Starting phenix.real_space_refine on Sun Oct 25 11:28:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sri_55141/10_2026/9sri_55141.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sri_55141/10_2026/9sri_55141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sri_55141/10_2026/9sri_55141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sri_55141/10_2026/9sri_55141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sri_55141/10_2026/9sri_55141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sri_55141/10_2026/9sri_55141.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.102 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 50 5.49 5 S 102 5.16 5 C 10170 2.51 5 N 2753 2.21 5 O 3227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16306 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9277 Classifications: {'peptide': 1140} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1081} Chain breaks: 1 Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "C" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "D" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1998 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain: "P" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 450 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "T" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 575 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4827 SG CYS A 651 76.644 77.954 53.803 1.00 32.27 S ATOM 4843 SG CYS A 654 79.687 79.246 48.100 1.00 30.77 S ATOM 5633 SG CYS A 747 73.410 77.299 48.354 1.00 20.22 S ATOM 4909 SG CYS A 663 74.321 82.559 49.853 1.00 27.89 S Time building chain proxies: 3.52, per 1000 atoms: 0.22 Number of scatterers: 16306 At special positions: 0 Unit cell: (109.225, 111.826, 150.835, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 102 16.00 P 50 15.00 O 3227 8.00 N 2753 7.00 C 10170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 661.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 654 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 663 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 747 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 651 " Number of angles added : 12 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 21 sheets defined 38.3% alpha, 25.7% beta 23 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 27 through 48 removed outlier: 4.081A pdb=" N ARG A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ARG A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 removed outlier: 3.744A pdb=" N LYS A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 159 through 180 Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.684A pdb=" N LEU A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 233 " --> pdb=" O HIS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.617A pdb=" N GLN A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.860A pdb=" N TRP A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 432 removed outlier: 3.765A pdb=" N LYS A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.824A pdb=" N MET A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N CYS A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR A 449 " --> pdb=" O CYS A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 482 removed outlier: 4.227A pdb=" N LEU A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 473 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N HIS A 475 " --> pdb=" O MET A 471 " (cutoff:3.500A) Proline residue: A 476 - end of helix Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.809A pdb=" N LEU A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 513 Processing helix chain 'A' and resid 563 through 572 removed outlier: 3.706A pdb=" N PHE A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 585 removed outlier: 3.549A pdb=" N GLU A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 595 through 613 removed outlier: 3.787A pdb=" N VAL A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU A 602 " --> pdb=" O GLU A 598 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.513A pdb=" N ASN A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 4.103A pdb=" N MET A 645 " --> pdb=" O PRO A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 652 Processing helix chain 'A' and resid 680 through 691 removed outlier: 3.945A pdb=" N ILE A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 710 removed outlier: 3.562A pdb=" N LEU A 710 " --> pdb=" O PHE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 731 removed outlier: 3.512A pdb=" N LYS A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 786 removed outlier: 3.601A pdb=" N TYR A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 784 " --> pdb=" O SER A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 821 removed outlier: 3.863A pdb=" N ARG A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 814 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 821 " --> pdb=" O GLY A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 854 removed outlier: 3.700A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 835 " --> pdb=" O MET A 831 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 905 removed outlier: 3.550A pdb=" N MET A 900 " --> pdb=" O MET A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 993 removed outlier: 3.657A pdb=" N LYS A 983 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 990 " --> pdb=" O GLN A 986 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU A 991 " --> pdb=" O SER A 987 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A 992 " --> pdb=" O SER A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1019 removed outlier: 3.829A pdb=" N TYR A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LYS A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A1010 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP A1015 " --> pdb=" O ASP A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1034 Processing helix chain 'A' and resid 1042 through 1047 removed