Starting phenix.real_space_refine on Sat Sep 12 22:03:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ifz_9659/09_2026/6ifz_9659.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ifz_9659/09_2026/6ifz_9659.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ifz_9659/09_2026/6ifz_9659.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ifz_9659/09_2026/6ifz_9659.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ifz_9659/09_2026/6ifz_9659.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ifz_9659/09_2026/6ifz_9659.map" model { file = "/net/cci-nas-00/data/ceres_data/6ifz_9659/09_2026/6ifz_9659.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ifz_9659/09_2026/6ifz_9659.cif" } resolution = 3.58 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= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 62 5.49 5 S 37 5.16 5 C 12029 2.51 5 N 3257 2.21 5 O 3799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19185 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5799 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 8, 'TRANS': 725} Chain breaks: 3 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 985 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1697 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1623 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2319 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2750 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 17, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 715 Classifications: {'RNAv2': 34} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 606 Classifications: {'RNAv2': 28} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2935 SG CYS A 404 55.785 30.462 65.300 1.00 51.21 S ATOM 3079 SG CYS A 422 58.862 33.242 65.609 1.00 46.39 S Time building chain proxies: 4.12, per 1000 atoms: 0.21 Number of scatterers: 19185 At special positions: 0 Unit cell: (93.6, 135.2, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 37 16.00 P 62 15.00 O 3799 8.00 N 3257 7.00 C 12029 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 777.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 404 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 422 " 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 23 sheets defined 37.2% alpha, 11.2% beta 21 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.805A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.832A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 4.341A pdb=" N GLN A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.639A pdb=" N THR A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.856A pdb=" N TYR A 141 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 145 through 148 Processing helix chain 'A' and resid 149 through 159 removed outlier: 4.048A pdb=" N ARG A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 179 removed outlier: 3.821A pdb=" N ASN A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 removed outlier: 4.041A pdb=" N PHE A 183 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 184 " --> pdb=" O LEU A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 197 through 219 removed outlier: 4.958A pdb=" N ARG A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.682A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 266 through 291 removed outlier: 3.964A pdb=" N ARG A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 335 removed outlier: 3.690A pdb=" N THR A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 378 removed outlier: 4.213A pdb=" N TYR A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLN A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.824A pdb=" N ASN A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 removed outlier: 4.608A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 removed outlier: 4.022A pdb=" N SER A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.684A pdb=" N LYS A 503 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 529 removed outlier: 3.776A pdb=" N ALA A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 558 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.219A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 638 removed outlier: 3.586A pdb=" N GLN A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.609A pdb=" N ILE A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 675 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.978A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.773A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 732 removed outlier: 3.795A pdb=" N LEU A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 Processing