Starting phenix.real_space_refine on Sat Aug 8 05:23:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i23_35130/08_2026/8i23_35130.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i23_35130/08_2026/8i23_35130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i23_35130/08_2026/8i23_35130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i23_35130/08_2026/8i23_35130.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i23_35130/08_2026/8i23_35130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i23_35130/08_2026/8i23_35130.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8i23_35130/08_2026/8i23_35130.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i23_35130/08_2026/8i23_35130.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 108 5.49 5 Mg 1 5.21 5 S 83 5.16 5 C 16279 2.51 5 N 4556 2.21 5 O 5243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26272 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1775 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain: "B" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1745 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} Chain: "C" Number of atoms: 9115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9115 Classifications: {'peptide': 1164} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 54, 'TRANS': 1109} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 8980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1154, 8980 Classifications: {'peptide': 1154} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 47, 'TRANS': 1106} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "E" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 497 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "F" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1943 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 4, 'TRANS': 225} Chain: "O" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1182 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "P" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1032 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain breaks: 2 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18876 SG CYS D 817 109.213 57.244 86.156 1.00 37.71 S ATOM 19446 SG CYS D 891 105.695 57.511 87.748 1.00 34.53 S ATOM 19500 SG CYS D 898 107.314 60.409 85.893 1.00 35.01 S ATOM 19520 SG CYS D 901 106.002 57.199 84.069 1.00 32.73 S ATOM 13086 SG CYS D 83 80.924 101.953 127.598 1.00 48.89 S ATOM 13102 SG CYS D 85 78.928 102.489 130.809 1.00 51.61 S ATOM 13212 SG CYS D 98 82.761 103.219 130.825 1.00 50.27 S ATOM 13237 SG CYS D 101 81.362 99.753 130.366 1.00 49.64 S Time building chain proxies: 5.82, per 1000 atoms: 0.22 Number of scatterers: 26272 At special positions: 0 Unit cell: (132.08, 162.24, 176.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 83 16.00 P 108 15.00 Mg 1 11.99 O 5243 8.00 N 4556 7.00 C 16279 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: 2.15 Conformation dependent library (CDL) restraints added in 959.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1201 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 901 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1201 " - pdb=" SG CYS D 817 " pdb=" ZN D1202 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 101 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 83 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1202 " - pdb=" SG CYS D 98 " Number of angles added : 12 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5668 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 43 sheets defined 40.4% alpha, 15.7% beta 20 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 31 through 48 removed outlier: 4.165A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 205 through 231 removed outlier: 4.338A pdb=" N LEU A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASP A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 74 through 85 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 205 through 226 removed outlier: 3.940A pdb=" N ILE B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE B 224 " --> pdb=" O HIS B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 51 removed outlier: 3.678A pdb=" N LYS C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N PHE C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.830A pdb=" N LYS C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU C 82 " --> pdb=" O ASP C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 210 Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.757A pdb=" N THR C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 240 Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 267 through 278 Processing helix chain 'C' and resid 279 through 284 removed outlier: 3.567A pdb=" N ARG C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 284' Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.710A pdb=" N ILE C 317 " --> pdb=" O LYS C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 373 Processing helix chain 'C' and resid 377 through 393 removed outlier: 3.659A pdb=" N GLN C 386 " --> pdb=" O LYS C 382 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP C 390 " --> pdb=" O GLN C 386 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 412 removed outlier: 3.590A pdb=" N ILE C 402 " --> pdb=" O THR C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 432 through 456 removed outlier: 3.860A pdb=" N GLN C 438 " --> pdb=" O GLY C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 472 through 485 Processing helix chain 'C' and resid 496 through 504 Processing helix chain 'C' and resid 528 through 532 removed outlier: 3.686A pdb=" N TYR C 532 " --> pdb=" O HIS C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 4.393A pdb=" N ASN C 545 " --> pdb=" O GLU C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 655 through 666 Processing helix chain 'C' and resid 684 through 692 Processing helix chain 'C' and resid 784 through 786 No H-bonds generated for 'chain 'C' and resid 784 through 786' Processing helix chain 'C' and resid 793 through 798 Processing helix chain 'C' and resid 831 through 836 removed outlier: 3.815A pdb=" N LYS C 836 " --> pdb=" O ASP C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 879 removed outlier: 3.999A pdb=" N LEU C 874 " --> pdb=" O ALA C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 912 No H-bonds generated for 'chain 'C' and resid 910 through 912' Processing helix chain 'C' and resid 954 through 958 Processing helix chain 'C' and resid 974 through 979 removed outlier: 4.165A pdb=" N SER C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 998 Processing helix chain 'C' and resid 1010 through 1021 Processing helix chain 'C' and resid 1090 through 1093 Processing helix chain 'C' and resid 1094 through 1101 Processing helix chain 'C' and resid 1102 through 1112 removed outlier: 3.637A pdb=" N LEU C1106 " --> pdb=" O ALA C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1130 removed outlier: 3.842A pdb=" N VAL C1121 " --> pdb=" O VAL C1117 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1152 removed outlier: 3.677A pdb=" N LYS C1143 " --> pdb=" O PRO C1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 107 through 113 removed outlier: 3.833A pdb=" N VAL D 110 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 removed outlier: 4.186A pdb=" N GLY D 132 " --> pdb=" O TRP D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.522A pdb=" N LEU D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 174 through 185 removed outlier: 4.003A pdb=" N GLU D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 206 through 219 removed outlier: 3.746A pdb=" N LYS D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 241 Processing helix chain 'D' and resid 245 through 248 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 275 through 296 removed outlier: 3.720A pdb=" N ASP D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 296 " --> pdb=" O LYS D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 320 Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 348 through 353 Processing helix chain 'D' and resid 382 through 389 Processing helix chain 'D' and resid 389 through 399 Processing helix chain 'D' and resid 405 through 415 Processing helix chain 'D' and resid 419 through 428 removed outlier: 4.180A pdb=" N VAL D 423 " --> pdb=" O GLU D 419 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU D 426 " --> pdb=" O ASP D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 444 No H-bonds generated for 'chain 'D' and resid 442 through 444' Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 485 through 495 Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'D' and resid 516 through 527 Processing helix chain 'D' and resid 541 through 551 Processing helix chain 'D' and resid 581 through 587 Processing helix chain 'D' and resid 616 through 630 Processing helix chain 'D' and resid 633 through 654 removed outlier: 3.727A pdb=" N THR D 651 " --> pdb=" O PHE D 647 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS D 652 " --> pdb=" O LYS D 648 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY D 653 " --> pdb=" O TYR D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 662 Processing helix chain 'D' and resid 667 through 685 removed outlier: 3.585A pdb=" N GLN D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 718 removed outlier: 3.818A pdb=" N ILE D 716 " --> pdb=" O THR D 712 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN D 717 " --> pdb=" O ARG D 713 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 731 Processing helix chain 'D' and resid 736 through 740 Processing helix chain 'D' and resid 771 through 778 removed outlier: 3.674A pdb=" N SER D 778 " --> pdb=" O GLU D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 807 removed outlier: 3.585A pdb=" N ALA D 782 " --> pdb=" O SER D 778 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR D 789 " --> pdb=" O GLY D 785 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA D 790 " --> pdb=" O LEU D 786 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP D 795 " --> pdb=" O LEU D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 843 removed outlier: 3.567A pdb=" N ILE D 842 " --> pdb=" O LEU D 838 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 843 " --> pdb=" O SER D 839 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 838 through 843' Processing helix chain 'D' and resid 868 through 879 Processing helix chain 'D' and resid 887 through 891 removed outlier: 3.568A pdb=" N CYS D 891 " --> pdb=" O VAL D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 903 Processing helix chain 'D' and resid 919 through 928 Processing helix chain 'D' and resid 929 through 933 removed outlier: 3.579A pdb=" N LEU D 933 " --> pdb=" O GLY D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 951 through 961 Processing helix chain 'D' and resid 1028 through 1055 removed outlier: 7.793A pdb=" N VAL D1038 " --> pdb=" O LYS D1034 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N GLU D1039 " --> pdb=" O ILE D1035 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA D1040 " --> pdb=" O LYS D1036 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D1041 " --> pdb=" O GLY D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1072 removed outlier: 4.232A pdb=" N ILE D1065 " --> pdb=" O ASN D1061 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D1068 " --> pdb=" O HIS D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1094 through 1108 removed outlier: 3.658A pdb=" N ALA D1104 " --> pdb=" O GLU D1100 " (cutoff:3.500A) Processing helix chain 'D' and resid 1130 through 1138 removed outlier: 3.532A pdb=" N ALA D1134 " --> pdb=" O SER D1130 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER D1136 " --> pdb=" O LEU D1132 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D1138 " --> pdb=" O ALA D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1151 Processing helix chain 'D' and resid 1159 through 1166 Processing helix chain 'D' and resid 1171 through 1174 Processing helix chain 'D' and resid 1175 through 1180 Processing helix chain 'E' and resid 15 through 21 Processing helix chain 'E' and resid 27 through 42 removed outlier: 3.531A pdb=" N ASP E 42 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 65 Processing helix chain 'F' and resid 19 through 31 Processing helix chain 'F' and resid 35 through 45 Processing helix chain 'F' and resid 45 through 58 removed outlier: 3.525A pdb=" N ILE F 49 " --> pdb=" O TYR F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.636A pdb=" N ILE F 71 " --> pdb=" O ASP F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 110 removed outlier: 3.617A pdb=" N PHE F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 121 No H-bonds generated for 'chain 'F' and resid 119 through 121' Processing helix chain 'F' and resid 141 through 160 Processing helix chain 'F' and resid 164 through 169 Processing helix chain 'F' and resid 173 through 190 Processing helix chain 'F' and resid 190 through 199 removed outlier: 3.505A pdb=" N TYR F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 212 removed outlier: 3.648A pdb=" N LEU F 208 " --> pdb=" O PRO F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 234 removed outlier: 4.232A pdb=" N TYR F 225 " --> pdb=" O ASN F 221 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA F 228 " --> pdb=" O LYS F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 247 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 9.580A pdb=" N ILE A 9 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLU A 26 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N CYS A 11 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL A 24 " --> pdb=" O CYS A 11 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 13 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TYR A 20 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR A 200 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LYS A 22 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL A 198 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 24 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU A 196 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU A 26 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU A 194 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR A 191 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ASN A 182 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 193 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL A 180 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR A 195 " --> pdb=" O TYR A 178 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR A 178 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU A 197 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL A 176 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TRP A 199 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113 removed outlier: 7.388A pdb=" N TYR A 137 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE A 58 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU A 139 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 56 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR A 141 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.886A pdb=" N ASN A 88 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 107 removed outlier: 3.619A pdb=" N GLY A 105 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 14 removed outlier: 8.825A pdb=" N ILE B 9 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLU B 26 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N CYS B 11 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 24 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B 13 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR B 20 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N THR B 200 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYS B 22 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N VAL B 198 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL B 24 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU B 196 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLU B 26 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU B 194 " --> pdb=" O GLU B 26 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 175 " --> pdb=" O TRP B 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 101 removed outlier: 7.965A pdb=" N TYR B 137 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE B 58 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLU B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE B 56 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 143 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 52 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AA9, first strand: chain 'B' and resid 106 through 108 removed outlier: 7.069A pdb=" N VAL B 107 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.519A pdb=" N HIS C 3 " --> pdb=" O SER C 14 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA C1002 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N MET C 13 " --> pdb=" O ALA C1002 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 61 through 68 removed outlier: 3.581A pdb=" N VAL C 65 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LYS C 94 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR C 67 " --> pdb=" O LYS C 92 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LYS C 92 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA C 89 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY C 113 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU C 91 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE C 111 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL C 93 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 109 " --> pdb=" O VAL C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 124 through 126 Processing sheet with id=AB4, first strand: chain 'C' and resid 428 through 431 removed outlier: 6.274A pdb=" N SER C 135 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 142 through 149 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 173 removed outlier: 3.828A pdb=" N GLU C 170 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 288 through 289 removed outlier: 4.167A pdb=" N ILE C 288 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 557 through 558 removed outlier: 6.981A pdb=" N ILE C 564 " --> pdb=" O LEU C 586 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 586 " --> pdb=" O ILE C 564 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N THR C 566 " --> pdb=" O VAL C 584 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL C 584 " --> pdb=" O THR C 566 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR C 568 " --> pdb=" O GLU C 582 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU C 582 " --> pdb=" O TYR C 568 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS C 570 