outlier: 3.686A pdb=" N TYR A1046 " --> pdb=" O LYS A1042 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A1047 " --> pdb=" O LEU A1043 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1042 through 1047' Processing helix chain 'A' and resid 1051 through 1065 Processing helix chain 'A' and resid 1066 through 1070 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1102 through 1115 Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.570A pdb=" N TYR A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1164 through 1175 Processing helix chain 'A' and resid 1182 through 1186 Processing helix chain 'B' and resid 9 through 23 removed outlier: 4.711A pdb=" N ASP B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 190 through 194 removed outlier: 3.742A pdb=" N ALA B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 removed outlier: 3.849A pdb=" N PHE B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'C' and resid 9 through 18 removed outlier: 3.562A pdb=" N LYS C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.562A pdb=" N PHE C 57 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 151 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 209 through 216 removed outlier: 4.091A pdb=" N PHE C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 Proline residue: C 220 - end of helix No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'D' and resid 8 through 20 removed outlier: 4.356A pdb=" N LEU D 12 " --> pdb=" O GLN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 140 through 151 removed outlier: 3.984A pdb=" N ARG D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 190 through 194 removed outlier: 3.720A pdb=" N ALA D 194 " --> pdb=" O GLU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 removed outlier: 3.607A pdb=" N PHE D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Proline residue: D 220 - end of helix No H-bonds generated for 'chain 'D' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 99 removed outlier: 3.613A pdb=" N ASN A 65 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A 87 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU A 63 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 57 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 136 removed outlier: 7.426A pdb=" N ASN A 151 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N THR A 108 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.607A pdb=" N GLY A 304 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N PHE A 335 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 306 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLU A 337 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR A 308 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET A 294 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 272 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET A 359 " --> pdb=" O MET A 405 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 3.541A pdb=" N GLN A 390 " --> pdb=" O LYS A 398 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 533 through 539 removed outlier: 4.171A pdb=" N VAL A 533 " --> pdb=" O MET A 676 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU A 674 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU A 537 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARG A 672 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR A 539 " --> pdb=" O GLN A 670 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N GLN A 670 " --> pdb=" O TYR A 539 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET A 667 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 546 removed outlier: 6.536A pdb=" N VAL A 867 " --> pdb=" O PRO A 856 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE A 622 " --> pdb=" O PRO A 936 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.632A pdb=" N ALA A 939 " --> pdb=" O PHE A 959 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AA9, first strand: chain 'A' and resid 876 through 879 Processing sheet with id=AB1, first strand: chain 'A' and resid 907 through 913 removed outlier: 5.779A pdb=" N ASP A 908 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLU A 926 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1035 through 1039 Processing sheet with id=AB3, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id=AB4, first strand: chain 'A' and resid 1189 through 1195 removed outlier: 3.550A pdb=" N GLY A1191 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 59 through 62 removed outlier: 3.772A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 88 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 111 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 66 through 71 removed outlier: 3.657A pdb=" N LEU B 66 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N SER B 230 " --> pdb=" O PRO B 234 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 203 through 208 removed outlier: 3.652A pdb=" N VAL B 203 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR D 59 " --> pdb=" O ARG D 5 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 62 removed outlier: 3.777A pdb=" N THR C 59 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER D 172 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALA D 157 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 25 through 30 Processing sheet with id=AC1, first strand: chain 'C' and resid 36 through 40 removed outlier: 3.787A pdb=" N LEU C 37 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.601A pdb=" N ASN D 36 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET D 68 " --> pdb=" O TRP D 28 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.731A pdb=" N VAL D 136 " --> pdb=" O GLU D 198 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 7029 1.43 - 1.64: 9529 1.64 - 1.85: 158 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 16728 Sorted by residual: bond pdb=" C3' DA T -3 " pdb=" C2' DA T -3 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.70e+01 bond pdb=" C3' DT P 10 " pdb=" C2' DT P 10 