Starting phenix.real_space_refine on Thu Mar 5 12:21:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wvj_21920/03_2026/6wvj_21920.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wvj_21920/03_2026/6wvj_21920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wvj_21920/03_2026/6wvj_21920.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wvj_21920/03_2026/6wvj_21920.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wvj_21920/03_2026/6wvj_21920.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wvj_21920/03_2026/6wvj_21920.map" } resolution = 3.36 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 ------------------------------------------------------------------------------- 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= -0.026 sd= 0.774 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 36 5.49 5 Mg 1 5.21 5 S 80 5.16 5 C 13981 2.51 5 N 3916 2.21 5 O 4351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 249 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22367 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1688 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1663 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 8688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8688 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1062} Chain breaks: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 90 Chain: "D" Number of atoms: 9085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9085 Classifications: {'peptide': 1176} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 52, 'TRANS': 1123} Chain breaks: 1 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 10, 'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 102 Chain: "F" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 478 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "T" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "R" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna3p': 7} Chain: "N" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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 12462 SG CYS D 60 68.748 73.881 117.814 1.00 93.04 S ATOM 12478 SG CYS D 62 65.848 73.909 119.750 1.00100.22 S ATOM 12586 SG CYS D 75 68.454 71.660 120.817 1.00 90.54 S ATOM 12611 SG CYS D 78 65.998 70.895 118.159 1.00 94.90 S ATOM 18378 SG CYS D 818 110.171 42.222 72.853 1.00 67.88 S ATOM 18963 SG CYS D 892 106.801 43.756 72.517 1.00 60.22 S ATOM 19012 SG CYS D 899 109.827 45.738 71.906 1.00 57.65 S ATOM 19038 SG CYS D 902 108.878 43.298 69.631 1.00 56.16 S Time building chain proxies: 4.76, per 1000 atoms: 0.21 Number of scatterers: 22367 At special positions: 0 Unit cell: (150.36, 136.08, 132.72, 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 80 16.00 P 36 15.00 Mg 1 11.99 O 4351 8.00 N 3916 7.00 C 13981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 78 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 902 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 899 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 818 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 892 " Number of angles added : 12 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5160 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 40 sheets defined 38.5% alpha, 17.2% beta 14 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 31 through 45 removed outlier: 3.737A pdb=" N THR A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 83 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 205 through 226 removed outlier: 3.846A pdb=" N LEU A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 74 through 83 Processing helix chain 'B' and resid 150 through 155 removed outlier: 3.556A pdb=" N ASN B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 221 removed outlier: 3.878A pdb=" N HIS B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'C' and resid 30 through 43 removed outlier: 4.177A pdb=" N THR C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 53 removed outlier: 3.583A pdb=" N GLN C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 52 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 191 through 198 removed outlier: 3.744A pdb=" N LEU C 195 " --> pdb=" O PRO C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 211 removed outlier: 4.403A pdb=" N ASP C 209 " --> pdb=" O GLN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 removed outlier: 4.779A pdb=" N ASP C 222 " --> pdb=" O ARG C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 239 removed outlier: 3.789A pdb=" N ARG C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 259 removed outlier: 3.652A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 280 Processing helix chain 'C' and resid 281 through 286 Processing helix chain 'C' and resid 377 through 393 removed outlier: 3.711A pdb=" N ILE C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 382 " --> pdb=" O PRO C 378 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 439 removed outlier: 3.502A pdb=" N GLN C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 423 " --> pdb=" O GLN C 419 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ARG C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 439 " --> pdb=" O MET C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 448 Processing helix chain 'C' and resid 451 through 465 removed outlier: 3.848A pdb=" N ILE C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.778A pdb=" N TYR C 511 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 572 removed outlier: 3.721A pdb=" N TYR C 572 " --> pdb=" O GLU C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 586 removed outlier: 3.659A pdb=" N ALA C 586 " --> pdb=" O ASP C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 618 Processing helix chain 'C' and resid 633 through 645 removed outlier: 4.048A pdb=" N ARG C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 670 Processing helix chain 'C' and resid 767 through 771 removed outlier: 4.053A pdb=" N ASN C 770 " --> pdb=" O ASP C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 784 Processing helix chain 'C' and resid 819 through 823 removed outlier: 3.556A pdb=" N ARG C 822 " --> pdb=" O ASP C 819 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN C 823 " --> pdb=" O ALA C 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 819 through 823' Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 960 through 965 removed outlier: 3.891A pdb=" N SER C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 965 " --> pdb=" O GLY C 961 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 960 through 965' Processing helix chain 'C' and resid 967 through 984 removed outlier: 4.179A pdb=" N VAL C 971 " --> pdb=" O ASN C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1008 Processing helix chain 'C' and resid 1043 through 1048 Processing helix chain 'C' and resid 1066 through 1070 Processing helix chain 'C' and resid 1076 through 1087 Processing helix chain 'C' and resid 1088 through 1097 Processing helix chain 'C' and resid 1102 through 1116 removed outlier: 4.095A pdb=" N VAL C1107 " --> pdb=" O VAL C1103 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1138 removed outlier: 3.647A pdb=" N LYS C1133 " --> pdb=" O LYS C1129 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.631A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 121 through 130 removed outlier: 4.216A pdb=" N GLU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 removed outlier: 4.682A pdb=" N LYS D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 180 removed outlier: 4.219A pdb=" N LEU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 200 through 219 removed outlier: 3.707A pdb=" N ARG D 205 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL D 212 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 252 through 275 removed outlier: 3.880A pdb=" N ASP D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 297 removed outlier: 3.582A pdb=" N ASP D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 321 removed outlier: 3.913A pdb=" N LEU D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.723A pdb=" N LEU D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU D 364 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 382 through 392 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.849A pdb=" N ASP D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU D 402 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 403 " --> pdb=" O ASP D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 421 No H-bonds generated for 'chain 'D' and resid 419 through 421' Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 442 through 447 Processing helix chain 'D' and resid 462 through 472 Processing helix chain 'D' and resid 493 through 504 Processing helix chain 'D' and resid 518 through 529 removed outlier: 