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 557 through 558 removed outlier: 3.500A pdb=" N ASP C 634 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 614 through 615 removed outlier: 3.726A pdb=" N VAL C 614 " --> pdb=" O VAL C 625 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 696 through 697 removed outlier: 6.453A pdb=" N ILE C 696 " --> pdb=" O ILE C 756 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 703 through 708 removed outlier: 6.916A pdb=" N ILE C 713 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL C 707 " --> pdb=" O GLU C 711 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU C 711 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 730 through 731 Processing sheet with id=AC5, first strand: chain 'C' and resid 762 through 763 Processing sheet with id=AC6, first strand: chain 'C' and resid 939 through 940 removed outlier: 4.735A pdb=" N THR C1045 " --> pdb=" O PHE C 777 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N ILE C 969 " --> pdb=" O ASN C 772 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU C 774 " --> pdb=" O ILE C 969 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU C 971 " --> pdb=" O LEU C 774 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY C 776 " --> pdb=" O LEU C 971 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 790 " --> pdb=" O VAL C 970 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE C 789 " --> pdb=" O SER C 950 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE C 952 " --> pdb=" O ILE C 789 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE C 791 " --> pdb=" O ILE C 952 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 939 through 940 Processing sheet with id=AC8, first strand: chain 'C' and resid 803 through 812 removed outlier: 3.838A pdb=" N ASP C 903 " --> pdb=" O TYR C 926 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA C 928 " --> pdb=" O VAL C 901 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL C 901 " --> pdb=" O ALA C 928 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N LYS C 930 " --> pdb=" O GLY C 899 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N GLY C 899 " --> pdb=" O LYS C 930 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 899 " --> pdb=" O VAL C 850 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 822 through 823 removed outlier: 3.799A pdb=" N ASP C 822 " --> pdb=" O VAL C 860 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 855 through 857 removed outlier: 6.990A pdb=" N LEU C 891 " --> pdb=" O LEU C 856 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1063 through 1065 removed outlier: 6.142A pdb=" N CYS D 378 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL D 454 " --> pdb=" O CYS D 378 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU D 380 " --> pdb=" O VAL D 454 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1087 through 1089 removed outlier: 3.742A pdb=" N GLN C1087 " --> pdb=" O VAL D 359 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1154 through 1159 Processing sheet with id=AD5, first strand: chain 'D' and resid 47 through 50 removed outlier: 5.331A pdb=" N SER D 47 " --> pdb=" O MET D 115 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N HIS D 117 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY D 49 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLU D 119 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 10.740A pdb=" N LEU D 120 " --> pdb=" O PRO D 255 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N ALA D 122 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL D 253 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 172 through 173 Processing sheet with id=AD7, first strand: chain 'D' and resid 264 through 266 removed outlier: 6.537A pdb=" N PHE D 272 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 538 through 539 Processing sheet with id=AD9, first strand: chain 'D' and resid 812 through 814 Processing sheet with id=AE1, first strand: chain 'D' and resid 823 through 825 removed outlier: 4.097A pdb=" N VAL D 883 " --> pdb=" O VAL D 825 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 828 through 829 removed outlier: 6.760A pdb=" N ILE D 828 " --> pdb=" O ILE D 835 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 851 through 852 removed outlier: 7.011A pdb=" N ILE D 851 " --> pdb=" O ILE D 860 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 967 through 968 Processing sheet with id=AE5, first strand: chain 'D' and resid 977 through 981 removed outlier: 3.942A pdb=" N VAL D 977 " --> pdb=" O SER D 992 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER D 992 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 979 " --> pdb=" O VAL D 990 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 990 " --> pdb=" O ILE D 979 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE D 988 " --> pdb=" O GLU D 981 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1091 through 1093 removed outlier: 4.864A pdb=" N LYS D1075 " --> pdb=" O ALA D1117 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D1113 " --> pdb=" O GLU D1079 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1183 through 1184 removed outlier: 3.655A pdb=" N THR E 69 " --> pdb=" O SER D1184 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2658 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6918 1.33 - 1.45: 4819 1.45 - 1.57: 14829 1.57 - 1.69: 212 1.69 - 1.82: 142 Bond restraints: 26920 Sorted by residual: bond pdb=" C1' DT P 99 " pdb=" N1 DT P 99 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.18e+01 bond pdb=" C1' DA P 92 " pdb=" N9 DA P 92 " ideal model delta sigma weight residual 1.468 1.390 0.078 1.40e-02 5.10e+03 3.12e+01 bond pdb=" C1' DG P 93 " pdb=" N9 DG P 93 " ideal model delta sigma weight residual 1.468 1.391 0.077 1.40e-02 5.10e+03 3.01e+01 bond pdb=" C1' DC P 98 " pdb=" N1 DC P 98 " ideal model delta sigma weight residual 1.468 1.544 -0.076 1.40e-02 5.10e+03 2.95e+01 bond pdb=" C1' DA P 101 " pdb=" N9 DA P 101 " ideal model delta sigma weight residual 1.468 1.405 0.063 1.40e-02 5.10e+03 2.01e+01 ... (remaining 26915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 35913 1.69 - 3.38: 806 3.38 - 5.07: 67 5.07 - 6.75: 16 6.75 - 8.44: 3 Bond angle restraints: 36805 Sorted by residual: angle pdb=" N ALA D1104 " pdb=" CA ALA D1104 " pdb=" C ALA D1104 " ideal model delta sigma weight residual 111.28 116.89 -5.61 1.09e+00 8.42e-01 2.65e+01 angle pdb=" N LYS D1110 " pdb=" CA LYS D1110 " pdb=" C LYS D1110 " ideal model delta sigma weight residual 109.64 115.50 -5.86 1.27e+00 6.20e-01 2.13e+01 angle pdb=" N3 DT O 55 " pdb=" C4 DT O 55 " pdb=" O4 DT O 55 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT P 127 " pdb=" C4 DT P 127 " pdb=" O4 DT P 127 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT P 85 " pdb=" C4 DT P 85 " pdb=" O4 DT P 85 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 ... (remaining 36800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.20: 15139 28.20 - 56.41: 1038 56.41 - 84.61: 93 84.61 - 112.81: 2 112.81 - 141.01: 3 Dihedral angle restraints: 16275 sinusoidal: 7451 harmonic: 8824 Sorted by residual: dihedral pdb=" CA GLU C1093 " pdb=" C GLU C1093 " pdb=" N VAL C1094 " pdb=" CA VAL C1094 " ideal model delta harmonic sigma weight residual 180.00 155.37 24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ASP E 24 " pdb=" C ASP E 24 " pdb=" N SER E 25 " pdb=" CA SER E 25 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE C 344 " pdb=" C ILE C 344 " pdb=" N LYS C 345 " pdb=" CA LYS C 345 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 16272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3329 0.054 - 0.109: 752 0.109 - 0.163: 101 0.163 - 0.217: 6 0.217 - 0.271: 4 Chirality restraints: 4192 Sorted by residual: chirality pdb=" CB ILE C 110 " pdb=" CA ILE C 110 " pdb=" CG1 ILE C 110 " pdb=" CG2 ILE C 110 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ALA D1104 " pdb=" N ALA D1104 " pdb=" C ALA D1104 " pdb=" CB ALA D1104 " both_signs ideal model delta sigma weight residual False 2.48 2.23 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA LYS D1110 " pdb=" N LYS D1110 " pdb=" C LYS D1110 " pdb=" CB LYS D1110 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4189 not shown) Planarity restraints: 4390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 626 " -0.052 5.00e-02 4.00e+02 7.86e-02 9.89e+00 pdb=" N PRO C 627 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO C 627 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 627 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 601 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO D 602 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 602 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 602 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 827 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO C 828 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 828 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 828 " 0.027 5.00e-02 4.00e+02 ... (remaining 4387 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 737 2.70 - 3.25: 25130 3.25 - 3.80: 41654 3.80 - 4.35: 55443 4.35 - 4.90: 90542 Nonbonded interactions: 213506 Sorted by model distance: nonbonded pdb=" O GLU C 867 " pdb=" OH TYR F 137 " model vdw 2.151 3.040 nonbonded pdb=" O ILE C 878 " pdb=" OH TYR F 225 " model vdw 2.152 3.040 nonbonded pdb=" OG SER C 677 " pdb=" OD1 ASP C 763 " model vdw 2.153 3.040 nonbonded pdb=" OG1 THR B 179 " pdb=" OG1 THR B 195 " model vdw 2.187 3.040 nonbonded pdb=" OD1 ASP D 472 " pdb="MG MG D1203 " model vdw 2.190 2.170 ... (remaining 213501 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 'A' and resid 5 through 229) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 29.470 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.004 0.079 26928 Z= 0.254 Angle : 0.578 8.659 36817 Z= 0.386 Chirality : 0.046 0.271 4192 Planarity : 0.004 0.079 4390 Dihedral : 16.990 141.013 10607 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.15 % Allowed : 0.15 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 3052 helix: 0.50 (0.16), residues: 1104 sheet: 0.59 (0.30), residues: 327 loop : -0.81 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 190 TYR 0.025 0.001 TYR F 225 PHE 0.018 0.001 PHE C 879 TRP 0.027 0.001 TRP C 999 HIS 0.008 0.001 HIS D 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.25 (26920) covalent geometry : angle 0.57300 / 0.39 (36805) hydrogen bonds : bond 0.19019 / 12.51 ( 993) hydrogen bonds : angle 6.64816 / 4.61 ( 2752) metal coordination : bond 0.01007 / 0.50 ( 8) metal coordination : angle 4.25807 / 2.