helix chain 'D' and resid 8 through 18 removed outlier: 3.652A pdb=" N ALA D 16 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 57 removed outlier: 3.569A pdb=" N LEU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 78 removed outlier: 4.029A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 removed outlier: 4.111A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 97 removed outlier: 3.626A pdb=" N LYS D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 4.166A pdb=" N ARG D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 122 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 18 Processing helix chain 'C' and resid 37 through 55 removed outlier: 4.749A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 64 through 78 removed outlier: 3.765A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 101 through 122 Processing helix chain 'G' and resid 48 through 62 removed outlier: 3.542A pdb=" N LEU G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 177 removed outlier: 3.742A pdb=" N ASP G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE G 167 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS G 168 " --> pdb=" O GLU G 164 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.669A pdb=" N LEU F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 83 removed outlier: 3.527A pdb=" N SER F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.634A pdb=" N PHE F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.523A pdb=" N GLY F 189 " --> pdb=" O GLY F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 211 removed outlier: 3.550A pdb=" N THR F 211 " --> pdb=" O ASP F 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 212 through 217 removed outlier: 3.867A pdb=" N LEU F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 61 removed outlier: 3.873A pdb=" N LYS E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 162 through 165 Processing helix chain 'E' and resid 166 through 178 removed outlier: 4.171A pdb=" N ASP E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 176 " --> pdb=" O ASP E 172 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.804A pdb=" N GLY E 189 " --> pdb=" O GLY E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 96 through 101 Processing helix chain 'B' and resid 110 through 118 removed outlier: 4.024A pdb=" N LEU B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.540A pdb=" N GLY B 185 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.649A pdb=" N ASP B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 52 through 54 No H-bonds generated for 'chain 'H' and resid 52 through 54' Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.582A pdb=" N LEU H 63 " --> pdb=" O PHE H 59 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.591A pdb=" N LEU H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 148 removed outlier: 4.065A pdb=" N ASN H 148 " --> pdb=" O PRO H 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 145 through 148' Processing helix chain 'H' and resid 236 through 245 removed outlier: 3.663A pdb=" N LEU H 242 " --> pdb=" O GLU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 259 removed outlier: 4.558A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 270 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 removed outlier: 4.418A pdb=" N GLN A 107 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.517A pdb=" N ALA A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 569 through 574 removed outlier: 4.754A pdb=" N ILE A 571 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 582 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 612 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 96 through 97 Processing sheet with id=AA7, first strand: chain 'G' and resid 102 through 103 removed outlier: 4.161A pdb=" N PHE G 102 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS G 5 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 118 through 122 Processing sheet with id=AA9, first strand: chain 'F' and resid 146 through 149 Processing sheet with id=AB1, first strand: chain 'F' and resid 146 through 149 removed outlier: 7.037A pdb=" N LYS F 5 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR F 202 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS F 7 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA F 200 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N SER F 9 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU F 198 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 118 through 123 Processing sheet with id=AB3, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 149 removed