3.662A pdb=" N ALA D 522 " --> pdb=" O ASN D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 544 No H-bonds generated for 'chain 'D' and resid 542 through 544' Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 582 through 588 Processing helix chain 'D' and resid 601 through 609 Processing helix chain 'D' and resid 616 through 631 removed outlier: 3.704A pdb=" N LEU D 620 " --> pdb=" O LYS D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 655 removed outlier: 3.666A pdb=" N LYS D 653 " --> pdb=" O LYS D 649 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA D 654 " --> pdb=" O TYR D 650 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY D 655 " --> pdb=" O SER D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 663 Processing helix chain 'D' and resid 668 through 690 removed outlier: 3.706A pdb=" N LYS D 679 " --> pdb=" O GLU D 675 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN D 682 " --> pdb=" O SER D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 720 removed outlier: 4.135A pdb=" N GLU D 699 " --> pdb=" O GLU D 695 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 702 " --> pdb=" O TYR D 698 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D 707 " --> pdb=" O SER D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 732 Processing helix chain 'D' and resid 737 through 746 removed outlier: 4.036A pdb=" N GLN D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 779 Processing helix chain 'D' and resid 780 through 808 removed outlier: 4.089A pdb=" N THR D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP D 796 " --> pdb=" O LEU D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 838 through 844 removed outlier: 3.545A pdb=" N ILE D 844 " --> pdb=" O GLU D 840 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 880 Processing helix chain 'D' and resid 888 through 892 Processing helix chain 'D' and resid 899 through 904 Processing helix chain 'D' and resid 918 through 929 Processing helix chain 'D' and resid 930 through 934 Processing helix chain 'D' and resid 952 through 961 removed outlier: 3.653A pdb=" N ILE D 956 " --> pdb=" O GLY D 952 " (cutoff:3.500A) Processing helix chain 'D' and resid 1030 through 1038 Processing helix chain 'D' and resid 1039 through 1059 removed outlier: 4.013A pdb=" N GLU D1045 " --> pdb=" O THR D1041 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR D1046 " --> pdb=" O THR D1042 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D1054 " --> pdb=" O GLU D1050 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR D1055 " --> pdb=" O VAL D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1063 through 1073 removed outlier: 3.927A pdb=" N VAL D1067 " --> pdb=" O GLY D1063 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET D1070 " --> pdb=" O HIS D1066 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN D1073 " --> pdb=" O VAL D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1096 through 1107 Processing helix chain 'D' and resid 1122 through 1128 removed outlier: 4.004A pdb=" N LEU D1128 " --> pdb=" O THR D1124 " (cutoff:3.500A) Processing helix chain 'D' and resid 1133 through 1138 Processing helix chain 'D' and resid 1141 through 1153 removed outlier: 3.514A pdb=" N ASP D1148 " --> pdb=" O ARG D1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1168 removed outlier: 3.640A pdb=" N ASN D1164 " --> pdb=" O GLY D1160 " (cutoff:3.500A) Processing helix chain 'D' and resid 1173 through 1176 Processing helix chain 'D' and resid 1177 through 1182 Processing helix chain 'F' and resid 5 through 11 Processing helix chain 'F' and resid 15 through 34 Processing helix chain 'F' and resid 45 through 54 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 14 removed outlier: 6.807A pdb=" N LYS A 22 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE A 14 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 20 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE A 20 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR A 200 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS A 22 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL A 198 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL A 24 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 196 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU A 26 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 194 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 185 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 191 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 175 " --> pdb=" O TRP A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 102 removed outlier: 7.161A pdb=" N ARG A 137 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE A 58 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARG A 139 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE A 56 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 6.608A 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 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 108 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 8 through 12 removed outlier: 6.606A pdb=" N ASP B 192 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR B 191 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 95 through 101 removed outlier: 7.176A pdb=" N ARG B 137 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE B 58 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG B 139 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 56 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 141 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 143 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 108 Processing sheet with id=AB1, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 8 removed outlier: 3.780A pdb=" N ARG C 12 " --> pdb=" O TYR C 8 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA C 988 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ARG C 15 " --> pdb=" O ALA C 988 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.707A pdb=" N ILE C 55 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU C 64 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE C 99 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N PHE C 66 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG C 97 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP C 68 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY C 114 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL C 94 " --> pdb=" O PHE C 112 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE C 112 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL C 96 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP C 110 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU C 98 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP C 108 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 125 through 127 Processing sheet with id=AB5, first strand: chain 'C' and resid 407 through 409 removed outlier: 3.940A pdb=" N SER C 136 " --> pdb=" O ARG C 485 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 147 removed outlier: 3.740A pdb=" N THR C 159 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 334 through 335 removed outlier: 3.762A pdb=" N VAL C 342 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 346 through 350 removed outlier: 3.536A pdb=" N ILE C 347 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 349 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 536 through 537 removed outlier: 5.754A pdb=" N ARG C 560 " --> pdb=" O ARG C 549 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 536 through 537 Processing sheet with id=AC2, first strand: chain 'C' and resid 674 through 675 removed outlier: 6.524A pdb=" N VAL C 674 " --> pdb=" O LEU C 742 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 707 through 711 removed outlier: 6.769A pdb=" N ASN C 689 " --> pdb=" O VAL C 685 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL C 685 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP C 691 " --> pdb=" O GLU C 683 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.664A pdb=" N VAL C 716 " --> pdb=" O TYR C 724 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 749 Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 763 removed outlier: 8.917A pdb=" N ILE C 955 " --> pdb=" O ASN C 758 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N MET C 760 " --> pdb=" O ILE C 955 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU C 957 " --> pdb=" O MET C 760 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY C 762 " --> pdb=" O LEU C 957 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE C 776 " --> pdb=" O MET C 956 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE C 775 " --> pdb=" O SER C 936 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 938 " --> pdb=" O ILE C 775 