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 598 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 15 SER cc_start: 0.8526 (p) cc_final: 0.8318 (p) REVERT: B 140 MET cc_start: 0.7190 (mpp) cc_final: 0.6855 (mpp) REVERT: C 147 MET cc_start: 0.7039 (tmm) cc_final: 0.6527 (tmm) REVERT: C 283 ARG cc_start: 0.7617 (mtt180) cc_final: 0.7280 (mtt180) REVERT: C 344 ILE cc_start: 0.7486 (mm) cc_final: 0.7184 (mm) REVERT: C 449 GLU cc_start: 0.7030 (pp20) cc_final: 0.6793 (pp20) REVERT: C 491 PHE cc_start: 0.8354 (t80) cc_final: 0.7998 (t80) REVERT: C 751 GLU cc_start: 0.7019 (mp0) cc_final: 0.6811 (mp0) REVERT: C 754 ASP cc_start: 0.6893 (m-30) cc_final: 0.6651 (m-30) REVERT: C 841 GLU cc_start: 0.7362 (mp0) cc_final: 0.6873 (mp0) REVERT: D 34 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6775 (ttm-80) REVERT: D 109 LYS cc_start: 0.7243 (pttp) cc_final: 0.7013 (ptmm) REVERT: D 316 ASP cc_start: 0.7023 (m-30) cc_final: 0.6699 (m-30) REVERT: D 577 ILE cc_start: 0.8156 (mm) cc_final: 0.7913 (mm) REVERT: D 709 GLU cc_start: 0.6617 (pp20) cc_final: 0.6182 (pp20) REVERT: F 169 ASN cc_start: 0.6659 (m110) cc_final: 0.6170 (m110) REVERT: F 201 LYS cc_start: 0.7851 (ptmt) cc_final: 0.7546 (ptmt) outliers start: 4 outliers final: 2 residues processed: 601 average time/residue: 0.2006 time to fit residues: 177.9678 Evaluate side-chains 573 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 571 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain F residue 115 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.0970 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN D 932 GLN ** D1061 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114124 restraints weight = 35005.670| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.98 r_work: 0.3315 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26928 Z= 0.179 Angle : 0.602 10.127 36817 Z= 0.325 Chirality : 0.047 0.289 4192 Planarity : 0.005 0.056 4390 Dihedral : 17.970 151.234 4561 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.33 % Allowed : 9.13 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3052 helix: 0.57 (0.16), residues: 1130 sheet: 0.68 (0.29), residues: 332 loop : -0.79 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 411 TYR 0.020 0.001 TYR F 225 PHE 0.020 0.001 PHE C 522 TRP 0.024 0.002 TRP C 999 HIS 0.005 0.001 HIS D 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (26920) covalent geometry : angle 0.59543 / 0.32 (36805) hydrogen bonds : bond 0.05474 / 3.75 ( 993) hydrogen bonds : angle 5.01298 / 3.52 ( 2752) metal coordination : bond 0.00932 / 0.47 ( 8) metal coordination : angle 4.96105 / 2.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 592 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 ASP cc_start: 0.6703 (t0) cc_final: 0.6319 (t0) REVERT: B 148 TYR cc_start: 0.7998 (t80) cc_final: 0.7623 (t80) REVERT: C 147 MET cc_start: 0.8119 (tmm) cc_final: 0.7836 (tmm) REVERT: C 283 ARG cc_start: 0.7944 (mtt180) cc_final: 0.7518 (mtt180) REVERT: C 344 ILE cc_start: 0.7767 (mm) cc_final: 0.7561 (mm) REVERT: C 449 GLU cc_start: 0.7746 (pp20) cc_final: 0.7384 (pp20) REVERT: C 481 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7624 (mm-30) REVERT: C 697 LEU cc_start: 0.8937 (mt) cc_final: 0.8725 (mt) REVERT: C 751 GLU cc_start: 0.7781 (mp0) cc_final: 0.7324 (mp0) REVERT: C 841 GLU cc_start: 0.8098 (mp0) cc_final: 0.7452 (mp0) REVERT: C 879 PHE cc_start: 0.8109 (m-10) cc_final: 0.7871 (m-10) REVERT: C 885 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6658 (mm-30) REVERT: C 1007 ASP cc_start: 0.8428 (p0) cc_final: 0.8126 (p0) REVERT: C 1011 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7382 (mm-30) REVERT: D 34 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.7987 (ttm-80) REVERT: D 150 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8523 (mtpp) REVERT: D 204 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7192 (mm-30) REVERT: D 249 MET cc_start: 0.8643 (mtt) cc_final: 0.8256 (mtt) REVERT: D 310 MET cc_start: 0.8674 (mmm) cc_final: 0.8452 (mmp) REVERT: D 316 ASP cc_start: 0.7682 (m-30) cc_final: 0.7281 (m-30) REVERT: D 342 MET cc_start: 0.8177 (mmt) cc_final: 0.7922 (mmt) REVERT: D 387 GLU cc_start: 0.7977 (tp30) cc_final: 0.7745 (tp30) REVERT: D 624 ASP cc_start: 0.7928 (t0) cc_final: 0.7652 (t0) REVERT: D 709 GLU cc_start: 0.7542 (pp20) cc_final: 0.7083 (pp20) REVERT: D 858 GLU cc_start: 0.7182 (pm20) cc_final: 0.6968 (pm20) REVERT: D 865 ARG cc_start: 0.8391 (ttp80) cc_final: 0.7813 (ttt180) REVERT: D 910 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: F 169 ASN cc_start: 0.7267 (m110) cc_final: 0.6665 (m110) REVERT: F 193 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.5418 (mtm) REVERT: F 201 LYS cc_start: 0.8080 (ptmt) cc_final: 0.7747 (ptmt) REVERT: F 231 LEU cc_start: 0.7981 (mt) cc_final: 0.7673 (mt) outliers start: 35 outliers final: 24 residues processed: 602 average time/residue: 0.2142 time to fit residues: 189.4960 Evaluate side-chains 602 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 576 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 516 GLN Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 910 GLU Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1113 VAL Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 193 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 65 optimal weight: 0.0670 chunk 284 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 516 GLN D 551 ASN D 932 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114546 restraints weight = 34950.279| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.98 r_work: 0.3317 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26928 Z= 0.142 Angle : 0.556 7.917 36817 Z= 0.302 Chirality : 0.045 0.327 4192 Planarity : 0.004 0.057 4390 Dihedral : 18.040 150.384 4558 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.02 % Allowed : 11.98 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 3052 helix: 0.68 (0.16), residues: 1133 sheet: 0.78 (0.29), residues: 338 loop : -0.77 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 557 TYR 0.020 0.001 TYR F 225 PHE 0.015 0.001 PHE C 522 TRP 0.019 0.001 TRP C 999 HIS 0.004 0.001 HIS D 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (26920) covalent geometry : angle 0.55152 / 0.30 (36805) hydrogen bonds : bond 0.04633 / 3.22 ( 993) hydrogen bonds : angle 4.74138 / 3.33 ( 2752) metal coordination : bond 0.00798 / 0.40 ( 8) metal coordination : angle 4.13312 / 2.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 584 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8036 (mtm) REVERT: B 17 ASP cc_start: 0.6685 (t0) cc_final: 0.6298 (t0) REVERT: B 148 TYR cc_start: 0.8043 (t80) cc_final: 0.7652 (t80) REVERT: C 283 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7499 (mtt180) REVERT: C 449 GLU cc_start: 0.7723 (pp20) cc_final: 0.7346 (pp20) REVERT: C 481 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7574 (mm-30) REVERT: C 491 PHE cc_start: 0.8642 (t80) cc_final: 0.8262 (t80) REVERT: C 697 LEU cc_start: 0.8946 (mt) cc_final: 0.8736 (mt) REVERT: C 751 GLU cc_start: 0.7842 (mp0) cc_final: 0.7329 (mp0) REVERT: C 836 LYS cc_start: 0.7558 (mtmm) cc_final: 0.7343 (mtmm) REVERT: C 885 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6662 (mm-30) REVERT: C 1007 ASP cc_start: 0.8428 (p0) cc_final: 0.8141 (p0) REVERT: C 1089 PHE cc_start: 0.8473 (t80) cc_final: 0.8009 (t80) REVERT: D 149 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7611 (mm-30) REVERT: D 150 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8516 (mtpp) REVERT: D 182 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7716 (pt) REVERT: D 204 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7056 (mm-30) REVERT: D 249 MET cc_start: 0.8683 (mtt) cc_final: 0.8273 (mtt) REVERT: D 310 MET cc_start: 0.8663 (mmm) cc_final: 0.8462 (mmp) REVERT: D 316 ASP cc_start: 0.7682 (m-30) cc_final: 0.7257 (m-30) REVERT: D 399 ASN cc_start: 0.7946 (OUTLIER) cc_final: 0.7704 (t0) REVERT: D 414 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: D 624 ASP cc_start: 0.7970 (t0) cc_final: 0.7656 (t0) REVERT: D 709 GLU cc_start: 0.7613 (pp20) cc_final: 0.7194 (pp20) REVERT: D 726 TYR cc_start: 0.7675 (t80) cc_final: 0.7342 (t80) REVERT: D 858 GLU