.6712 (ttm-80) REVERT: C 188 GLN cc_start: 0.7301 (mt0) cc_final: 0.7076 (mm-40) REVERT: C 218 GLN cc_start: 0.7788 (tt0) cc_final: 0.7496 (tt0) REVERT: C 228 ASN cc_start: 0.5366 (OUTLIER) cc_final: 0.5034 (m-40) REVERT: C 236 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7531 (ttpt) REVERT: C 238 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 267 GLU cc_start: 0.7443 (tp30) cc_final: 0.7014 (tp30) REVERT: C 288 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8621 (mt) REVERT: C 289 LYS cc_start: 0.8194 (tppt) cc_final: 0.7970 (tppt) REVERT: C 313 MET cc_start: 0.7766 (ttm) cc_final: 0.7403 (ttm) REVERT: C 326 LYS cc_start: 0.7202 (mmmt) cc_final: 0.6934 (mmtm) REVERT: C 354 ARG cc_start: 0.7482 (ttp80) cc_final: 0.7009 (ttp80) REVERT: C 393 ASP cc_start: 0.7270 (t0) cc_final: 0.7058 (t70) REVERT: C 410 THR cc_start: 0.8224 (t) cc_final: 0.7996 (p) REVERT: C 416 MET cc_start: 0.8140 (mmm) cc_final: 0.7783 (mmm) REVERT: C 422 MET cc_start: 0.8759 (ttp) cc_final: 0.8547 (ttm) REVERT: C 424 GLU cc_start: 0.7582 (mp0) cc_final: 0.7186 (mp0) REVERT: C 429 GLU cc_start: 0.7725 (tt0) cc_final: 0.7489 (tt0) REVERT: C 444 LYS cc_start: 0.6545 (OUTLIER) cc_final: 0.6334 (tptp) REVERT: C 454 MET cc_start: 0.8089 (mmm) cc_final: 0.7801 (tpt) REVERT: C 469 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8293 (mmtp) REVERT: C 473 MET cc_start: 0.8259 (ttt) cc_final: 0.7155 (tpp) REVERT: C 513 TRP cc_start: 0.7830 (m100) cc_final: 0.7031 (m100) REVERT: C 533 GLU cc_start: 0.8006 (tp30) cc_final: 0.7421 (tp30) REVERT: C 673 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.7095 (mmtt) REVERT: C 689 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7514 (ptpt) REVERT: C 690 GLU cc_start: 0.7113 (pp20) cc_final: 0.6517 (pp20) REVERT: C 693 GLN cc_start: 0.7988 (pp30) cc_final: 0.7372 (pp30) REVERT: C 697 ASP cc_start: 0.7724 (m-30) cc_final: 0.7383 (m-30) REVERT: C 700 LYS cc_start: 0.8240 (mttt) cc_final: 0.7236 (mttt) REVERT: C 701 HIS cc_start: 0.7798 (m170) cc_final: 0.7322 (m170) REVERT: C 711 MET cc_start: 0.6226 (mmt) cc_final: 0.5856 (mmt) REVERT: C 725 GLU cc_start: 0.7572 (tt0) cc_final: 0.7051 (tp30) REVERT: C 731 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7521 (ttmm) REVERT: C 744 ARG cc_start: 0.8364 (ttm170) cc_final: 0.7526 (tpt-90) outliers start: 86 outliers final: 72 residues processed: 535 average time/residue: 0.3338 time to fit residues: 251.2192 Evaluate side-chains 567 residues out of total 1759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 484 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 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 151 GLN Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 386 ARG 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 500 CYS 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 773 MET 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 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 974 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1013 LYS Chi-restraints excluded: chain A residue 1052 LEU Chi-restraints excluded: chain A residue 1060 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 436 LEU 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 613 PHE 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 729 GLN Chi-restraints excluded: chain C residue 735 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.3980 chunk 47 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 154 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 158 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.0870 chunk 135 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 847 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.145631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.122999 restraints weight = 32056.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.127147 restraints weight = 17235.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.129891 restraints weight = 10794.894| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 15761 Z= 0.287 Angle : 0.973 59.199 21287 Z= 0.527 Chirality : 0.047 0.522 2490 Planarity : 0.006 0.116 2711 Dihedral : 6.168 58.392 2128 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.37 % Favored : 90.37 % Rotamer: Outliers : 4.79 % Allowed : 34.97 % Favored : 60.24 % 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: -0.28 (0.19), residues: 1942 helix: 1.02 (0.14), residues: 1338 sheet: -0.60 (1.43), residues: 13 loop : -3.13 (0.22), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 933 HIS 0.010 0.001 HIS A 847 PHE 0.032 0.002 PHE A 395 TYR 0.029 0.002 TYR C 431 ARG 0.033 0.001 ARG C 629 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4613.25 seconds wall clock time: 84 minutes 54.02 seconds (5094.02 seconds total)