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N MET C 777 " --> pdb=" O ILE C 938 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 788 through 800 removed outlier: 6.491A pdb=" N SER C 789 " --> pdb=" O LYS C 916 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS C 916 " --> pdb=" O SER C 789 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HIS C 791 " --> pdb=" O VAL C 914 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 914 " --> pdb=" O HIS C 791 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU C 793 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N TYR C 912 " --> pdb=" O GLU C 793 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR C 795 " --> pdb=" O ARG C 910 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG C 910 " --> pdb=" O TYR C 795 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER C 797 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LEU C 908 " --> pdb=" O SER C 797 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA C 799 " --> pdb=" O ASN C 906 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP C 889 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 914 " --> pdb=" O ILE C 887 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE C 887 " --> pdb=" O VAL C 914 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N LYS C 916 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N GLY C 885 " --> pdb=" O LYS C 916 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 808 through 809 Processing sheet with id=AC9, first strand: chain 'C' and resid 1049 through 1051 removed outlier: 3.505A pdb=" N SER D 342 " --> pdb=" O MET D 455 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AD2, first strand: chain 'D' and resid 9 through 11 Processing sheet with id=AD3, first strand: chain 'D' and resid 93 through 102 removed outlier: 3.515A pdb=" N LEU D 97 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASP D 229 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 10.645A pdb=" N ALA D 99 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 10.548A pdb=" N ILE D 227 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 149 through 150 removed outlier: 7.047A pdb=" N GLN D 167 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 241 through 243 Processing sheet with id=AD6, first strand: chain 'D' and resid 515 through 516 removed outlier: 3.673A pdb=" N ALA D 540 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D 557 " --> pdb=" O LEU D 596 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 752 through 753 removed outlier: 3.786A pdb=" N GLY D 756 " --> pdb=" O ASN D 753 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 812 through 813 removed outlier: 6.284A pdb=" N ILE D 812 " --> pdb=" O VAL D 898 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 824 through 826 Processing sheet with id=AE1, first strand: chain 'D' and resid 829 through 831 removed outlier: 6.685A pdb=" N LEU D 829 " --> pdb=" O ILE D 836 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU D 834 " --> pdb=" O GLU D 831 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 852 through 854 removed outlier: 7.194A pdb=" N VAL D 852 " --> pdb=" O LEU D 861 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLU D 859 " --> pdb=" O HIS D 854 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 978 through 981 Processing sheet with id=AE4, first strand: chain 'D' and resid 1093 through 1095 removed outlier: 7.217A pdb=" N THR D1115 " --> pdb=" O ILE D1081 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2349 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 4.58 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7321 1.34 - 1.46: 3139 1.46 - 1.57: 12137 1.57 - 1.69: 70 1.69 - 1.81: 145 Bond restraints: 22812 Sorted by residual: bond pdb=" CZ ARG B 30 " pdb=" NH2 ARG B 30 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.21e+00 bond pdb=" CZ ARG C 811 " pdb=" NH2 ARG C 811 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.10e+00 bond pdb=" CZ ARG C 800 " pdb=" NH2 ARG C 800 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.03e+00 bond pdb=" CZ ARG C 878 " pdb=" NH2 ARG C 878 " ideal model delta sigma weight residual 1.330 1.301 0.029 1.30e-02 5.92e+03 4.97e+00 bond pdb=" CZ ARG C 811 " pdb=" NH1 ARG C 811 " ideal model delta sigma weight residual 1.323 1.292 0.031 1.40e-02 5.10e+03 4.86e+00 ... (remaining 22807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 29825 1.71 - 3.43: 1091 3.43 - 5.14: 114 5.14 - 6.85: 18 6.85 - 8.57: 6 Bond angle restraints: 31054 Sorted by residual: angle pdb=" CA GLU C 339 " pdb=" C GLU C 339 " pdb=" O GLU C 339 " ideal model delta sigma weight residual 117.94 121.81 -3.87 5.80e-01 2.97e+00 4.44e+01 angle pdb=" C GLN D1140 " pdb=" CA GLN D1140 " pdb=" CB GLN D1140 " ideal model delta sigma weight residual 116.63 109.31 7.32 1.16e+00 7.43e-01 3.98e+01 angle pdb=" N GLU B 26 " pdb=" CA GLU B 26 " pdb=" C GLU B 26 " ideal model delta sigma weight residual 108.22 112.48 -4.26 9.00e-01 1.23e+00 2.24e+01 angle pdb=" C ALA C1041 " pdb=" CA ALA C1041 " pdb=" CB ALA C1041 " ideal model delta sigma weight residual 116.54 111.22 5.32 1.15e+00 7.56e-01 2.14e+01 angle pdb=" C VAL B 25 " pdb=" CA VAL B 25 " pdb=" CB VAL B 25 " ideal model delta sigma weight residual 110.12 116.04 -5.92 1.36e+00 5.41e-01 1.90e+01 ... (remaining 31049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 11814 17.96 - 35.92: 1518 35.92 - 53.87: 380 53.87 - 71.83: 95 71.83 - 89.79: 27 Dihedral angle restraints: 13834 sinusoidal: 5795 harmonic: 8039 Sorted by residual: dihedral pdb=" CA ASP B 192 " pdb=" C ASP B 192 " pdb=" N LYS B 193 " pdb=" CA LYS B 193 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ILE D 110 " pdb=" C ILE D 110 " pdb=" N PRO D 111 " pdb=" CA PRO D 111 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA GLU C 105 " pdb=" C GLU C 105 " pdb=" N VAL C 106 " pdb=" CA VAL C 106 " ideal model delta harmonic sigma weight residual -180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 13831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2866 0.053 - 0.106: 614 0.106 - 0.159: 90 0.159 - 0.212: 10 0.212 - 0.265: 3 Chirality restraints: 3583 Sorted by residual: chirality pdb=" CA LYS C 845 " pdb=" N LYS C 845 " pdb=" C LYS C 845 " pdb=" CB LYS C 845 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE B 120 " pdb=" CA ILE B 120 " pdb=" CG1 ILE B 120 " pdb=" CG2 ILE B 120 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ASP C 812 " pdb=" N ASP C 812 " pdb=" C ASP C 812 " pdb=" CB ASP C 812 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 3580 not shown) Planarity restraints: 3918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 32 " -0.056 2.00e-02 2.50e+03 3.93e-02 3.08e+01 pdb=" CG TYR B 32 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR B 32 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 32 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR B 32 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR B 32 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 32 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR B 32 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 191 " -0.032 2.00e-02 2.50e+03 1.84e-02 6.79e+00 pdb=" CG TYR B 191 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 191 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 191 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 191 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 191 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 191 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 191 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG T 10 " -0.009 2.00e-02 2.50e+03 1.28e-02 4.89e+00 pdb=" N9 DG T 10 " 0.009 2.00e-02 2.50e+03 pdb=" C8 DG T 10 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG T 10 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG T 10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG T 10 " 0.010 2.00e-02 2.50e+03 pdb=" O6 DG T 10 " -0.023 2.00e-02 2.50e+03 pdb=" N1 DG T 10 " 0.029 2.00e-02 2.50e+03 pdb=" C2 DG T 10 " -0.019 2.00e-02 2.50e+03 pdb=" N2 DG T 10 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG T 10 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG T 10 " 0.001 2.00e-02 2.50e+03 ... (remaining 3915 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 418 2.64 - 3.21: 21363 3.21 - 3.77: 33598 3.77 - 4.34: 47339 4.34 - 4.90: 78706 Nonbonded interactions: 181424 Sorted by model distance: nonbonded pdb=" OD1 ASP D 453 " pdb="MG MG D2001 " model vdw 2.079 2.170 nonbonded pdb=" OD1 ASP D 449 " pdb="MG MG D2001 " model vdw 2.082 2.170 nonbonded pdb=" OD1 ASP D 451 " pdb="MG MG D2001 " model vdw 2.083 2.170 nonbonded pdb=" O TRP C 766 " pdb=" OG1 THR D 652 " model vdw 2.118 3.040 nonbonded pdb=" O GLN C 419 " pdb=" OG SER C 457 " model vdw 2.152 