cc_start: 0.7110 (pm20) cc_final: 0.6815 (pm20) REVERT: D 865 ARG cc_start: 0.8368 (ttp80) cc_final: 0.7801 (ttt180) REVERT: D 910 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: F 67 ASP cc_start: 0.7604 (m-30) cc_final: 0.7345 (m-30) REVERT: F 147 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7203 (mt-10) REVERT: F 157 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6443 (pm20) REVERT: F 169 ASN cc_start: 0.7317 (m110) cc_final: 0.6679 (m110) REVERT: F 193 MET cc_start: 0.5727 (OUTLIER) cc_final: 0.5417 (mtm) REVERT: F 201 LYS cc_start: 0.8047 (ptmt) cc_final: 0.7753 (ptmt) REVERT: F 231 LEU cc_start: 0.7982 (mt) cc_final: 0.7614 (mt) outliers start: 53 outliers final: 32 residues processed: 604 average time/residue: 0.2020 time to fit residues: 180.2788 Evaluate side-chains 611 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 572 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 661 MET Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1093 GLU Chi-restraints excluded: chain C residue 1121 VAL Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 399 ASN Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 516 GLN Chi-restraints excluded: chain D residue 910 GLU Chi-restraints excluded: chain D residue 956 GLU Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 193 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 168 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 932 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.138865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112529 restraints weight = 34628.891| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.96 r_work: 0.3280 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 26928 Z= 0.219 Angle : 0.603 9.027 36817 Z= 0.322 Chirality : 0.047 0.368 4192 Planarity : 0.004 0.057 4390 Dihedral : 18.158 149.860 4557 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.43 % Allowed : 13.69 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 3052 helix: 0.56 (0.15), residues: 1137 sheet: 0.68 (0.29), residues: 334 loop : -0.81 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 734 TYR 0.027 0.002 TYR C 347 PHE 0.017 0.002 PHE F 92 TRP 0.026 0.002 TRP C 999 HIS 0.007 0.001 HIS D 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 (26920) covalent geometry : angle 0.59570 / 0.32 (36805) hydrogen bonds : bond 0.04797 / 3.33 ( 993) hydrogen bonds : angle 4.69904 / 3.29 ( 2752) metal coordination : bond 0.01093 / 0.54 ( 8) metal coordination : angle 5.20821 / 2.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 593 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.6472 (pm20) cc_final: 0.6150 (pm20) REVERT: B 17 ASP cc_start: 0.6702 (t0) cc_final: 0.6276 (t0) REVERT: B 139 GLU cc_start: 0.6460 (pp20) cc_final: 0.5690 (pp20) REVERT: C 344 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7586 (mm) REVERT: C 388 ARG cc_start: 0.7707 (mtp85) cc_final: 0.6909 (mtp85) REVERT: C 449 GLU cc_start: 0.7819 (pp20) cc_final: 0.7326 (pp20) REVERT: C 481 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7528 (mm-30) REVERT: C 491 PHE cc_start: 0.8782 (t80) cc_final: 0.8508 (t80) REVERT: C 557 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7840 (ttm170) REVERT: C 751 GLU cc_start: 0.7864 (mp0) cc_final: 0.7352 (mp0) REVERT: C 885 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6659 (mm-30) REVERT: C 1007 ASP cc_start: 0.8411 (p0) cc_final: 0.8144 (p0) REVERT: D 150 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8547 (mtpp) REVERT: D 182 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7724 (pt) REVERT: D 193 MET cc_start: 0.7302 (ptm) cc_final: 0.7062 (ttt) REVERT: D 249 MET cc_start: 0.8860 (mtt) cc_final: 0.8453 (mtt) REVERT: D 316 ASP cc_start: 0.7662 (m-30) cc_final: 0.7301 (m-30) REVERT: D 387 GLU cc_start: 0.7994 (tp30) cc_final: 0.7763 (tp30) REVERT: D 414 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: D 604 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7853 (ptpp) REVERT: D 628 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8374 (mtpt) REVERT: D 709 GLU cc_start: 0.7626 (pp20) cc_final: 0.7162 (pp20) REVERT: D 858 GLU cc_start: 0.7077 (pm20) cc_final: 0.6750 (pm20) REVERT: D 865 ARG cc_start: 0.8370 (ttp80) cc_final: 0.7782 (ttt180) REVERT: D 910 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: F 39 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: F 67 ASP cc_start: 0.7718 (m-30) cc_final: 0.7448 (m-30) REVERT: F 85 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7720 (mt) REVERT: F 147 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7269 (mt-10) REVERT: F 157 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6616 (pm20) REVERT: F 169 ASN cc_start: 0.7373 (m110) cc_final: 0.6722 (m110) REVERT: F 193 MET cc_start: 0.5853 (OUTLIER) cc_final: 0.5557 (mtm) REVERT: F 201 LYS cc_start: 0.8043 (ptmt) cc_final: 0.7806 (ptmt) REVERT: F 202 ASN cc_start: 0.6593 (m-40) cc_final: 0.6221 (m-40) outliers start: 64 outliers final: 43 residues processed: 617 average time/residue: 0.2057 time to fit residues: 186.6134 Evaluate side-chains 638 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 586 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1093 GLU Chi-restraints excluded: chain C residue 1121 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 628 LYS Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 910 GLU Chi-restraints excluded: chain D residue 956 GLU Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain D residue 1146 GLU Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 193 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 94 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 516 GLN ** D 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112861 restraints weight = 34613.424| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.96 r_work: 0.3294 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26928 Z= 0.171 Angle : 0.576 8.792 36817 Z= 0.308 Chirality : 0.045 0.372 4192 Planarity : 0.004 0.056 4390 Dihedral : 18.184 149.878 4557 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.93 % Allowed : 14.68 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.15), residues: 3052 helix: 0.63 (0.15), residues: 1135 sheet: 0.67 (0.29), residues: 343 loop : -0.82 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 190 TYR 0.028 0.001 TYR D 726 PHE 0.015 0.001 PHE F 92 TRP 0.020 0.001 TRP C 999 HIS 0.004 0.001 HIS D 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (26920) covalent geometry : angle 0.56920 / 0.31 (36805) hydrogen bonds : bond 0.04432 / 3.08 ( 993) hydrogen bonds : angle 4.59951 / 3.22 ( 2752) metal coordination : bond 0.00862 / 0.42 ( 8) metal coordination : angle 4.92101 / 2.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 580 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.6457 (pm20) cc_final: 0.6127 (pm20) REVERT: C 71 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7836 (mm-30) REVERT: C 79 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7163 (pm20) REVERT: C 312 GLU cc_start: 0.6941 (tm-30) cc_final: 0.6538 (tm-30) REVERT: C 449 GLU cc_start: 0.7763 (pp20) cc_final: 0.7446 (pp20) REVERT: C 557 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.7868 (ttm170) REVERT: C 751 GLU cc_start: 0.7886 (mp0) cc_final: 0.7352 (mp0) REVERT: C 836 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7255 (mtmm) REVERT: C 885 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6662 (mm-30) REVERT: C 1007 ASP cc_start: 0.8432 (p0) cc_final: 0.8151 (p0) REVERT: D 45 GLU cc_start: 0.7170 (tp30) cc_final: 0.6839 (tp30) REVERT: D 107 ARG cc_start: 0.7777 (mmt180) cc_final: 0.7487 (mmt-90) REVERT: D 150 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8538 (mtpp) REVERT: D 181 SER cc_start: 0.8421 (m) cc_final: 0.8167 (m) REVERT: D 182 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7734 (pt) REVERT: D 184 LYS cc_start: 0.8477 (tmtt) cc_final: 0.8248 (tttt) REVERT: D 193 MET cc_start: 0.7267 (ptm) cc_final: 0.6989 (ttt) REVERT: D 249 MET cc_start: 0.8851 (mtt) cc_final: 0.8479 (mtt) REVERT: D 316 ASP cc_start: 0.7654 (m-30) cc_final: 0.7275 (m-30) REVERT: D 323 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.7612 (ttp80) REVERT: D 387 GLU cc_start: 0.7976 (tp30) cc_final: 0.7744 (tp30) REVERT: D 414 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: D 604 LYS cc_start: 0.8067 (ptpp) cc_final: 0.7813 (ptpp) REVERT: D 628 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8473 (mppt) REVERT: D 670 LYS cc_start: 0.7534 (ttpt) cc_final: 0.7235 (tmmt) REVERT: D 709 GLU cc_start: 0.7689 (pp20) cc_final: 0.7099 (pp20) REVERT: D 858 GLU cc_start: 0.7040 (pm20) cc_final: 0.6684 (pm20) REVERT: D 865 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7758 (ttt180) REVERT: D 910 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: D 1105 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7487 (tt) REVERT: F 39 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: F 44 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6991 (tm-30) REVERT: F 67 ASP cc_start: 0.7654 (m-30) cc_final: 0.7365 (m-30) REVERT: F 85 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7748 (mt) REVERT: F 147 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7252 (mt-10) REVERT: F 157 GLN cc_start: 0.6940 (OUTLIER) cc_final: 0.6557 (pm20) REVERT: F 169 ASN cc_start: 0.7369 (m110) cc_final: 0.6721 (m110) REVERT: F 193 MET cc_start: 0.5816 (OUTLIER) cc_final: 0.5528 (mtm) REVERT: F 202 ASN cc_start: 0.6633 (m-40) cc_final: 0.6390 (m-40) outliers start: 77 outliers final: 46 residues processed: 613 average time/residue: 0.2024 time to fit residues: 182.8389 Evaluate side-chains 632 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 575 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain C residue 836 LYS Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1093 GLU Chi-restraints excluded: chain C residue 1121 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 516 GLN Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 628 LYS Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 910 GLU Chi-restraints excluded: chain D residue 956 GLU Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 231 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 151 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 300 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN ** D 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.112744 restraints weight = 34765.748| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.95 r_work: 0.3289 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26928 Z= 0.168 Angle : 0.578 13.196 36817 Z= 0.307 Chirality : 0.045 0.371 4192 Planarity : 0.004 0.056 4390 Dihedral : 18.205 149.592 4557 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.00 % Allowed : 15.79 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 3052 helix: 0.66 (0.16), residues: 1137 sheet: 0.70 (0.29), residues: 343 loop : -0.81 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 388 TYR 0.024 0.001 TYR C 75 PHE 0.016 0.001 PHE F 92 TRP 0.017 0.001 TRP C 999 HIS 0.004 0.001 HIS D 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (26920) covalent geometry : angle 0.57144 / 0.31 (36805) hydrogen bonds : bond 0.04355 / 3.02 ( 993) hydrogen bonds : angle 4.57059 / 3.19 ( 2752) metal coordination : bond 0.00835 / 0.41 ( 8) metal coordination : angle 4.94624 / 2.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 588 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 MET cc_start: 0.8633 (mtm) cc_final: 0.8350 (mtt) REVERT: B 16 GLU cc_start: 0.6439 (pm20) cc_final: 0.6104 (pm20) REVERT: C 71 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7843 (mm-30) REVERT: C 79 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: C 96 ARG cc_start: 0.7782 (ptm160) cc_final: 0.7526 (ptp-170) REVERT: C 312 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6630 (tm-30) REVERT: C 344 ILE cc_start: 0.7690 (mm) cc_final: 0.7473 (mm) REVERT: C 388 ARG cc_start: 0.7717 (mtp85) cc_final: 0.6961 (mtp85) REVERT: C 449 GLU cc_start: 0.7784 (pp20) cc_final: 0.7418 (pp20) REVERT: C 481 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7522 (tm-30) REVERT: C 557 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7880 (ttm170) REVERT: C 751 GLU cc_start: 0.7880 (mp0) cc_final: 0.7359 (mp0) REVERT: C 836 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7211 (mtmm) REVERT: C 885 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6700 (mm-30) REVERT: C 1007 ASP cc_start: 0.8423 (p0) cc_final: 0.8168 (p0) REVERT: C 1089 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: D 45 GLU cc_start: 0.7142 (tp30) cc_final: 0.6865 (tp30) REVERT: D 107 ARG cc_start: 0.7766 (mmt180) cc_final: 0.7458 (mmt-90) REVERT: D 181 SER cc_start: 0.8432 (m) cc_final: 0.8175 (m) REVERT: D 182 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7733 (pt) REVERT: D 193 MET cc_start: 0.7215 (ptm) cc_final: 0.6970 (ttt) REVERT: D 249 MET cc_start: 0.8859 (mtt) cc_final: 0.8490 (mtt) REVERT: D 310 MET cc_start: 0.8664 (mmm) cc_final: 0.8435 (mmp) REVERT: D 316 ASP cc_start: 0.7660 (m-30) cc_final: 0.7283 (m-30) REVERT: D 414 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7302 (mt-10) REVERT: D 604 LYS cc_start: 0.8068 (ptpp) cc_final: 0.7863 (ptpp) REVERT: D 670 LYS cc_start: 0.7521 (ttpt) cc_final: 0.7303 (tmmt) REVERT: D 709 GLU cc_start: 0.7688 (pp20) cc_final: 0.7304 (pp20) REVERT: D 865 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7739 (ttt180) REVERT: D 910 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: D 1105 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7435 (tt) REVERT: F 39 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: F 44 GLU cc_start: 0.7296 (tm-30) cc_final: 0.7031 (tm-30) REVERT: F 67 ASP cc_start: 0.7662 (m-30) cc_final: 0.7374 (m-30) REVERT: F 85 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7756 (mt) REVERT: F 147 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7269 (mt-10) REVERT: F 157 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6515 (pm20) REVERT: F 169 ASN cc_start: 0.7378 (m110) cc_final: 0.6730 (m110) REVERT: F 193 MET cc_start: 0.5788 (OUTLIER) cc_final: 0.5511 (mtm) outliers start: 79 outliers final: 53 residues processed: 626 average time/residue: 0.2117 time to fit residues: 195.9385 Evaluate side-chains 644 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 580 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 491 PHE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain C residue 836 LYS Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1093 GLU Chi-restraints excluded: chain C residue 1121 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 784 LYS Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 910 GLU Chi-restraints excluded: chain D residue 956 GLU Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 231 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 130 optimal weight: 0.6980 chunk 262 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 313 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 299 optimal weight: 0.4980 chunk 198 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 GLN D 551 ASN ** D 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.139567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113328 restraints weight = 34530.445| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.96 r_work: 0.3291 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26928 Z= 0.142 Angle : 0.565 15.652 36817 Z= 0.300 Chirality : 0.045 0.365 4192 Planarity : 0.004 0.056 4390 Dihedral : 18.211 149.272 4557 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.93 % Allowed : 16.39 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3052 helix: 0.73 (0.16), residues: 1135 sheet: 0.74 (0.29), residues: 346 loop : -0.77 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 388 TYR 0.021 0.001 TYR D 726 PHE 0.014 0.001 PHE F 92 TRP 0.015 0.001 TRP C 999 HIS 0.005 0.001 HIS D 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (26920) covalent geometry : angle 0.55844 / 0.30 (36805) hydrogen bonds : bond 0.04132 / 2.87 ( 993) hydrogen bonds : angle 4.51385 / 3.15 ( 2752) metal coordination : bond 0.00682 / 0.34 ( 8) metal coordination : angle 4.63910 / 2.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 582 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.6417 (pm20) cc_final: 0.6080 (pm20) REVERT: C 71 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7851 (mm-30) REVERT: C 79 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7175 (pm20) REVERT: C 96 ARG cc_start: 0.7764 (ptm160) cc_final: 0.7518 (ptp-170) REVERT: C 312 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6712 (tm-30) REVERT: C 387 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6693 (pm20) REVERT: C 388 ARG cc_start: 0.7707 (mtp85) cc_final: 0.6939 (mtp85) REVERT: C 449 GLU cc_start: 0.7747 (pp20) cc_final: 0.7413 (pp20) REVERT: C 481 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7526 (tm-30) REVERT: C 751 GLU cc_start: 0.7893 (mp0) cc_final: 0.7369 (mp0) REVERT: C 766 GLU cc_start: 0.8148 (pt0) cc_final: 0.7870 (pt0) REVERT: C 885 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6656 (mm-30) REVERT: C 1007 ASP cc_start: 0.8405 (p0) cc_final: 0.8117 (p0) REVERT: C 1089 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: D 45 GLU cc_start: 0.7174 (tp30) cc_final: 0.6890 (tp30) REVERT: D 107 ARG cc_start: 0.7773 (mmt180) cc_final: 0.7453 (mmt-90) REVERT: D 181 SER cc_start: 0.8430 (m) cc_final: 0.8167 (m) REVERT: D 182 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7735 (pt) REVERT: D 249 MET cc_start: 0.8847 (mtt) cc_final: 0.8495 (mtt) REVERT: D 310 MET cc_start: 0.8684 (mmm) cc_final: 0.8457 (mmp) REVERT: D 316 ASP cc_start: 0.7682 (m-30) cc_final: 0.7275 (m-30) REVERT: D 414 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: D 604 LYS cc_start: 0.8046 (ptpp) cc_final: 0.7817 (ptpp) REVERT: D 670 LYS cc_start: 0.7503 (ttpt) cc_final: 0.7282 (tmmt) REVERT: D 709 GLU cc_start: 0.7696 (pp20) cc_final: 0.7322 (pp20) REVERT: D 865 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7723 (ttt180) REVERT: D 910 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: D 1105 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7378 (tt) REVERT: F 39 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: F 44 GLU cc_start: 0.7301 (tm-30) cc_final: 0.7010 (tm-30) REVERT: F 67 ASP cc_start: 0.7680 (m-30) cc_final: 0.7381 (m-30) REVERT: F 85 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7713 (mt) REVERT: F 147 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7241 (mt-10) REVERT: F 157 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6509 (pm20) REVERT: F 159 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6444 (t80) REVERT: F 169 ASN cc_start: 0.7394 (m110) cc_final: 0.6726 (m110) REVERT: F 193 MET cc_start: 0.5736 (OUTLIER) cc_final: 0.5474 (mtm) outliers start: 77 outliers final: 55 residues processed: 622 average time/residue: 0.2159 time to fit residues: 198.4625 Evaluate side-chains 641 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 574 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 491 PHE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 764 ASN Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1093 GLU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 910 GLU Chi-restraints excluded: chain D residue 956 GLU Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain D residue 1105 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 231 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 79 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 278 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 chunk 191 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN ** D 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.139471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.113195 restraints weight = 34748.261| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.96 r_work: 0.3293 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26928 Z= 0.148 Angle : 0.566 12.605 36817 Z= 0.301 Chirality : 0.044 0.357 4192 Planarity : 0.004 0.056 4390 Dihedral : 18.214 148.445 4557 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.97 % Allowed : 16.62 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.15), residues: 3052 helix: 0.77 (0.16), residues: 1135 sheet: 0.71 (0.29), residues: 347 loop : -0.77 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 388 TYR 0.019 0.001 TYR F 225 PHE 0.017 0.001 PHE C 259 TRP 0.012 0.001 TRP C 999 HIS 0.004 0.001 HIS D 442 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (26920) covalent geometry : angle 0.56021 / 0.30 (36805) hydrogen bonds : bond 0.04076 / 2.82 ( 993) hydrogen bonds : angle 4.47241 / 3.12 ( 2752) metal coordination : bond 0.00704 / 0.35 ( 8) metal coordination : angle 4.67931 / 2.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 578 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7016 (m-30) REVERT: B 16 GLU cc_start: 0.6424 (pm20) cc_final: 0.6082 (pm20) REVERT: B 77 GLU cc_start: 0.7870 (tp30) cc_final: 0.7604 (tp30) REVERT: B 139 GLU cc_start: 0.6179 (pp20) cc_final: 0.5883 (pp20) REVERT: C 45 GLU cc_start: 0.6999 (tm-30) cc_final: 0.6778 (tm-30) REVERT: C 71 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7845 (mm-30) REVERT: C 79 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7292 (pm20) REVERT: C 96 ARG cc_start: 0.7765 (ptm160) cc_final: 0.7527 (ptp-170) REVERT: C 205 GLU cc_start: 0.6507 (pt0) cc_final: 0.6141 (pt0) REVERT: C 312 GLU cc_start: 0.6924 (tm-30) cc_final: 0.6691 (tm-30) REVERT: C 387 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6693 (pm20) REVERT: C 388 ARG cc_start: 0.7687 (mtp85) cc_final: 0.6879 (mtp85) REVERT: C 449 GLU cc_start: 0.7809 (pp20) cc_final: 0.7447 (pp20) REVERT: C 481 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7523 (tm-30) REVERT: C 619 LYS cc_start: 0.7857 (ptpp) cc_final: 0.7522 (mtmm) REVERT: C 751 GLU cc_start: 0.7892 (mp0) cc_final: 0.7361 (mp0) REVERT: C 836 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7193 (mtmm) REVERT: C 885 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6685 (mm-30) REVERT: C 1007 ASP cc_start: 0.8422 (p0) cc_final: 0.8156 (p0) REVERT: C 1089 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: D 45 GLU cc_start: 0.7177 (tp30) cc_final: 0.6886 (tp30) REVERT: D 107 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7429 (mmt-90) REVERT: D 182 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7744 (pt) REVERT: D 193 MET cc_start: 0.7185 (ptm) cc_final: 0.6896 (ttt) REVERT: D 249 MET cc_start: 0.8867 (mtt) cc_final: 0.8533 (mtt) REVERT: D 310 MET cc_start: 0.8671 (mmm) cc_final: 0.8463 (mmp) REVERT: D 316 ASP cc_start: 0.7681 (m-30) cc_final: 0.7280 (m-30) REVERT: D 414 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7321 (mt-10) REVERT: D 509 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8428 (mptt) REVERT: D 559 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8399 (tmtt) REVERT: D 604 LYS cc_start: 0.7999 (ptpp) cc_final: 0.7780 (ptpp) REVERT: D 709 GLU cc_start: 0.7708 (pp20) cc_final: 0.7331 (pp20) REVERT: D 830 ASP cc_start: 0.7288 (p0) cc_final: 0.7051 (p0) REVERT: D 865 ARG cc_start: 0.8318 (ttp80) cc_final: 0.7783 (ttt180) REVERT: D 871 ASP cc_start: 0.7433 (m-30) cc_final: 0.6811 (m-30) REVERT: D 910 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: D 1059 ASP cc_start: 0.7461 (p0) cc_final: 0.7036 (p0) REVERT: F 39 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: F 44 GLU cc_start: 0.7351 (tm-30) cc_final: 0.7092 (tm-30) REVERT: F 67 ASP cc_start: 0.7655 (m-30) cc_final: 0.7363 (m-30) REVERT: F 85 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7716 (mt) REVERT: F 115 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7561 (mm-30) REVERT: F 147 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7266 (mt-10) REVERT: F 157 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6483 (pm20) REVERT: F 159 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6473 (t80) REVERT: F 169 ASN cc_start: 0.7418 (m110) cc_final: 0.6739 (m110) REVERT: F 193 MET cc_start: 0.5634 (OUTLIER) cc_final: 0.5365 (mtm) outliers start: 78 outliers final: 58 residues processed: 615 average time/residue: 0.1965 time to fit residues: 177.8911 Evaluate side-chains 648 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 576 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 491 PHE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain C residue 836 LYS Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1093 GLU Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 559 LYS Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 810 VAL Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 910 GLU Chi-restraints excluded: chain D residue 956 GLU Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1023 THR Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 231 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 74 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 0.0060 chunk 246 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN ** D 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.140501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114360 restraints weight = 34788.068| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.93 r_work: 0.3315 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26928 Z= 0.120 Angle : 0.550 10.545 36817 Z= 0.294 Chirality : 0.044 0.347 4192 Planarity : 0.004 0.056 4390 Dihedral : 18.177 147.786 4557 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.47 % Allowed : 17.65 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3052 helix: 0.86 (0.16), residues: 1135 sheet: 0.71 (0.29), residues: 347 loop : -0.74 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 190 TYR 0.026 0.001 TYR D 726 PHE 0.012 0.001 PHE F 92 TRP 0.010 0.001 TRP C 999 HIS 0.004 0.001 HIS D 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (26920) covalent geometry : angle 0.54499 / 0.29 (36805) hydrogen bonds : bond 0.03749 / 2.60 ( 993) hydrogen bonds : angle 4.40489 / 3.07 ( 2752) metal coordination : bond 0.00584 / 0.29 ( 8) metal coordination : angle 4.06763 / 2.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 581 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: B 16 GLU cc_start: 0.6376 (pm20) cc_final: 0.6038 (pm20) REVERT: C 45 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6776 (tm-30) REVERT: C 79 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: C 96 ARG cc_start: 0.7777 (ptm160) cc_final: 0.7549 (ptp-170) REVERT: C 205 GLU cc_start: 0.6509 (pt0) cc_final: 0.6146 (pt0) REVERT: C 222 LYS cc_start: 0.8262 (tppp) cc_final: 0.8060 (tptp) REVERT: C 387 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6666 (pm20) REVERT: C 388 ARG cc_start: 0.7644 (mtp85) cc_final: 0.6841 (mtp85) REVERT: C 449 GLU cc_start: 0.7737 (pp20) cc_final: 0.7374 (pp20) REVERT: C 481 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7511 (tm-30) REVERT: C 751 GLU cc_start: 0.7890 (mp0) cc_final: 0.7337 (mp0) REVERT: C 766 GLU cc_start: 0.8150 (pt0) cc_final: 0.7861 (pt0) REVERT: C 885 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6696 (mm-30) REVERT: C 958 MET cc_start: 0.8302 (mmp) cc_final: 0.7607 (mmt) REVERT: C 1007 ASP cc_start: 0.8417 (p0) cc_final: 0.8160 (p0) REVERT: C 1089 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: D 45 GLU cc_start: 0.7118 (tp30) cc_final: 0.6834 (tp30) REVERT: D 107 ARG cc_start: 0.7712 (mmt180) cc_final: 0.7396 (mmt-90) REVERT: D 182 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7733 (pt) REVERT: D 193 MET cc_start: 0.7073 (ptm) cc_final: 0.6815 (ttt) REVERT: D 249 MET cc_start: 0.8846 (mtt) cc_final: 0.8498 (mtt) REVERT: D 310 MET cc_start: 0.8658 (mmm) cc_final: 0.8447 (mmp) REVERT: D 316 ASP cc_start: 0.7675 (m-30) cc_final: 0.7247 (m-30) REVERT: D 414 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: D 426 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7435 (mm-30) REVERT: D 515 THR cc_start: 0.8477 (t) cc_final: 0.8224 (p) REVERT: D 559 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8386 (tmtt) REVERT: D 670 LYS cc_start: 0.7452 (ttpt) cc_final: 0.7229 (tmmt) REVERT: D 709 GLU cc_start: 0.7697 (pp20) cc_final: 0.7317 (pp20) REVERT: D 830 ASP cc_start: 0.7300 (p0) cc_final: 0.7072 (p0) REVERT: D 858 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: D 865 ARG cc_start: 0.8301 (ttp80) cc_final: 0.7807 (ttt180) REVERT: D 871 ASP cc_start: 0.7431 (m-30) cc_final: 0.6782 (m-30) REVERT: D 910 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: D 1059 ASP cc_start: 0.7432 (p0) cc_final: 0.6995 (p0) REVERT: D 1110 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7942 (mmmm) REVERT: F 39 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: F 44 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7079 (tm-30) REVERT: F 67 ASP cc_start: 0.7689 (m-30) cc_final: 0.7384 (m-30) REVERT: F 85 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7648 (mt) REVERT: F 115 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7525 (mm-30) REVERT: F 147 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7190 (mt-10) REVERT: F 157 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6425 (pm20) REVERT: F 159 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6506 (t80) REVERT: F 169 ASN cc_start: 0.7421 (m110) cc_final: 0.6725 (m110) REVERT: F 193 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.5378 (mtm) outliers start: 65 outliers final: 47 residues processed: 613 average time/residue: 0.2237 time to fit residues: 202.3140 Evaluate side-chains 632 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 571 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain C residue 854 ASP Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1093 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 559 LYS Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 858 GLU Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 910 GLU Chi-restraints excluded: chain D residue 956 GLU Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 189 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 250 optimal weight: 0.1980 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 301 optimal weight: 0.5980 chunk 265 optimal weight: 5.9990 chunk 223 optimal weight: 0.5980 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN ** D 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.140395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114140 restraints weight = 34725.354| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.96 r_work: 0.3315 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26928 Z= 0.128 Angle : 0.556 9.831 36817 Z= 0.296 Chirality : 0.044 0.342 4192 Planarity : 0.004 0.056 4390 Dihedral : 18.165 146.709 4557 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.55 % Allowed : 17.57 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3052 helix: 0.89 (0.16), residues: 1135 sheet: 0.53 (0.29), residues: 361 loop : -0.72 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 190 TYR 0.024 0.001 TYR D 726 PHE 0.018 0.001 PHE C 259 TRP 0.009 0.001 TRP C 999 HIS 0.004 0.001 HIS D 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (26920) covalent geometry : angle 0.55068 / 0.30 (36805) hydrogen bonds : bond 0.03799 / 2.64 ( 993) hydrogen bonds : angle 4.38228 / 3.06 ( 2752) metal coordination : bond 0.00610 / 0.30 ( 8) metal coordination : angle 4.26302 / 2.23 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6104 Ramachandran restraints generated. 3052 Oldfield, 0 Emsley, 3052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 569 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6978 (m-30) REVERT: B 16 GLU cc_start: 0.6390 (pm20) cc_final: 0.6050 (pm20) REVERT: B 77 GLU cc_start: 0.7885 (tp30) cc_final: 0.7598 (tp30) REVERT: B 208 GLU cc_start: 0.7010 (pm20) cc_final: 0.6749 (pm20) REVERT: C 48 LYS cc_start: 0.7751 (pttp) cc_final: 0.7504 (pttp) REVERT: C 79 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: C 96 ARG cc_start: 0.7771 (ptm160) cc_final: 0.7565 (ptp-170) REVERT: C 205 GLU cc_start: 0.6518 (pt0) cc_final: 0.6156 (pt0) REVERT: C 222 LYS cc_start: 0.8267 (tppp) cc_final: 0.8060 (tptp) REVERT: C 387 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6661 (pm20) REVERT: C 388 ARG cc_start: 0.7647 (mtp85) cc_final: 0.6845 (mtp85) REVERT: C 449 GLU cc_start: 0.7777 (pp20) cc_final: 0.7397 (pp20) REVERT: C 481 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7521 (tm-30) REVERT: C 604 ASP cc_start: 0.7374 (p0) cc_final: 0.7173 (p0) REVERT: C 751 GLU cc_start: 0.7890 (mp0) cc_final: 0.7358 (mp0) REVERT: C 766 GLU cc_start: 0.8153 (pt0) cc_final: 0.7952 (pt0) REVERT: C 885 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6733 (mm-30) REVERT: C 1007 ASP cc_start: 0.8418 (p0) cc_final: 0.8160 (p0) REVERT: C 1089 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: C 1138 ILE cc_start: 0.8479 (mm) cc_final: 0.8239 (mt) REVERT: D 45 GLU cc_start: 0.7146 (tp30) cc_final: 0.6864 (tp30) REVERT: D 107 ARG cc_start: 0.7721 (mmt180) cc_final: 0.7442 (mmt-90) REVERT: D 182 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7746 (pt) REVERT: D 193 MET cc_start: 0.7091 (ptm) cc_final: 0.6846 (ttt) REVERT: D 249 MET cc_start: 0.8861 (mtt) cc_final: 0.8510 (mtt) REVERT: D 310 MET cc_start: 0.8666 (mmm) cc_final: 0.8460 (mmp) REVERT: D 316 ASP cc_start: 0.7687 (m-30) cc_final: 0.7262 (m-30) REVERT: D 414 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: D 426 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7447 (mm-30) REVERT: D 515 THR cc_start: 0.8491 (t) cc_final: 0.8241 (p) REVERT: D 559 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8399 (tmtt) REVERT: D 670 LYS cc_start: 0.7483 (ttpt) cc_final: 0.7263 (tmmt) REVERT: D 709 GLU cc_start: 0.7661 (pp20) cc_final: 0.7286 (pp20) REVERT: D 830 ASP cc_start: 0.7332 (p0) cc_final: 0.7110 (p0) REVERT: D 865 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7786 (ttt180) REVERT: D 871 ASP cc_start: 0.7446 (m-30) cc_final: 0.6808 (m-30) REVERT: D 910 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7294 (mp0) REVERT: D 1059 ASP cc_start: 0.7387 (p0) cc_final: 0.6980 (p0) REVERT: D 1103 LYS cc_start: 0.8234 (ttpp) cc_final: 0.7956 (ttmm) REVERT: D 1110 LYS cc_start: 0.8241 (mmmm) cc_final: 0.7929 (mmmm) REVERT: F 39 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: F 44 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7080 (tm-30) REVERT: F 67 ASP cc_start: 0.7678 (m-30) cc_final: 0.7382 (m-30) REVERT: F 85 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7649 (mt) REVERT: F 115 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7510 (mm-30) REVERT: F 147 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7240 (mt-10) REVERT: F 157 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.6422 (pm20) REVERT: F 159 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6538 (t80) REVERT: F 169 ASN cc_start: 0.7407 (m110) cc_final: 0.6725 (m110) REVERT: F 193 MET cc_start: 0.5608 (OUTLIER) cc_final: 0.5359 (mtm) outliers start: 67 outliers final: 50 residues processed: 602 average time/residue: 0.1982 time to fit residues: 175.5532 Evaluate side-chains 633 residues out of total 2653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 570 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 219 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 612 ASN Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 779 THR Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain C residue 920 ASN Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1093 GLU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 414 GLU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 559 LYS Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 644 GLU Chi-restraints excluded: chain D residue 843 ILE Chi-restraints excluded: chain D residue 887 SER Chi-restraints excluded: chain D residue 910 GLU Chi-restraints excluded: chain D residue 956 GLU Chi-restraints excluded: chain D residue 1022 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1096 ASP Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 159 PHE Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 231 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 230 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 211 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN ** C 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN ** D 913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 GLN ** F 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113659 restraints weight = 34670.431| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.95 r_work: 0.3302 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26928 Z= 0.145 Angle : 0.573 14.418 36817 Z= 0.302 Chirality : 0.045 0.364 4192 Planarity : 0.004 0.056 4390 Dihedral : 18.159 145.685 4557 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.78 % Allowed : 17.54 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3052 helix: 0.89 (0.16), residues: 1132 sheet: 0.61 (0.29), residues: 351 loop : -0.73 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 83 TYR 0.050 0.001 TYR D 726 PHE 0.013 0.001 PHE F 92 TRP 0.009 0.001 TRP C 999 HIS 0.005 0.001 HIS D 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (26920) covalent geometry : angle 0.56714 / 0.30 (36805) hydrogen bonds : bond 0.03909 / 2.71 ( 993) hydrogen bonds : angle 4.40431 / 3.07 ( 2752) metal coordination : bond 0.00657 / 0.33 ( 8) metal coordination : angle 4.55780 / 2.39 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7530.55 seconds wall clock time: 129 minutes 7.63 seconds (7747.63 seconds total)