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DC P 16 " pdb=" C2' DC P 16 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DC P 12 " pdb=" C2' DC P 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DC P 11 " pdb=" C2' DC P 11 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 16723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 21941 1.43 - 2.87: 722 2.87 - 4.30: 106 4.30 - 5.73: 48 5.73 - 7.16: 2 Bond angle restraints: 22819 Sorted by residual: angle pdb=" O4' DA P 15 " pdb=" C1' DA P 15 " pdb=" N9 DA P 15 " ideal model delta sigma weight residual 108.00 104.93 3.07 7.00e-01 2.04e+00 1.92e+01 angle pdb=" O4' DG T 23 " pdb=" C4' DG T 23 " pdb=" C3' DG T 23 " ideal model delta sigma weight residual 106.00 103.47 2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT T 10 " pdb=" C4 DT T 10 " pdb=" O4 DT T 10 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT P 10 " pdb=" C4 DT P 10 " pdb=" O4 DT P 10 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT T 3 " pdb=" C4 DT T 3 " pdb=" O4 DT T 3 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 22814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 8964 17.72 - 35.43: 778 35.43 - 53.15: 257 53.15 - 70.86: 74 70.86 - 88.58: 17 Dihedral angle restraints: 10090 sinusoidal: 4454 harmonic: 5636 Sorted by residual: dihedral pdb=" CA SER A 615 " pdb=" C SER A 615 " pdb=" N ARG A 616 " pdb=" CA ARG A 616 " ideal model delta harmonic sigma weight residual 180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE C 197 " pdb=" C ILE C 197 " pdb=" N GLU C 198 " pdb=" CA GLU C 198 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA TRP D 28 " pdb=" C TRP D 28 " pdb=" N ASP D 29 " pdb=" CA ASP D 29 " ideal model delta harmonic sigma weight residual 180.00 153.58 26.42 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 10087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.215: 2542 4.215 - 8.430: 0 8.430 - 12.645: 0 12.645 - 16.861: 0 16.861 - 21.076: 4 Chirality restraints: 2546 Sorted by residual: chirality pdb="FE1 SF4 A1301 " pdb=" S2 SF4 A1301 " pdb=" S3 SF4 A1301 " pdb=" S4 SF4 A1301 " both_signs ideal model delta sigma weight residual False -10.55 10.52 -21.08 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4 A1301 " pdb=" S1 SF4 A1301 " pdb=" S2 SF4 A1301 " pdb=" S4 SF4 A1301 " both_signs ideal model delta sigma weight residual False -10.55 10.52 -21.07 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE2 SF4 A1301 " pdb=" S1 SF4 A1301 " pdb=" S3 SF4 A1301 " pdb=" S4 SF4 A1301 " both_signs ideal model delta sigma weight residual False 10.55 -10.50 21.05 2.00e-01 2.50e+01 1.11e+04 ... (remaining 2543 not shown) Planarity restraints: 2768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT P 10 " -0.037 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" N1 DT P 10 " 0.064 2.00e-02 2.50e+03 pdb=" C2 DT P 10 " -0.020 2.00e-02 2.50e+03 pdb=" O2 DT P 10 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT P 10 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT P 10 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT P 10 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DT P 10 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT P 10 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT P 10 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 163 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C ALA D 163 " -0.062 2.00e-02 2.50e+03 pdb=" O ALA D 163 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS D 164 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT P 9 " -0.036 2.00e-02 2.50e+03 2.21e-02 1.22e+01 pdb=" N1 DT P 9 " 0.058 2.00e-02 2.50e+03 pdb=" C2 DT P 9 " -0.011 2.00e-02 2.50e+03 pdb=" O2 DT P 9 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT P 9 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT P 9 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT P 9 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DT P 9 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT P 9 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DT P 9 " 0.000 2.00e-02 2.50e+03 ... (remaining 2765 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3707 2.80 - 3.32: 15073 3.32 - 3.85: 24775 3.85 - 4.37: 29731 4.37 - 4.90: 50595 Nonbonded interactions: 123881 Sorted by model distance: nonbonded pdb=" OE2 GLU A 137 " pdb=" NZ LYS A 149 " model vdw 2.269 3.120 nonbonded pdb=" OG1 THR A 528 " pdb=" OD1 ASP A 530 " model vdw 2.316 3.040 nonbonded pdb=" O ALA A 480 " pdb=" OG1 THR A 483 " model vdw 2.328 3.040 nonbonded pdb=" NH1 ARG C 64 " pdb=" OD2 ASP C 94 " model vdw 2.329 3.120 nonbonded pdb=" OD1 ASP C 41 " pdb=" N SER C 42 " model vdw 2.331 3.120 ... (remaining 123876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and resid 1 through 258) selection = chain 'C' selection = (chain 'D' and resid 1 through 258) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.630 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16732 Z= 0.230 Angle : 0.725 31.117 22831 Z= 0.415 Chirality : 0.836 21.076 2546 Planarity : 0.008 0.107 2768 Dihedral : 15.953 88.576 6436 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.12 % Allowed : 3.84 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.18), residues: 1908 helix: -2.02 (0.17), residues: 593 sheet: 0.79 (0.21), residues: 556 loop : -0.26 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG A1059 TYR 0.033 0.005 TYR A 470 PHE 0.014 0.002 PHE A1063 TRP 0.024 0.003 TRP A 671 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.23 (16728) covalent geometry : angle 0.64988 / 0.41 (22819) hydrogen bonds : bond 0.11842 / 7.84 ( 819) hydrogen bonds : angle 6.37223 / 4.42 ( 2229) metal coordination : bond 0.02393 / 1.22 ( 4) metal coordination : angle 14.02987 / 7.