3.040 ... (remaining 181419 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 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 62 or (resid 63 through 64 and (name \ N or name CA or name C or name O or name CB )) or resid 65 through 68 or (resid \ 69 and (name N or name CA or name C or name O or name CB )) or resid 70 through \ 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or res \ id 89 through 101 or (resid 102 and (name N or name CA or name C or name O or na \ me CB )) or resid 103 through 131 or (resid 132 through 134 and (name N or name \ CA or name C or name O or name CB )) or resid 135 through 156 or (resid 157 and \ (name N or name CA or name C or name O or name CB )) or resid 158 through 228)) selection = (chain 'B' and (resid 5 through 7 or (resid 8 and (name N or name CA or name C o \ r name O or name CB )) or resid 9 through 28 or (resid 29 and (name N or name CA \ or name C or name O or name CB )) or resid 30 through 58 or (resid 59 and (name \ N or name CA or name C or name O or name CB )) or resid 60 through 91 or (resid \ 92 through 93 and (name N or name CA or name C or name O or name CB )) or resid \ 94 through 228)) } 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.090 Find NCS groups from input model: 0.210 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.005 0.256 22820 Z= 0.253 Angle : 0.752 10.454 31066 Z= 0.454 Chirality : 0.045 0.265 3583 Planarity : 0.004 0.047 3918 Dihedral : 17.450 89.788 8674 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.75 % Favored : 93.14 % Rotamer: Outliers : 5.36 % Allowed : 19.46 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % 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: -2.98 (0.14), residues: 2786 helix: -1.63 (0.15), residues: 927 sheet: -1.57 (0.26), residues: 386 loop : -2.33 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 84 TYR 0.075 0.002 TYR B 32 PHE 0.020 0.001 PHE A 20 TRP 0.015 0.001 TRP B 199 HIS 0.006 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00489 (22812) covalent geometry : angle 0.74615 (31054) hydrogen bonds : bond 0.16352 ( 875) hydrogen bonds : angle 6.58545 ( 2411) metal coordination : bond 0.13450 ( 8) metal coordination : angle 4.67032 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 375 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: A 215 LYS cc_start: 0.7917 (ttpp) cc_final: 0.7701 (ttpp) REVERT: B 57 GLN cc_start: 0.7913 (tt0) cc_final: 0.7634 (tt0) REVERT: B 181 GLU cc_start: 0.8097 (mp0) cc_final: 0.7512 (pm20) REVERT: B 191 TYR cc_start: 0.7664 (m-80) cc_final: 0.7413 (m-80) REVERT: B 199 TRP cc_start: 0.7713 (m-90) cc_final: 0.7312 (m-90) REVERT: C 30 ILE cc_start: 0.9012 (pt) cc_final: 0.8739 (mt) REVERT: C 264 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7759 (mmm-85) REVERT: C 286 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: C 486 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8491 (mt) REVERT: C 1115 LYS cc_start: 0.8331 (tmtt) cc_final: 0.8122 (tptt) REVERT: D 177 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7510 (mmtt) REVERT: D 205 ARG cc_start: 0.8099 (ptp90) cc_final: 0.7790 (ptp90) REVERT: D 214 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6671 (mm-30) REVERT: D 267 ARG cc_start: 0.6931 (ttp-170) cc_final: 0.6585 (ttp-170) REVERT: D 289 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7302 (tp40) REVERT: D 536 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7269 (mtp180) REVERT: D 593 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7843 (ttp-170) REVERT: D 689 ARG cc_start: 0.7839 (mmp80) cc_final: 0.7509 (mmp80) outliers start: 124 outliers final: 86 residues processed: 485 average time/residue: 0.1873 time to fit residues: 133.9110 Evaluate side-chains 417 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 325 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain C residue 533 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 686 GLU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 536 ARG Chi-restraints excluded: chain D residue 557 LEU Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 639 MET Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1175 THR Chi-restraints excluded: chain D residue 1177 MET Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 7 ASP Chi-restraints excluded: chain F residue 19 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 220 HIS B 57 GLN B 154 ASN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 GLN C 689 ASN C 823 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN D 957 GLN D 989 GLN D1140 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.112243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.094809 restraints weight = 48302.048| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.59 r_work: 0.3138 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 22820 Z= 0.259 Angle : 0.695 17.593 31066 Z= 0.357 Chirality : 0.046 0.270 3583 Planarity : 0.005 0.052 3918 Dihedral : 11.835 73.686 3645 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.10 % Favored : 94.76 % Rotamer: Outliers : 5.71 % Allowed : 22.49 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % 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: -2.16 (0.15), residues: 2786 helix: -0.76 (0.16), residues: 948 sheet: -1.35 (0.25), residues: 396 loop : -1.91 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 539 TYR 0.016 0.002 TYR F 46 PHE 0.021 0.002 PHE C 470 TRP 0.012 0.002 TRP B 199 HIS 0.004 0.001 HIS D1097 Details of bonding type rmsd covalent geometry : bond 0.00608 (22812) covalent geometry : angle 0.68038 (31054) hydrogen bonds : bond 0.05760 ( 875) hydrogen bonds : angle 5.27007 ( 2411) metal coordination : bond 0.01215 ( 8) metal coordination : angle 7.15168 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 330 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7412 (tp) REVERT: B 30 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8032 (mtp-110) REVERT: B 44 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8828 (mp) REVERT: B 57 GLN cc_start: 0.8571 (tt0) cc_final: 0.8154 (tm-30) REVERT: B 140 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8694 (mt) REVERT: B 191 TYR cc_start: 0.7965 (m-80) cc_final: 0.7671 (m-80) REVERT: B 199 TRP cc_start: 0.7837 (m-90) cc_final: 0.7496 (m-90) REVERT: C 149 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8169 (tmmt) REVERT: C 264 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.7979 (mmm-85) REVERT: C 419 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: C 485 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8893 (ptp-110) REVERT: C 595 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7307 (ptt-90) REVERT: C 1115 LYS cc_start: 0.8460 (tmtt) cc_final: 0.8259 (tptt) REVERT: D 36 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7864 (m-80) REVERT: D 205 ARG cc_start: 0.8728 (ptp90) cc_final: 0.8414 (ptp90) REVERT: D 208 LYS cc_start: 0.9122 (mmtm) cc_final: 0.8764 (mmtm) REVERT: D 214 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7436 (mm-30) REVERT: D 287 MET cc_start: 0.8564 (ttp) cc_final: 0.8334 (ttp) REVERT: D 289 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7452 (tp40) REVERT: D 320 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8238 (mt) REVERT: D 593 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8015 (ttp80) REVERT: D 689 ARG cc_start: 0.8066 (mmp80) cc_final: 0.7709 (mmp80) REVERT: D 864 GLU cc_start: 0.8190 (pt0) cc_final: 0.7810 (tt0) outliers start: 132 outliers final: 91 residues processed: 439 average time/residue: 0.1968 time to fit residues: 126.2469 Evaluate side-chains 418 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 317 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 188 ARG Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 419 GLN Chi-restraints excluded: chain C residue 441 ASN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 692 ILE Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 898 VAL Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1078 VAL Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 63 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 200 optimal weight: 0.0970 chunk 44 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 126 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 HIS ** D 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.114232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096854 restraints weight = 48087.241| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.54 r_work: 0.3177 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22820 Z= 0.161 Angle : 0.677 49.163 31066 Z= 0.316 Chirality : 0.043 0.187 3583 Planarity : 0.004 0.054 3918 Dihedral : 11.263 73.626 3570 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.63 % Favored : 95.26 % Rotamer: Outliers : 5.49 % Allowed : 23.79 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.15), residues: 2786 helix: -0.16 (0.17), residues: 942 sheet: -1.07 (0.26), residues: 385 loop : -1.57 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 267 TYR 0.014 0.001 TYR D 130 PHE 0.016 0.001 PHE C 470 TRP 0.013 0.001 TRP B 199 HIS 0.005 0.001 HIS D1097 Details of bonding type rmsd covalent geometry : bond 0.00376 (22812) covalent geometry : angle 0.59653 (31054) hydrogen bonds : bond 0.04892 ( 875) hydrogen bonds : angle 4.95237 ( 2411) metal coordination : bond 0.01243 ( 8) metal coordination : angle 16.32848 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 356 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7387 (tp) REVERT: B 30 ARG cc_start: 0.8322 (ttp80) cc_final: 0.8054 (mtp180) REVERT: B 45 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8712 (mp) REVERT: B 57 GLN cc_start: 0.8419 (tt0) cc_final: 0.8181 (tm-30) REVERT: B 137 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7638 (ttp80) REVERT: B 140 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8673 (mt) REVERT: B 181 GLU cc_start: 0.7956 (mp0) cc_final: 0.7721 (mp0) REVERT: B 199 TRP cc_start: 0.7807 (m-90) cc_final: 0.7478 (m-90) REVERT: C 42 ASP cc_start: 0.7852 (m-30) cc_final: 0.7592 (m-30) REVERT: C 264 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.8009 (mmm-85) REVERT: C 485 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8851 (ptp-110) REVERT: C 584 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: C 595 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7302 (ptt-90) REVERT: D 36 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: D 158 TYR cc_start: 0.7961 (m-80) cc_final: 0.7759 (m-80) REVERT: D 205 ARG cc_start: 0.8713 (ptp90) cc_final: 0.8444 (ptp90) REVERT: D 208 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8771 (mmtm) REVERT: D 214 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7420 (mm-30) REVERT: D 287 MET cc_start: 0.8276 (ttp) cc_final: 0.7955 (ttp) REVERT: D 289 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: D 593 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8013 (ttp80) REVERT: D 670 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7772 (tp40) REVERT: D 674 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7492 (mm-30) REVERT: D 689 ARG cc_start: 0.8018 (mmp80) cc_final: 0.7705 (mmp80) REVERT: D 864 GLU cc_start: 0.8017 (pt0) cc_final: 0.7757 (tt0) REVERT: F 25 ARG cc_start: 0.8221 (ptp-170) cc_final: 0.7888 (ptp-170) outliers start: 127 outliers final: 77 residues processed: 465 average time/residue: 0.1947 time to fit residues: 131.4552 Evaluate side-chains 412 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 326 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 97 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 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 16 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 204 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 220 HIS B 126 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN ** D 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1097 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096149 restraints weight = 48250.399| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.54 r_work: 0.3163 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22820 Z= 0.198 Angle : 0.685 43.515 31066 Z= 0.326 Chirality : 0.044 0.310 3583 Planarity : 0.005 0.050 3918 Dihedral : 11.096 73.732 3548 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 5.75 % Allowed : 24.35 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 2786 helix: 0.04 (0.17), residues: 939 sheet: -1.01 (0.27), residues: 386 loop : -1.48 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 700 TYR 0.015 0.001 TYR F 46 PHE 0.018 0.001 PHE C 420 TRP 0.011 0.001 TRP B 199 HIS 0.006 0.001 HIS D1097 Details of bonding type rmsd covalent geometry : bond 0.00467 (22812) covalent geometry : angle 0.62161 (31054) hydrogen bonds : bond 0.04996 ( 875) hydrogen bonds : angle 4.94339 ( 2411) metal coordination : bond 0.00879 ( 8) metal coordination : angle 14.71540 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 341 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8423 (p) REVERT: B 14 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7385 (tp) REVERT: B 30 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8062 (mtp-110) REVERT: B 44 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8839 (mp) REVERT: B 140 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8697 (mt) REVERT: B 199 TRP cc_start: 0.7835 (m-90) cc_final: 0.7339 (m-90) REVERT: C 264 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.8023 (mmm-85) REVERT: C 485 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8855 (ptp-110) REVERT: C 584 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7570 (pt0) REVERT: C 595 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7361 (ptt-90) REVERT: D 158 TYR cc_start: 0.7974 (m-80) cc_final: 0.7758 (m-80) REVERT: D 190 MET cc_start: 0.8481 (tmm) cc_final: 0.8215 (tmm) REVERT: D 208 LYS cc_start: 0.9123 (mmtm) cc_final: 0.8816 (mmtm) REVERT: D 214 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7462 (mm-30) REVERT: D 289 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7185 (tt0) REVERT: D 593 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7976 (ttp80) REVERT: D 670 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7719 (tp40) REVERT: D 674 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7631 (mm-30) REVERT: D 689 ARG cc_start: 0.8021 (mmp80) cc_final: 0.7734 (mmp80) REVERT: D 864 GLU cc_start: 0.7901 (pt0) cc_final: 0.7658 (tt0) REVERT: F 25 ARG cc_start: 0.8212 (ptp-170) cc_final: 0.7889 (ptp-170) outliers start: 133 outliers final: 95 residues processed: 449 average time/residue: 0.1929 time to fit residues: 126.9353 Evaluate side-chains 428 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 324 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 967 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 730 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 744 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 812 ILE Chi-restraints excluded: chain D residue 827 LYS Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 271 optimal weight: 8.9990 chunk 166 optimal weight: 7.9990 chunk 227 optimal weight: 0.0870 chunk 243 optimal weight: 3.9990 chunk 192 optimal weight: 0.0970 chunk 34 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 109 optimal weight: 7.9990 chunk 265 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 overall best weight: 3.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 126 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.115893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098573 restraints weight = 47637.571| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.55 r_work: 0.3210 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22820 Z= 0.129 Angle : 0.629 35.673 31066 Z= 0.303 Chirality : 0.043 0.235 3583 Planarity : 0.004 0.055 3918 Dihedral : 10.898 73.574 3546 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 4.71 % Allowed : 25.17 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.16), residues: 2786 helix: 0.27 (0.17), residues: 940 sheet: -0.84 (0.27), residues: 386 loop : -1.32 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 700 TYR 0.012 0.001 TYR F 46 PHE 0.013 0.001 PHE D1139 TRP 0.010 0.001 TRP B 199 HIS 0.004 0.001 HIS C 393 Details of bonding type rmsd covalent geometry : bond 0.00295 (22812) covalent geometry : angle 0.57698 (31054) hydrogen bonds : bond 0.04413 ( 875) hydrogen bonds : angle 4.71459 ( 2411) metal coordination : bond 0.00775 ( 8) metal coordination : angle 12.69504 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 351 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9142 (OUTLIER) cc_final: 0.8419 (p) REVERT: B 8 LYS cc_start: 0.7665 (pptt) cc_final: 0.7448 (pptt) REVERT: B 14 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7353 (tp) REVERT: B 24 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8698 (p) REVERT: B 26 GLU cc_start: 0.8517 (pm20) cc_final: 0.8308 (pm20) REVERT: B 30 ARG cc_start: 0.8265 (ttp80) cc_final: 0.8043 (mtp-110) REVERT: B 44 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8770 (mp) REVERT: B 45 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8829 (mp) REVERT: B 90 TYR cc_start: 0.7901 (m-80) cc_final: 0.7603 (m-80) REVERT: B 119 GLU cc_start: 0.7496 (mp0) cc_final: 0.7011 (mp0) REVERT: B 130 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7776 (mt) REVERT: B 137 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7591 (tmt170) REVERT: B 140 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8650 (mt) REVERT: B 