outlier: 6.301A pdb=" N SER E 9 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU E 198 " --> pdb=" O SER E 9 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.748A pdb=" N LEU E 44 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 118 through 123 Processing sheet with id=AB7, first strand: chain 'B' and resid 64 through 65 removed outlier: 4.020A pdb=" N PHE B 64 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 158 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA B 160 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS B 4 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB9, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AC1, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.512A pdb=" N TYR B 143 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 211 through 213 Processing sheet with id=AC3, first strand: chain 'H' and resid 227 through 230 Processing sheet with id=AC4, first strand: chain 'H' and resid 32 through 33 Processing sheet with id=AC5, first strand: chain 'H' and resid 203 through 206 598 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 50 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3478 1.32 - 1.45: 5330 1.45 - 1.57: 10677 1.57 - 1.69: 123 1.69 - 1.82: 66 Bond restraints: 19674 Sorted by residual: bond pdb=" C GLN H 275 " pdb=" N TYR H 276 " ideal model delta sigma weight residual 1.331 1.422 -0.091 2.07e-02 2.33e+03 1.95e+01 bond pdb=" N TYR G 181 " pdb=" CA TYR G 181 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.32e-02 5.74e+03 9.20e+00 bond pdb=" N LEU A 160 " pdb=" CA LEU A 160 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 8.07e+00 bond pdb=" CA ARG H 158 " pdb=" C ARG H 158 " ideal model delta sigma weight residual 1.523 1.562 -0.040 1.41e-02 5.03e+03 7.89e+00 bond pdb=" N ILE E 29 " pdb=" CA ILE E 29 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.47e+00 ... (remaining 19669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 26364 3.77 - 7.54: 417 7.54 - 11.32: 38 11.32 - 15.09: 8 15.09 - 18.86: 2 Bond angle restraints: 26829 Sorted by residual: angle pdb=" N GLY H 314 " pdb=" CA GLY H 314 " pdb=" C GLY H 314 " ideal model delta sigma weight residual 112.73 127.67 -14.94 1.20e+00 6.94e-01 1.55e+02 angle pdb=" N SER H 107 " pdb=" CA SER H 107 " pdb=" C SER H 107 " ideal model delta sigma weight residual 112.45 95.21 17.24 1.39e+00 5.18e-01 1.54e+02 angle pdb=" N ARG F 95 " pdb=" CA ARG F 95 " pdb=" C ARG F 95 " ideal model delta sigma weight residual 112.24 126.42 -14.18 1.28e+00 6.10e-01 1.23e+02 angle pdb=" N ARG E 95 " pdb=" CA ARG E 95 " pdb=" C ARG E 95 " ideal model delta sigma weight residual 112.24 125.39 -13.15 1.28e+00 6.10e-01 1.06e+02 angle pdb=" N LYS H 161 " pdb=" CA LYS H 161 " pdb=" C LYS H 161 " ideal model delta sigma weight residual 110.23 121.06 -10.83 1.45e+00 4.76e-01 5.57e+01 ... (remaining 26824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.15: 11149 32.15 - 64.30: 509 64.30 - 96.45: 33 96.45 - 128.60: 0 128.60 - 160.75: 2 Dihedral angle restraints: 11693 sinusoidal: 5098 harmonic: 6595 Sorted by residual: dihedral pdb=" C4' G I 9 " pdb=" C3' G I 9 " pdb=" C2' G I 9 " pdb=" C1' G I 9 " ideal model delta sinusoidal sigma weight residual 36.34 -41.02 77.36 1 3.10e+00 1.04e-01 7.80e+02 dihedral pdb=" C4' G I 3 " pdb=" C3' G I 3 " pdb=" C2' G I 3 " pdb=" C1' G I 3 " ideal model delta sinusoidal sigma weight residual 36.34 -40.61 76.96 1 3.10e+00 1.04e-01 7.73e+02 dihedral pdb=" C4' A I 27 " pdb=" C3' A I 27 " pdb=" C2' A I 27 " pdb=" C1' A I 27 " ideal model delta sinusoidal sigma weight residual 36.34 -38.08 74.43 1 3.10e+00 1.04e-01 7.31e+02 ... (remaining 11690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2751 0.119 - 0.239: 217 0.239 - 0.358: 52 0.358 - 0.477: 5 0.477 - 0.596: 4 Chirality restraints: 3029 Sorted by residual: chirality pdb=" CA PHE H 159 " pdb=" N PHE H 159 " pdb=" C PHE H 159 " pdb=" CB PHE H 159 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.89e+00 chirality pdb=" CA ARG F 95 " pdb=" N ARG F 95 " pdb=" C ARG F 95 " pdb=" CB ARG F 95 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" CA ARG E 95 " pdb=" N ARG E 95 " pdb=" C ARG E 95 " pdb=" CB ARG E 95 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.40e+00 ... (remaining 3026 not shown) Planarity restraints: 3226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " 0.066 2.00e-02 2.50e+03 2.89e-02 2.50e+01 pdb=" N9 G I 21 " -0.071 2.00e-02 2.50e+03 pdb=" C8 G I 21 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G I 21 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G I 21 " 0.024 2.00e-02 