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 378 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 GLU cc_start: 0.6782 (tt0) cc_final: 0.6519 (tt0) REVERT: A 383 MET cc_start: 0.8049 (tpp) cc_final: 0.7564 (tpp) REVERT: A 443 ASP cc_start: 0.6830 (m-30) cc_final: 0.6551 (m-30) REVERT: A 586 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5489 (mm-30) REVERT: A 860 ASP cc_start: 0.7621 (t0) cc_final: 0.7377 (t0) REVERT: A 878 PHE cc_start: 0.8182 (m-80) cc_final: 0.7865 (m-10) REVERT: A 896 MET cc_start: 0.7593 (tmm) cc_final: 0.6966 (ttp) REVERT: C 256 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7029 (mp0) REVERT: D 81 CYS cc_start: 0.7173 (m) cc_final: 0.6283 (m) REVERT: D 119 MET cc_start: 0.7446 (ptp) cc_final: 0.7218 (ptp) outliers start: 2 outliers final: 0 residues processed: 379 average time/residue: 0.1548 time to fit residues: 81.6619 Evaluate side-chains 184 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN A 217 ASN A 342 HIS A 345 GLN A 390 GLN A 394 GLN A 592 GLN A1175 ASN B 213 ASN C 38 GLN C 213 ASN D 131 GLN D 177 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.128025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097303 restraints weight = 27364.876| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.07 r_work: 0.3234 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.274 16732 Z= 0.307 Angle : 1.565 50.718 22831 Z= 0.885 Chirality : 0.255 6.437 2546 Planarity : 0.005 0.059 2768 Dihedral : 15.636 79.586 2615 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.07 % Allowed : 10.17 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1908 helix: -0.28 (0.20), residues: 583 sheet: 0.73 (0.21), residues: 580 loop : -0.08 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 109 TYR 0.020 0.002 TYR D 211 PHE 0.022 0.002 PHE A 94 TRP 0.023 0.002 TRP A 671 HIS 0.005 0.001 HIS A1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.31 (16728) covalent geometry : angle 1.38456 / 0.88 (22819) hydrogen bonds : bond 0.05358 / 3.54 ( 819) hydrogen bonds : angle 5.28452 / 3.64 ( 2229) metal coordination : bond 0.04621 / 2.28 ( 4) metal coordination : angle 31.84195 / 19.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.621 Fit side-chains REVERT: A 51 GLU cc_start: 0.7760 (pp20) cc_final: 0.7530 (pp20) REVERT: A 169 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7699 (tm-30) REVERT: A 223 GLU cc_start: 0.7584 (tt0) cc_final: 0.7223 (tt0) REVERT: A 444 MET cc_start: 0.7938 (mtm) cc_final: 0.7733 (mtm) REVERT: A 447 MET cc_start: 0.8177 (mmt) cc_final: 0.7741 (mmm) REVERT: A 878 PHE cc_start: 0.8679 (m-80) cc_final: 0.8234 (m-10) REVERT: A 896 MET cc_start: 0.8591 (tmm) cc_final: 0.8274 (ttp) REVERT: A 1067 GLN cc_start: 0.8404 (mp10) cc_final: 0.8104 (mp10) REVERT: A 1068 MET cc_start: 0.8541 (mmm) cc_final: 0.8274 (mmm) REVERT: B 1 MET cc_start: 0.4990 (mtp) cc_final: 0.4201 (ppp) REVERT: B 150 ASP cc_start: 0.8743 (m-30) cc_final: 0.7957 (t0) REVERT: B 164 LYS cc_start: 0.4859 (mmtm) cc_final: 0.3817 (mmmt) REVERT: B 199 MET cc_start: 0.6611 (ttp) cc_final: 0.6126 (ttp) REVERT: C 1 MET cc_start: 0.5235 (ttm) cc_final: 0.4991 (ttm) REVERT: C 2 PHE cc_start: 0.7892 (t80) cc_final: 0.7443 (t80) REVERT: C 256 GLU cc_start: 0.7569 (mm-30) cc_final: 0.6835 (mp0) REVERT: D 81 CYS cc_start: 0.8068 (m) cc_final: 0.6641 (m) REVERT: D 121 LEU cc_start: 0.7322 (tp) cc_final: 0.7028 (tp) outliers start: 35 outliers final: 16 residues processed: 222 average time/residue: 0.1392 time to fit residues: 45.3090 Evaluate side-chains 190 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 170 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [94, 75, 164, 128, 34, 73, 172, 30, 105, 26, 184] chunk 94 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 164 optimal weight: 5.9990 chunk 128 optimal weight: 0.0570 chunk 34 optimal weight: 0.0570 chunk 73 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 HIS B 8 GLN B 184 GLN D 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100228 restraints weight = 27372.235| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.11 r_work: 0.3279 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.249 16732 Z= 0.244 Angle : 1.515 50.561 22831 Z= 0.862 Chirality : 0.253 6.332 2546 Planarity : 0.004 0.056 2768 Dihedral : 15.306 76.180 2615 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.77 % Allowed : 12.35 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.19), residues: 1908 helix: 0.39 (0.21), residues: 586 sheet: 0.94 (0.21), residues: 574 loop : 0.07 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 91 TYR 0.014 0.001 TYR A 244 PHE 0.017 0.001 PHE A1030 TRP 0.019 0.001 TRP A 671 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.24 (16728) covalent geometry : angle 1.33003 / 0.86 (22819) hydrogen bonds : bond 0.04160 / 2.77 ( 819) hydrogen bonds : angle 4.87501 / 3.34 ( 2229) metal coordination : bond 0.02879 / 1.43 ( 4) metal coordination : angle 31.63588 / 18.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7700 (pp20) cc_final: 0.7466 (pp20) REVERT: A 169 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7696 (tm-30) REVERT: A 447 MET cc_start: 0.7930 (mmt) cc_final: 0.7485 (mmm) REVERT: A 471 MET cc_start: 0.8770 (tpp) cc_final: 0.8498 (tpp) REVERT: A 666 LYS cc_start: 0.8660 (mttt) cc_final: 0.8277 (mtpp) REVERT: A 721 ARG cc_start: 0.8359 (tpp80) cc_final: 0.8128 (ttp80) REVERT: A 864 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7892 (pt) REVERT: A 878 PHE cc_start: 0.8753 (m-80) cc_final: 0.8412 (m-10) REVERT: A 880 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7974 (t) REVERT: A 1067 GLN cc_start: 0.8332 (mp10) cc_final: 0.8079 (mp10) REVERT: B 1 MET cc_start: 0.4873 (mtp) cc_final: 0.4170 (ppp) REVERT: B 150 ASP cc_start: 0.8748 (m-30) cc_final: 0.8160 (t0) REVERT: B 164 LYS cc_start: 0.4893 (mmtm) cc_final: 0.3830 (mmmt) REVERT: B 199 MET cc_start: 0.6611 (ttp) cc_final: 0.6075 (ttp) REVERT: C 2 PHE cc_start: 0.7809 (t80) cc_final: 0.7339 (t80) REVERT: C 199 MET cc_start: 0.7307 (tmm) cc_final: 0.7013 (ttp) REVERT: C 256 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6852 (mp0) REVERT: D 30 ILE cc_start: 0.8737 (mm) cc_final: 0.8101 (mt) REVERT: D 121 LEU cc_start: 0.7417 (tp) cc_final: 0.7085 (tp) REVERT: D 159 VAL cc_start: 0.9137 (p) cc_final: 0.8928 (t) REVERT: D 174 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7587 (tm-30) REVERT: D 250 TYR cc_start: 0.8087 (m-80) cc_final: 0.7709 (m-80) outliers start: 30 outliers final: 16 residues processed: 226 average time/residue: 0.1382 time to fit residues: 45.8201 Evaluate side-chains 197 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain D residue 147 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [17, 134, 75, 143, 46, 167, 177, 148, 61, 141, 50] chunk 17 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 141 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN B 125 GLN B 131 GLN D 8 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098324 restraints weight = 27444.083| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.09 r_work: 0.3252 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 16732 Z= 0.257 Angle : 1.514 50.578 22831 Z= 0.862 Chirality : 0.254 6.346 2546 Planarity : 0.004 0.056 2768 Dihedral : 15.241 75.524 2615 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.48 % Allowed : 12.88 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1908 helix: 0.62 (0.22), residues: 584 sheet: 0.95 (0.22), residues: 567 loop : 0.05 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 178 TYR 0.018 0.002 TYR D 133 PHE 0.040 0.002 PHE D 215 TRP 0.016 0.001 TRP A 671 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.26 (16728) covalent geometry : angle 1.33115 / 0.86 (22819) hydrogen bonds : bond 0.04282 / 2.84 ( 819) hydrogen bonds : angle 4.78931 / 3.29 ( 2229) metal coordination : bond 0.01832 / 0.92 ( 4) metal coordination : angle 31.52422 / 18.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7842 (pp20) cc_final: 0.7539 (pp20) REVERT: A 169 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7803 (tm-30) REVERT: A 244 TYR cc_start: 0.8913 (m-80) cc_final: 0.8346 (m-80) REVERT: A 295 MET cc_start: 0.8226 (mtm) cc_final: 0.7875 (mtt) REVERT: A 383 MET cc_start: 0.8276 (ttm) cc_final: 0.7621 (ttm) REVERT: A 447 MET cc_start: 0.7887 (mmt) cc_final: 0.7392 (mmm) REVERT: A 471 MET cc_start: 0.8771 (tpp) cc_final: 0.8486 (tpp) REVERT: A 666 LYS cc_start: 0.8681 (mttt) cc_final: 0.8339 (mtpp) REVERT: A 864 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7836 (pt) REVERT: A 878 PHE cc_start: 0.8711 (m-80) cc_final: 0.8298 (m-10) REVERT: A 880 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.8079 (t) REVERT: A 1067 GLN cc_start: 0.8391 (mp10) cc_final: 0.8122 (mp10) REVERT: B 1 MET cc_start: 0.4842 (mtp) cc_final: 0.3870 (ppp) REVERT: B 149 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8054 (ttp-110) REVERT: B 164 LYS cc_start: 0.4993 (mmtm) cc_final: 0.3767 (mmmt) REVERT: B 199 MET cc_start: 0.6645 (ttp) cc_final: 0.6109 (ttp) REVERT: C 2 PHE cc_start: 0.7920 (t80) cc_final: 0.7430 (t80) REVERT: C 256 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6900 (mp0) REVERT: D 30 ILE cc_start: 0.8596 (mm) cc_final: 0.8065 (mt) REVERT: D 121 LEU cc_start: 0.7514 (tp) cc_final: 0.7182 (tp) REVERT: D 174 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7602 (tm-30) REVERT: D 177 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7462 (t0) REVERT: D 199 MET cc_start: 0.7189 (tpp) cc_final: 0.6880 (tpp) REVERT: D 250 TYR cc_start: 0.8201 (m-80) cc_final: 0.7750 (m-10) outliers start: 42 outliers final: 28 residues processed: 220 average time/residue: 0.1331 time to fit residues: 43.5256 Evaluate side-chains 206 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 820 MET Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 923 THR Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1188 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 177 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [80, 148, 50, 142, 67, 118, 122, 183, 152, 112, 119] chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 50 optimal weight: 0.0980 chunk 142 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 183 optimal weight: 0.4980 chunk 152 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS D 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.131353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.100446 restraints weight = 27122.633| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 3.11 r_work: 0.3287 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.245 16732 Z= 0.238 Angle : 1.499 50.603 22831 Z= 0.854 Chirality : 0.253 6.315 2546 Planarity : 0.004 0.052 2768 Dihedral : 15.110 73.158 2615 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.07 % Allowed : 14.01 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1908 helix: 0.88 (0.22), residues: 585 sheet: 1.07 (0.22), residues: 558 loop : 0.01 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 178 TYR 0.015 0.001 TYR D 211 PHE 0.044 0.001 PHE D 215 TRP 0.014 0.001 TRP A 671 HIS 0.002 0.000 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.24 (16728) covalent geometry : angle 1.31338 / 0.85 (22819) hydrogen bonds : bond 0.03681 / 2.44 ( 819) hydrogen bonds : angle 4.63479 / 3.20 ( 2229) metal coordination : bond 0.01522 / 0.76 ( 4) metal coordination : angle 31.49783 / 18.