199 TRP cc_start: 0.7776 (m-90) cc_final: 0.7545 (m-90) REVERT: C 106 VAL cc_start: 0.7515 (p) cc_final: 0.7303 (t) REVERT: C 264 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7882 (mtm180) REVERT: C 286 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: C 339 GLU cc_start: 0.0815 (OUTLIER) cc_final: 0.0071 (mt-10) REVERT: C 485 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8818 (ptp-110) REVERT: C 489 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8254 (mt) REVERT: C 584 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7524 (pt0) REVERT: C 595 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7312 (ptt-90) REVERT: D 158 TYR cc_start: 0.7973 (m-80) cc_final: 0.7745 (m-80) REVERT: D 177 LYS cc_start: 0.8273 (mmtt) cc_final: 0.8051 (mtpt) REVERT: D 205 ARG cc_start: 0.8643 (ptp90) cc_final: 0.8288 (ptp90) REVERT: D 208 LYS cc_start: 0.9129 (mmtm) cc_final: 0.8872 (mmtm) REVERT: D 214 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7479 (mm-30) REVERT: D 289 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7133 (tp40) REVERT: D 593 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7884 (ttp80) REVERT: D 670 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7669 (tp40) REVERT: D 674 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7742 (mm-30) REVERT: D 689 ARG cc_start: 0.7967 (mmp80) cc_final: 0.7723 (mmp80) REVERT: D 700 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7617 (mtp180) REVERT: D 950 THR cc_start: 0.8238 (p) cc_final: 0.7905 (p) REVERT: D 963 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7831 (mtt90) outliers start: 109 outliers final: 68 residues processed: 446 average time/residue: 0.1937 time to fit residues: 126.0095 Evaluate side-chains 414 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 330 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1134 GLU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 86 optimal weight: 0.0060 chunk 204 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 232 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 overall best weight: 7.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 126 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 743 GLN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 ASN D 957 GLN ** D 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.096261 restraints weight = 47928.324| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.56 r_work: 0.3162 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22820 Z= 0.218 Angle : 0.677 36.009 31066 Z= 0.329 Chirality : 0.045 0.282 3583 Planarity : 0.004 0.047 3918 Dihedral : 10.930 73.814 3537 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer: Outliers : 6.14 % Allowed : 24.78 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2786 helix: 0.27 (0.17), residues: 933 sheet: -0.88 (0.27), residues: 386 loop : -1.28 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 139 TYR 0.014 0.001 TYR D 500 PHE 0.018 0.001 PHE C 470 TRP 0.010 0.001 TRP B 199 HIS 0.004 0.001 HIS D1097 Details of bonding type rmsd covalent geometry : bond 0.00514 (22812) covalent geometry : angle 0.62888 (31054) hydrogen bonds : bond 0.05055 ( 875) hydrogen bonds : angle 4.84316 ( 2411) metal coordination : bond 0.00898 ( 8) metal coordination : angle 12.83081 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 331 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9296 (OUTLIER) cc_final: 0.8785 (p) REVERT: B 14 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7346 (tp) REVERT: B 30 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8100 (mtp-110) REVERT: B 44 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8822 (mp) REVERT: B 140 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8664 (mt) REVERT: B 181 GLU cc_start: 0.7872 (mp0) cc_final: 0.7260 (pm20) REVERT: B 199 TRP cc_start: 0.7871 (m-90) cc_final: 0.7410 (m-90) REVERT: C 264 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8027 (mmm-85) REVERT: C 339 GLU cc_start: 0.0891 (OUTLIER) cc_final: 0.0130 (mt-10) REVERT: C 485 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8848 (ptp-110) REVERT: C 489 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8317 (mt) REVERT: C 584 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7558 (pt0) REVERT: C 595 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7316 (ptt-90) REVERT: C 944 MET cc_start: 0.8859 (mmm) cc_final: 0.8648 (mmm) REVERT: C 1140 MET cc_start: 0.8802 (mmp) cc_final: 0.8248 (mmp) REVERT: D 180 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: D 205 ARG cc_start: 0.8677 (ptp90) cc_final: 0.8302 (ptp90) REVERT: D 208 LYS cc_start: 0.9145 (mmtm) cc_final: 0.8891 (mmtm) REVERT: D 214 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7548 (mm-30) REVERT: D 289 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: D 593 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7914 (ttp80) REVERT: D 670 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7664 (tp40) REVERT: D 674 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7739 (mm-30) REVERT: D 963 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7393 (mtt90) REVERT: F 25 ARG cc_start: 0.8263 (ptp-170) cc_final: 0.7942 (ptp-170) outliers start: 142 outliers final: 101 residues processed: 452 average time/residue: 0.1880 time to fit residues: 125.3886 Evaluate side-chains 431 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 317 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 827 LYS Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1003 THR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 72 optimal weight: 10.0000 chunk 273 optimal weight: 9.9990 chunk 262 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 258 optimal weight: 7.9990 chunk 76 optimal weight: 50.0000 chunk 252 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 263 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 ASN ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.114871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.097515 restraints weight = 47593.379| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.56 r_work: 0.3185 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22820 Z= 0.161 Angle : 0.652 33.473 31066 Z= 0.317 Chirality : 0.044 0.322 3583 Planarity : 0.004 0.045 3918 Dihedral : 10.862 73.697 3537 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 5.71 % Allowed : 25.74 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % 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: -0.93 (0.16), residues: 2786 helix: 0.40 (0.17), residues: 927 sheet: -0.84 (0.27), residues: 398 loop : -1.21 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 139 TYR 0.020 0.001 TYR D 162 PHE 0.016 0.001 PHE A 224 TRP 0.012 0.001 TRP B 199 HIS 0.004 0.001 HIS D1097 Details of bonding type rmsd covalent geometry : bond 0.00380 (22812) covalent geometry : angle 0.60593 (31054) hydrogen bonds : bond 0.04632 ( 875) hydrogen bonds : angle 4.72681 ( 2411) metal coordination : bond 0.00779 ( 8) metal coordination : angle 12.24552 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 334 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9302 (OUTLIER) cc_final: 0.8612 (p) REVERT: B 14 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7347 (tp) REVERT: B 30 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8065 (mtp-110) REVERT: B 44 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8804 (mp) REVERT: B 45 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8864 (mp) REVERT: B 90 TYR cc_start: 0.7966 (m-80) cc_final: 0.7530 (m-80) REVERT: B 137 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7557 (tmt170) REVERT: B 140 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8654 (mt) REVERT: B 181 GLU cc_start: 0.7836 (mp0) cc_final: 0.7196 (pm20) REVERT: B 199 TRP cc_start: 0.7833 (m-90) cc_final: 0.7392 (m-90) REVERT: C 42 ASP cc_start: 0.7808 (m-30) cc_final: 0.7591 (m-30) REVERT: C 264 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.7904 (mtm180) REVERT: C 339 GLU cc_start: 0.0944 (OUTLIER) cc_final: 0.0206 (mt-10) REVERT: C 485 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8818 (ptp-110) REVERT: C 489 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8297 (mt) REVERT: C 505 ASP cc_start: 0.8248 (t0) cc_final: 0.7624 (t0) REVERT: C 584 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7513 (pt0) REVERT: C 595 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7328 (ptt-90) REVERT: C 944 MET cc_start: 0.8867 (mmm) cc_final: 0.8627 (mmm) REVERT: D 180 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8197 (pm20) REVERT: D 205 ARG cc_start: 0.8653 (ptp90) cc_final: 0.8303 (ptp90) REVERT: D 208 LYS cc_start: 0.9156 (mmtm) cc_final: 0.8880 (mmtm) REVERT: D 214 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7529 (mm-30) REVERT: D 289 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: D 593 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.7852 (ttp80) REVERT: D 669 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.8057 (tttm) REVERT: D 785 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7596 (ttmm) REVERT: D 963 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7713 (mtt90) REVERT: F 25 ARG cc_start: 0.8256 (ptp-170) cc_final: 0.7927 (ptp-170) outliers start: 132 outliers final: 93 residues processed: 445 average time/residue: 0.1950 time to fit residues: 126.6561 Evaluate side-chains 422 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 313 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1095 ILE Chi-restraints excluded: chain C residue 1108 LYS Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 785 LYS Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 827 LYS Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 152 optimal weight: 0.0070 chunk 274 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 126 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.114885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.097489 restraints weight = 47659.224| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.54 r_work: 0.3186 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22820 Z= 0.173 Angle : 0.668 32.997 31066 Z= 0.324 Chirality : 0.044 0.422 3583 Planarity : 0.004 0.044 3918 Dihedral : 10.847 73.709 3534 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 5.75 % Allowed : 25.69 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.16), residues: 2786 helix: 0.40 (0.17), residues: 929 sheet: -0.75 (0.28), residues: 379 loop : -1.18 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 188 TYR 0.020 0.001 TYR D 162 PHE 0.015 0.001 PHE C 470 TRP 0.010 0.001 TRP B 199 HIS 0.004 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00410 (22812) covalent geometry : angle 0.62451 (31054) hydrogen bonds : bond 0.04702 ( 875) hydrogen bonds : angle 4.73238 ( 2411) metal coordination : bond 0.00785 ( 8) metal coordination : angle 12.11379 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 325 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9300 (OUTLIER) cc_final: 0.8794 (p) REVERT: B 14 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7354 (tp) REVERT: B 30 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8067 (mtp-110) REVERT: B 44 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8815 (mp) REVERT: B 45 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8836 (mp) REVERT: B 119 GLU cc_start: 0.7760 (pm20) cc_final: 0.7265 (pm20) REVERT: B 137 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7563 (tmt170) REVERT: B 140 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8660 (mt) REVERT: B 181 GLU cc_start: 0.7839 (mp0) cc_final: 0.7196 (pm20) REVERT: B 199 TRP cc_start: 0.7803 (m-90) cc_final: 0.7537 (m-90) REVERT: C 264 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.7894 (mtm180) REVERT: C 339 GLU cc_start: 0.0933 (OUTLIER) cc_final: 0.0204 (mt-10) REVERT: C 485 ARG cc_start: 0.9109 (OUTLIER) cc_final: 0.8807 (ptp-110) REVERT: C 489 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8319 (mt) REVERT: C 584 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7503 (pt0) REVERT: C 595 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7346 (ptt-90) REVERT: C 932 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8356 (mttp) REVERT: C 1140 MET cc_start: 0.8746 (mmp) cc_final: 0.8261 (mmp) REVERT: D 180 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: D 205 ARG cc_start: 0.8647 (ptp90) cc_final: 0.8252 (ptp90) REVERT: D 208 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8873 (mmtm) REVERT: D 214 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7536 (mm-30) REVERT: D 289 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7043 (tp40) REVERT: D 593 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7910 (ttp80) REVERT: D 669 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7998 (tttp) REVERT: D 674 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8031 (mm-30) REVERT: D 785 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7750 (ttmm) REVERT: D 933 GLN cc_start: 0.7184 (mp-120) cc_final: 0.6926 (mp-120) REVERT: D 950 THR cc_start: 0.8310 (p) cc_final: 0.7863 (p) REVERT: D 951 GLN cc_start: 0.8440 (pm20) cc_final: 0.8164 (mm-40) REVERT: D 963 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7396 (mtt90) REVERT: F 25 ARG cc_start: 0.8247 (ptp-170) cc_final: 0.7919 (ptp-170) outliers start: 133 outliers final: 103 residues processed: 437 average time/residue: 0.1878 time to fit residues: 120.0822 Evaluate side-chains 435 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 316 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 57 GLN Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1058 LEU Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1108 LYS Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 785 LYS Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 827 LYS Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 266 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 258 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.115223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097850 restraints weight = 47536.357| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.55 r_work: 0.3189 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22820 Z= 0.162 Angle : 0.678 32.079 31066 Z= 0.329 Chirality : 0.044 0.424 3583 Planarity : 0.004 0.043 3918 Dihedral : 10.837 73.688 3534 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 5.45 % Allowed : 25.91 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % 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: -0.84 (0.16), residues: 2786 helix: 0.45 (0.17), residues: 928 sheet: -0.70 (0.28), residues: 375 loop : -1.17 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 735 TYR 0.018 0.001 TYR D 162 PHE 0.014 0.001 PHE C 470 TRP 0.011 0.001 TRP B 199 HIS 0.004 0.001 HIS D1097 Details of bonding type rmsd covalent geometry : bond 0.00385 (22812) covalent geometry : angle 0.63634 (31054) hydrogen bonds : bond 0.04621 ( 875) hydrogen bonds : angle 4.69870 ( 2411) metal coordination : bond 0.00761 ( 8) metal coordination : angle 11.89726 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 324 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.8810 (p) REVERT: B 14 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7337 (tp) REVERT: B 30 ARG cc_start: 0.8279 (ttp80) cc_final: 0.8060 (mtp-110) REVERT: B 44 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8792 (mp) REVERT: B 45 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8859 (mp) REVERT: B 137 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7561 (tmt170) REVERT: B 140 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8640 (mt) REVERT: B 181 GLU cc_start: 0.7810 (mp0) cc_final: 0.7171 (pm20) REVERT: B 199 TRP cc_start: 0.7792 (m-90) cc_final: 0.7416 (m-90) REVERT: C 218 ARG cc_start: 0.6521 (ptp-170) cc_final: 0.6035 (ptp-170) REVERT: C 264 ARG cc_start: 0.8465 (mmm-85) cc_final: 0.7917 (mtp180) REVERT: C 286 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.7218 (m-80) REVERT: C 339 GLU cc_start: 0.0902 (OUTLIER) cc_final: 0.0172 (mt-10) REVERT: C 438 GLN cc_start: 0.7198 (tm-30) cc_final: 0.6943 (tm-30) REVERT: C 485 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8798 (ptp-110) REVERT: C 489 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8301 (mt) REVERT: C 584 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: C 595 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7324 (ptt-90) REVERT: C 944 MET cc_start: 0.8882 (mmm) cc_final: 0.8635 (mmm) REVERT: C 1140 MET cc_start: 0.8758 (mmp) cc_final: 0.8272 (mmp) REVERT: D 180 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: D 205 ARG cc_start: 0.8690 (ptp90) cc_final: 0.8300 (ptp90) REVERT: D 208 LYS cc_start: 0.9137 (mmtm) cc_final: 0.8851 (mmtm) REVERT: D 214 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7573 (mm-30) REVERT: D 289 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: D 593 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7879 (ttp80) REVERT: D 669 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7966 (tttp) REVERT: D 674 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8162 (mm-30) REVERT: D 834 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7469 (tm-30) REVERT: D 933 GLN cc_start: 0.7183 (mp-120) cc_final: 0.6930 (mp-120) REVERT: D 950 THR cc_start: 0.8301 (p) cc_final: 0.7854 (p) REVERT: D 951 GLN cc_start: 0.8416 (pm20) cc_final: 0.8142 (mm-40) REVERT: D 963 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7357 (mtt90) REVERT: F 25 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.7887 (ptp-170) outliers start: 126 outliers final: 106 residues processed: 431 average time/residue: 0.1990 time to fit residues: 125.1807 Evaluate side-chains 440 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 318 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 643 MET Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 827 LYS Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1107 LEU Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 226 optimal weight: 20.0000 chunk 259 optimal weight: 7.9990 chunk 265 optimal weight: 9.9990 chunk 24 optimal weight: 0.0370 chunk 52 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 152 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN B 126 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.115221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097762 restraints weight = 47828.379| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.57 r_work: 0.3187 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22820 Z= 0.174 Angle : 0.686 31.810 31066 Z= 0.333 Chirality : 0.045 0.426 3583 Planarity : 0.004 0.044 3918 Dihedral : 10.850 73.691 3534 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 5.62 % Allowed : 25.74 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.40 % 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: -0.83 (0.16), residues: 2786 helix: 0.44 (0.17), residues: 929 sheet: -0.69 (0.28), residues: 375 loop : -1.15 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 218 TYR 0.018 0.001 TYR D 162 PHE 0.015 0.001 PHE C 470 TRP 0.011 0.001 TRP B 199 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00412 (22812) covalent geometry : angle 0.64547 (31054) hydrogen bonds : bond 0.04705 ( 875) hydrogen bonds : angle 4.71936 ( 2411) metal coordination : bond 0.00778 ( 8) metal coordination : angle 11.85015 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 317 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 SER cc_start: 0.9309 (OUTLIER) cc_final: 0.8821 (p) REVERT: B 14 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7348 (tp) REVERT: B 30 ARG cc_start: 0.8292 (ttp80) cc_final: 0.8074 (mtp-110) REVERT: B 44 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8809 (mp) REVERT: B 45 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8879 (mp) REVERT: B 140 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8673 (mt) REVERT: B 181 GLU cc_start: 0.7798 (mp0) cc_final: 0.7190 (pm20) REVERT: B 199 TRP cc_start: 0.7804 (m-90) cc_final: 0.7440 (m-90) REVERT: C 218 ARG cc_start: 0.6456 (ptp-170) cc_final: 0.5753 (ptp90) REVERT: C 264 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.7901 (mtp180) REVERT: C 339 GLU cc_start: 0.1038 (OUTLIER) cc_final: 0.0383 (mt-10) REVERT: C 489 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8314 (mt) REVERT: C 505 ASP cc_start: 0.8357 (t0) cc_final: 0.7639 (t0) REVERT: C 584 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: C 595 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7352 (ptt-90) REVERT: C 932 LYS cc_start: 0.8479 (mtmt) cc_final: 0.8240 (mttp) REVERT: C 944 MET cc_start: 0.8900 (mmm) cc_final: 0.8659 (mmm) REVERT: C 1140 MET cc_start: 0.8757 (mmp) cc_final: 0.8304 (mmp) REVERT: D 158 TYR cc_start: 0.8033 (m-80) cc_final: 0.7794 (m-80) REVERT: D 180 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8068 (pm20) REVERT: D 205 ARG cc_start: 0.8661 (ptp90) cc_final: 0.8271 (ptp90) REVERT: D 208 LYS cc_start: 0.9154 (mmtm) cc_final: 0.8843 (mmtm) REVERT: D 214 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7136 (mm-30) REVERT: D 218 ASN cc_start: 0.8354 (m110) cc_final: 0.7645 (m110) REVERT: D 289 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7056 (tp40) REVERT: D 593 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7918 (ttp80) REVERT: D 669 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8011 (tttp) REVERT: D 670 GLN cc_start: 0.8369 (tp40) cc_final: 0.7940 (tp40) REVERT: D 785 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7635 (ttmm) REVERT: D 834 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7482 (tm-30) REVERT: D 853 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8502 (mmpt) REVERT: D 933 GLN cc_start: 0.7183 (mp-120) cc_final: 0.6932 (mp-120) REVERT: D 936 MET cc_start: 0.5773 (tpt) cc_final: 0.4616 (tpt) REVERT: D 951 GLN cc_start: 0.8435 (pm20) cc_final: 0.8163 (mm-40) REVERT: D 963 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7367 (mtt90) REVERT: F 25 ARG cc_start: 0.8255 (ptp-170) cc_final: 0.7924 (ptp-170) outliers start: 130 outliers final: 112 residues processed: 424 average time/residue: 0.2046 time to fit residues: 126.3859 Evaluate side-chains 441 residues out of total 2411 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 314 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 49 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 339 GLU Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 530 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 584 GLU Chi-restraints excluded: chain C residue 589 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain C residue 600 ASN Chi-restraints excluded: chain C residue 616 LYS Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 643 MET Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 749 GLU Chi-restraints excluded: chain C residue 873 ARG Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 949 ASP Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1031 SER Chi-restraints excluded: chain C residue 1094 GLU Chi-restraints excluded: chain C residue 1098 VAL Chi-restraints excluded: chain D residue 9 TYR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 60 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 278 SER Chi-restraints excluded: chain D residue 283 ASN Chi-restraints excluded: chain D residue 289 GLN Chi-restraints excluded: chain D residue 359 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 473 MET Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 593 ARG Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 661 SER Chi-restraints excluded: chain D residue 665 VAL Chi-restraints excluded: chain D residue 669 LYS Chi-restraints excluded: chain D residue 719 SER Chi-restraints excluded: chain D residue 740 ASN Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 785 LYS Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 827 LYS Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 861 LEU Chi-restraints excluded: chain D residue 960 PHE Chi-restraints excluded: chain D residue 963 ARG Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 992 VAL Chi-restraints excluded: chain D residue 1002 TYR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1060 VAL Chi-restraints excluded: chain D residue 1080 VAL Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1108 LEU Chi-restraints excluded: chain D residue 1123 ILE Chi-restraints excluded: chain D residue 1135 SER Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain F residue 16 LYS Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 208 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 276 optimal weight: 0.0770 chunk 174 optimal weight: 40.0000 chunk 101 optimal weight: 5.9990 chunk 202 optimal weight: 0.0370 chunk 135 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 overall best weight: 3.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 126 HIS ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 931 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.114988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097550 restraints weight = 47684.463| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.58 r_work: 0.3189 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 22820 Z= 0.246 Angle : 0.933 59.200 31066 Z= 0.548 Chirality : 0.047 0.952 3583 Planarity : 0.005 0.091 3918 Dihedral : 10.854 73.678 3534 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 5.62 % Allowed : 25.91 % Favored : 68.47 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.40 % 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: -0.84 (0.16), residues: 2786 helix: 0.42 (0.17), residues: 929 sheet: -0.69 (0.28), residues: 375 loop : -1.15 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.001 ARG D 388 TYR 0.017 0.001 TYR D 162 PHE 0.015 0.001 PHE C 470 TRP 0.011 0.001 TRP B 199 HIS 0.142 0.002 HIS F 44 Details of bonding type rmsd covalent geometry : bond 0.00487 (22812) covalent geometry : angle 0.90334 (31054) hydrogen bonds : bond 0.04714 ( 875) hydrogen bonds : angle 4.73657 ( 2411) metal coordination : bond 0.00763 ( 8) metal coordination : angle 11.83862 ( 12) =============================================================================== Job complete usr+sys time: 4726.68 seconds wall clock time: 82 minutes 2.30 seconds (4922.30 seconds total)