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7959 (pp20) cc_final: 0.7623 (pp20) REVERT: A 169 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 244 TYR cc_start: 0.8890 (m-80) cc_final: 0.8422 (m-80) REVERT: A 299 MET cc_start: 0.8900 (mtp) cc_final: 0.8501 (mtp) REVERT: A 383 MET cc_start: 0.8164 (ttm) cc_final: 0.7814 (ttm) REVERT: A 447 MET cc_start: 0.7751 (mmt) cc_final: 0.7283 (mmm) REVERT: A 471 MET cc_start: 0.8695 (tpp) cc_final: 0.8412 (tpp) REVERT: A 666 LYS cc_start: 0.8658 (mttt) cc_final: 0.8338 (mtpp) REVERT: A 722 ARG cc_start: 0.7916 (tpp80) cc_final: 0.7645 (tpp80) REVERT: A 864 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7902 (pt) REVERT: A 880 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.8080 (t) REVERT: A 1067 GLN cc_start: 0.8396 (mp10) cc_final: 0.8128 (mp10) REVERT: B 1 MET cc_start: 0.4342 (mtp) cc_final: 0.4071 (ppp) REVERT: B 149 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8324 (ttp-110) REVERT: B 164 LYS cc_start: 0.4862 (mmtm) cc_final: 0.3639 (mmmt) REVERT: C 1 MET cc_start: 0.4837 (ttm) cc_final: 0.4052 (ttp) REVERT: C 2 PHE cc_start: 0.7742 (t80) cc_final: 0.7289 (t80) REVERT: C 41 ASP cc_start: 0.7402 (t0) cc_final: 0.7114 (t70) REVERT: C 241 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7125 (tt) REVERT: C 256 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6809 (mp0) REVERT: D 30 ILE cc_start: 0.8585 (mm) cc_final: 0.8058 (mt) REVERT: D 121 LEU cc_start: 0.7510 (tp) cc_final: 0.7229 (tp) REVERT: D 174 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7600 (tm-30) REVERT: D 192 GLU cc_start: 0.7063 (pt0) cc_final: 0.6734 (pp20) REVERT: D 199 MET cc_start: 0.7142 (tpp) cc_final: 0.6889 (tpp) REVERT: D 250 TYR cc_start: 0.8099 (m-10) cc_final: 0.7858 (m-10) outliers start: 35 outliers final: 15 residues processed: 220 average time/residue: 0.1377 time to fit residues: 44.2367 Evaluate side-chains 190 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 147 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [23, 100, 24, 185, 191, 45, 3, 118, 149, 49, 186] chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 118 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.130553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099723 restraints weight = 27206.917| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.09 r_work: 0.3275 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 16732 Z= 0.243 Angle : 1.498 50.547 22831 Z= 0.854 Chirality : 0.253 6.334 2546 Planarity : 0.004 0.056 2768 Dihedral : 15.113 72.693 2615 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.13 % Allowed : 14.95 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.20), residues: 1908 helix: 0.99 (0.22), residues: 584 sheet: 1.05 (0.22), residues: 563 loop : -0.01 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 53 TYR 0.014 0.001 TYR D 211 PHE 0.034 0.001 PHE D 215 TRP 0.013 0.001 TRP A 671 HIS 0.003 0.001 HIS D 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.24 (16728) covalent geometry : angle 1.31346 / 0.85 (22819) hydrogen bonds : bond 0.03750 / 2.48 ( 819) hydrogen bonds : angle 4.58000 / 3.16 ( 2229) metal coordination : bond 0.01210 / 0.61 ( 4) metal coordination : angle 31.47607 / 18.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.556 Fit side-chains REVERT: A 51 GLU cc_start: 0.7987 (pp20) cc_final: 0.7629 (pp20) REVERT: A 169 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 244 TYR cc_start: 0.8884 (m-80) cc_final: 0.8379 (m-80) REVERT: A 299 MET cc_start: 0.8920 (mtp) cc_final: 0.8523 (mtp) REVERT: A 383 MET cc_start: 0.8248 (ttm) cc_final: 0.7607 (ttm) REVERT: A 447 MET cc_start: 0.7795 (mmt) cc_final: 0.7304 (mmm) REVERT: A 471 MET cc_start: 0.8744 (tpp) cc_final: 0.8512 (tpp) REVERT: A 666 LYS cc_start: 0.8722 (mttt) cc_final: 0.8378 (mtpp) REVERT: A 722 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7646 (tpp80) REVERT: A 864 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7834 (pt) REVERT: A 880 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8122 (t) REVERT: A 1067 GLN cc_start: 0.8361 (mp10) cc_final: 0.8097 (mp10) REVERT: A 1113 TRP cc_start: 0.7202 (m-10) cc_final: 0.6616 (m-10) REVERT: A 1171 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7606 (tt) REVERT: B 1 MET cc_start: 0.4257 (mtp) cc_final: 0.3923 (ppp) REVERT: B 164 LYS cc_start: 0.4919 (mmtm) cc_final: 0.3667 (mmmt) REVERT: C 1 MET cc_start: 0.4611 (ttm) cc_final: 0.3845 (ttp) REVERT: C 41 ASP cc_start: 0.7537 (t0) cc_final: 0.7291 (t70) REVERT: C 199 MET cc_start: 0.6786 (tmm) cc_final: 0.6073 (tmm) REVERT: C 241 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7176 (tt) REVERT: C 256 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6809 (mp0) REVERT: D 121 LEU cc_start: 0.7527 (tp) cc_final: 0.7251 (tp) REVERT: D 174 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7651 (tm-30) REVERT: D 192 GLU cc_start: 0.7134 (pt0) cc_final: 0.6776 (pp20) outliers start: 36 outliers final: 20 residues processed: 206 average time/residue: 0.1269 time to fit residues: 38.9494 Evaluate side-chains 198 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 147 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [175, 101, 125, 141, 179, 57, 44, 127, 48, 111, 156] chunk 175 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 735 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.130705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099761 restraints weight = 27183.798| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.10 r_work: 0.3276 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 16732 Z= 0.239 Angle : 1.495 50.547 22831 Z= 0.852 Chirality : 0.253 6.315 2546 Planarity : 0.004 0.053 2768 Dihedral : 15.042 71.754 2615 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.13 % Allowed : 15.43 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.20), residues: 1908 helix: 1.09 (0.22), residues: 584 sheet: 1.03 (0.22), residues: 561 loop : 0.02 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 178 TYR 0.012 0.001 TYR D 211 PHE 0.030 0.001 PHE D 215 TRP 0.012 0.001 TRP A 671 HIS 0.003 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00678 / 0.24 (16728) covalent geometry : angle 1.31010 / 0.85 (22819) hydrogen bonds : bond 0.03642 / 2.41 ( 819) hydrogen bonds : angle 4.52229 / 3.12 ( 2229) metal coordination : bond 0.01187 / 0.60 ( 4) metal coordination : angle 31.43772 / 18.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8009 (pp20) cc_final: 0.7642 (pp20) REVERT: A 169 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 215 LEU cc_start: 0.6884 (mt) cc_final: 0.6548 (tp) REVERT: A 244 TYR cc_start: 0.8853 (m-80) cc_final: 0.8372 (m-80) REVERT: A 299 MET cc_start: 0.8879 (mtp) cc_final: 0.8485 (mtp) REVERT: A 383 MET cc_start: 0.8279 (ttm) cc_final: 0.7651 (ttm) REVERT: A 447 MET cc_start: 0.7835 (mmt) cc_final: 0.7310 (mmm) REVERT: A 471 MET cc_start: 0.8808 (tpp) cc_final: 0.8495 (tpp) REVERT: A 666 LYS cc_start: 0.8749 (mttt) cc_final: 0.8409 (mtpp) REVERT: A 722 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7641 (tpp80) REVERT: A 864 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7830 (pt) REVERT: A 1028 GLU cc_start: 0.7689 (mp0) cc_final: 0.7443 (mp0) REVERT: A 1067 GLN cc_start: 0.8367 (mp10) cc_final: 0.8099 (mp10) REVERT: A 1113 TRP cc_start: 0.7158 (m-10) cc_final: 0.6521 (m-10) REVERT: A 1171 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7621 (tt) REVERT: B 1 MET cc_start: 0.4415 (mtp) cc_final: 0.4137 (ppp) REVERT: B 164 LYS cc_start: 0.4899 (mmtm) cc_final: 0.3660 (mmmt) REVERT: B 199 MET cc_start: 0.6572 (ttp) cc_final: 0.6232 (ttp) REVERT: C 1 MET cc_start: 0.4641 (ttm) cc_final: 0.3910 (ttp) REVERT: C 2 PHE cc_start: 0.7680 (t80) cc_final: 0.7287 (t80) REVERT: C 199 MET cc_start: 0.6761 (tmm) cc_final: 0.6053 (tmm) REVERT: C 241 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7170 (tt) REVERT: C 256 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6804 (mp0) REVERT: D 121 LEU cc_start: 0.7505 (tp) cc_final: 0.7289 (tp) REVERT: D 174 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7654 (tm-30) REVERT: D 192 GLU cc_start: 0.6990 (pt0) cc_final: 0.6606 (pp20) outliers start: 36 outliers final: 23 residues processed: 208 average time/residue: 0.1293 time to fit residues: 39.9987 Evaluate side-chains 203 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 162 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [9, 30, 77, 180, 112, 117, 132, 159, 55, 43, 129] chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 180 optimal weight: 6.9990 chunk 112 optimal weight: 0.2980 chunk 117 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.131597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100621 restraints weight = 27273.410| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.12 r_work: 0.3290 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 16732 Z= 0.236 Angle : 1.491 50.526 22831 Z= 0.850 Chirality : 0.253 6.308 2546 Planarity : 0.003 0.054 2768 Dihedral : 14.956 70.021 2615 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.07 % Allowed : 15.72 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1908 helix: 1.15 (0.22), residues: 594 sheet: 1.04 (0.22), residues: 568 loop : 0.02 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 91 TYR 0.012 0.001 TYR D 211 PHE 0.024 0.001 PHE D 215 TRP 0.013 0.001 TRP A 671 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.24 (16728) covalent geometry : angle 1.30621 / 0.85 (22819) hydrogen bonds : bond 0.03438 / 2.27 ( 819) hydrogen bonds : angle 4.44885 / 3.07 ( 2229) metal coordination : bond 0.01201 / 0.61 ( 4) metal coordination : angle 31.36800 / 18.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8031 (pp20) cc_final: 0.7656 (pp20) REVERT: A 169 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 215 LEU cc_start: 0.6943 (mt) cc_final: 0.6595 (tp) REVERT: A 244 TYR cc_start: 0.8758 (m-80) cc_final: 0.8345 (m-80) REVERT: A 383 MET cc_start: 0.8420 (ttm) cc_final: 0.7780 (ttt) REVERT: A 447 MET cc_start: 0.7823 (mmt) cc_final: 0.7299 (mmm) REVERT: A 471 MET cc_start: 0.8787 (tpp) cc_final: 0.8453 (tpp) REVERT: A 666 LYS cc_start: 0.8757 (mttt) cc_final: 0.8421 (mtpp) REVERT: A 864 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7775 (pt) REVERT: A 1067 GLN cc_start: 0.8328 (mp10) cc_final: 0.8068 (mp10) REVERT: A 1171 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7607 (tt) REVERT: B 1 MET cc_start: 0.4418 (mtp) cc_final: 0.4160 (ppp) REVERT: B 164 LYS cc_start: 0.4923 (mmtm) cc_final: 0.3692 (mmmt) REVERT: B 199 MET cc_start: 0.6427 (ttp) cc_final: 0.6173 (ttp) REVERT: C 1 MET cc_start: 0.4924 (ttm) cc_final: 0.4172 (ttp) REVERT: C 2 PHE cc_start: 0.7745 (t80) cc_final: 0.7382 (t80) REVERT: C 199 MET cc_start: 0.6642 (tmm) cc_final: 0.5977 (tmm) REVERT: C 241 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7077 (tt) REVERT: C 244 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6155 (mmp) REVERT: C 256 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6797 (mp0) REVERT: D 121 LEU cc_start: 0.7448 (tp) cc_final: 0.7225 (tp) REVERT: D 174 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7632 (tm-30) outliers start: 35 outliers final: 26 residues processed: 210 average time/residue: 0.1259 time to fit residues: 39.7058 Evaluate side-chains 202 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 651 CYS Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 162 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [83, 6, 37, 36, 82, 183, 153, 14, 58, 28, 165] chunk 83 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.131349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100332 restraints weight = 27412.764| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.12 r_work: 0.3285 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 16732 Z= 0.238 Angle : 1.493 50.536 22831 Z= 0.851 Chirality : 0.253 6.303 2546 Planarity : 0.004 0.070 2768 Dihedral : 14.930 69.195 2615 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.95 % Allowed : 16.13 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1908 helix: 1.23 (0.22), residues: 595 sheet: 1.00 (0.22), residues: 577 loop : 0.04 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 146 TYR 0.011 0.001 TYR D 249 PHE 0.017 0.001 PHE A1030 TRP 0.012 0.001 TRP A 671 HIS 0.003 0.001 HIS A 684 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.24 (16728) covalent geometry : angle 1.30878 / 0.85 (22819) hydrogen bonds : bond 0.03461 / 2.29 ( 819) hydrogen bonds : angle 4.43112 / 3.07 ( 2229) metal coordination : bond 0.01032 / 0.52 ( 4) metal coordination : angle 31.35248 / 18.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 39 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: A 51 GLU cc_start: 0.8045 (pp20) cc_final: 0.7688 (pp20) REVERT: A 169 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7783 (tm-30) REVERT: A 215 LEU cc_start: 0.6977 (mt) cc_final: 0.6644 (tp) REVERT: A 244 TYR cc_start: 0.8756 (m-80) cc_final: 0.8342 (m-80) REVERT: A 383 MET cc_start: 0.8404 (ttm) cc_final: 0.7757 (ttm) REVERT: A 447 MET cc_start: 0.7826 (mmt) cc_final: 0.7294 (mmm) REVERT: A 471 MET cc_start: 0.8789 (tpp) cc_final: 0.8438 (tpp) REVERT: A 666 LYS cc_start: 0.8791 (mttt) cc_final: 0.8433 (mtpp) REVERT: A 864 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7771 (pt) REVERT: A 1036 ASN cc_start: 0.8558 (t0) cc_final: 0.7864 (m110) REVERT: A 1067 GLN cc_start: 0.8236 (mp10) cc_final: 0.7979 (mp10) REVERT: A 1171 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7617 (tt) REVERT: B 1 MET cc_start: 0.4352 (mtp) cc_final: 0.4098 (ppp) REVERT: B 164 LYS cc_start: 0.4927 (mmtm) cc_final: 0.3691 (mmmt) REVERT: B 199 MET cc_start: 0.6432 (ttp) cc_final: 0.6183 (ttp) REVERT: C 1 MET cc_start: 0.5014 (ttm) cc_final: 0.4347 (ttp) REVERT: C 2 PHE cc_start: 0.7741 (t80) cc_final: 0.7388 (t80) REVERT: C 241 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7140 (tt) REVERT: C 256 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6787 (mp0) REVERT: D 121 LEU cc_start: 0.7440 (tp) cc_final: 0.7230 (tp) REVERT: D 174 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7642 (tm-30) outliers start: 33 outliers final: 24 residues processed: 196 average time/residue: 0.1223 time to fit residues: 36.3590 Evaluate side-chains 195 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 170 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [191, 168, 93, 156, 63, 190, 114, 152, 72, 153, 33] chunk 191 optimal weight: 20.0000 chunk 168 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 63 optimal weight: 0.0370 chunk 190 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098536 restraints weight = 27207.091| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.09 r_work: 0.3259 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 16732 Z= 0.257 Angle : 1.506 50.563 22831 Z= 0.857 Chirality : 0.253 6.308 2546 Planarity : 0.004 0.066 2768 Dihedral : 14.986 70.560 2615 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.83 % Allowed : 16.55 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1908 helix: 1.16 (0.22), residues: 595 sheet: 0.91 (0.22), residues: 580 loop : -0.02 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 146 TYR 0.016 0.001 TYR D 249 PHE 0.018 0.001 PHE A1030 TRP 0.011 0.001 TRP A 669 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.26 (16728) covalent geometry : angle 1.32268 / 0.85 (22819) hydrogen bonds : bond 0.03931 / 2.59 ( 819) hydrogen bonds : angle 4.54463 / 3.14 ( 2229) metal coordination : bond 0.01119 / 0.57 ( 4) metal coordination : angle 31.39257 / 18.41 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 39 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: A 51 GLU cc_start: 0.8041 (pp20) cc_final: 0.7677 (pp20) REVERT: A 169 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 215 LEU cc_start: 0.7079 (mt) cc_final: 0.6767 (tp) REVERT: A 244 TYR cc_start: 0.8829 (m-80) cc_final: 0.8315 (m-80) REVERT: A 383 MET cc_start: 0.8373 (ttm) cc_final: 0.7694 (ttm) REVERT: A 447 MET cc_start: 0.7800 (mmt) cc_final: 0.7268 (mmm) REVERT: A 471 MET cc_start: 0.8822 (tpp) cc_final: 0.8455 (tpp) REVERT: A 666 LYS cc_start: 0.8806 (mttt) cc_final: 0.8484 (mtpp) REVERT: A 1067 GLN cc_start: 0.8258 (mp10) cc_final: 0.7997 (mp10) REVERT: A 1171 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7633 (tt) REVERT: B 1 MET cc_start: 0.4402 (mtp) cc_final: 0.4119 (ppp) REVERT: B 164 LYS cc_start: 0.4828 (mmtm) cc_final: 0.3596 (mmmt) REVERT: B 199 MET cc_start: 0.6355 (ttp) cc_final: 0.6100 (ttp) REVERT: C 1 MET cc_start: 0.4909 (ttm) cc_final: 0.4249 (ttp) REVERT: C 2 PHE cc_start: 0.7890 (t80) cc_final: 0.7529 (t80) REVERT: C 199 MET cc_start: 0.7155 (tmm) cc_final: 0.6378 (tmm) REVERT: C 241 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7168 (tt) REVERT: C 256 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6802 (mp0) REVERT: D 117 LYS cc_start: 0.7444 (mttt) cc_final: 0.7038 (mmmm) REVERT: D 174 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7666 (tm-30) outliers start: 31 outliers final: 22 residues processed: 192 average time/residue: 0.1276 time to fit residues: 36.4083 Evaluate side-chains 193 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 536 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 794 CYS Chi-restraints excluded: chain A residue 866 CYS Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 162 CYS Chi-restraints excluded: chain D residue 170 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [14, 93, 150, 112, 175, 69, 49, 7, 184, 32, 190] chunk 14 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 184 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100020 restraints weight = 27366.108| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.12 r_work: 0.3282 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 16732 Z= 0.239 Angle : 1.495 50.546 22831 Z= 0.852 Chirality : 0.253 6.306 2546 Planarity : 0.004 0.066 2768 Dihedral : 14.945 69.471 2615 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.71 % Allowed : 16.78 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.20), residues: 1908 helix: 1.25 (0.22), residues: 593 sheet: 0.97 (0.22), residues: 580 loop : -0.03 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 146 TYR 0.010 0.001 TYR A 468 PHE 0.014 0.001 PHE A1030 TRP 0.012 0.001 TRP A 671 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.24 (16728) covalent geometry : angle 1.31175 / 0.85 (22819) hydrogen bonds : bond 0.03565 / 2.35 ( 819) hydrogen bonds : angle 4.47802 / 3.09 ( 2229) metal coordination : bond 0.01022 / 0.52 ( 4) metal coordination : angle 31.32780 / 18.34 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3245.20 seconds wall clock time: 56 minutes 32.23 seconds (3392.23 seconds total)