2.50e+03 pdb=" N1 G I 21 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G I 21 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G I 21 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G I 21 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G I 21 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 638 " 0.023 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C GLY A 638 " -0.082 2.00e-02 2.50e+03 pdb=" O GLY A 638 " 0.031 2.00e-02 2.50e+03 pdb=" N ASN A 639 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " 0.055 2.00e-02 2.50e+03 2.62e-02 1.88e+01 pdb=" N9 A I 27 " -0.065 2.00e-02 2.50e+03 pdb=" C8 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A I 27 " 0.005 2.00e-02 2.50e+03 pdb=" C5 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A I 27 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A I 27 " 0.015 2.00e-02 2.50e+03 pdb=" N1 A I 27 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A I 27 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A I 27 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A I 27 " -0.005 2.00e-02 2.50e+03 ... (remaining 3223 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 7 1.99 - 2.71: 1307 2.71 - 3.44: 26631 3.44 - 4.17: 47514 4.17 - 4.90: 85260 Nonbonded interactions: 160719 Sorted by model distance: nonbonded pdb=" ND2 ASN A 639 " pdb=" OG SER A 643 " model vdw 1.258 3.120 nonbonded pdb=" CD1 LEU H 225 " pdb=" CD2 LEU H 335 " model vdw 1.771 3.880 nonbonded pdb=" CD2 LEU C 46 " pdb=" O ALA G 25 " model vdw 1.838 3.460 nonbonded pdb=" OG1 THR H 97 " pdb=" O ILE H 198 " model vdw 1.873 3.040 nonbonded pdb=" CG MET B 8 " pdb=" O LEU B 156 " model vdw 1.930 3.440 ... (remaining 160714 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 'C' selection = (chain 'D' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 99 or (resid 100 and (name N or nam \ e CA or name C or name O or name CB )) or resid 101 through 123)) } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB )) or resid 161 through 217)) selection = (chain 'F' and (resid 2 through 66 or resid 76 through 156 or (resid 157 through \ 160 and (name N or name CA or name C or name O or name CB )) or resid 161 throu \ gh 217)) selection = (chain 'G' and (resid 2 through 66 or resid 76 through 158 or (resid 159 through \ 160 and (name N or name CA or name C or name O or name CB )) or resid 161 throu \ gh 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.050 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.009 0.294 19677 Z= 0.405 Angle : 1.192 18.860 26829 Z= 0.660 Chirality : 0.079 0.596 3029 Planarity : 0.006 0.060 3226 Dihedral : 17.307 160.748 7439 Min Nonbonded Distance : 1.258 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.45 % Allowed : 10.74 % Favored : 88.81 % Rotamer: Outliers : 0.96 % Allowed : 10.93 % Favored : 88.11 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -5.16 (0.13), residues: 2226 helix: -3.36 (0.12), residues: 785 sheet: -3.36 (0.23), residues: 362 loop : -3.46 (0.14), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 136 TYR 0.028 0.003 TYR D 9 PHE 0.045 0.003 PHE F 98 TRP 0.066 0.003 TRP A 732 HIS 0.008 0.002 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00842 / 0.39 (19674) covalent geometry : angle 1.19197 / 0.66 (26829) hydrogen bonds : bond 0.17704 / 11.68 ( 630) hydrogen bonds : angle 7.97612 / 5.53 ( 1777) metal coordination : bond 0.26834 / 13.33 ( 2) Misc. bond : bond 0.06567 / 3.46 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 523 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ILE cc_start: 0.7013 (tp) cc_final: 0.6494 (tt) REVERT: A 183 PHE cc_start: 0.6605 (m-80) cc_final: 0.6281 (m-80) REVERT: A 228 LEU cc_start: 0.7736 (mp) cc_final: 0.7318 (tp) REVERT: A 384 TYR cc_start: 0.6242 (t80) cc_final: 0.6015 (t80) REVERT: A 527 PHE cc_start: 0.6482 (t80) cc_final: 0.5536 (m-10) REVERT: A 623 SER cc_start: 0.8495 (m) cc_final: 0.8269 (p) REVERT: A 641 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6452 (tttp) REVERT: D 22 ARG cc_start: 0.6446 (mpt-90) cc_final: 0.6178 (mpt-90) REVERT: D 44 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8691 (tp) REVERT: G 8 PHE cc_start: 0.7715 (m-80) cc_final: 0.7475 (m-80) REVERT: G 70 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6229 (tp30) REVERT: G 127 ASP cc_start: 0.7909 (t0) cc_final: 0.7683 (t0) REVERT: E 156 THR cc_start: 0.6417 (t) cc_final: 0.5931 (p) REVERT: B 219 LEU cc_start: 0.8059 (tt) cc_final: 0.7686 (tp) REVERT: B 278 ARG cc_start: 0.8148 (ttp-170) cc_final: 0.7891 (ttm170) REVERT: H 50 MET cc_start: 0.7759 (tmm) cc_final: 0.7552 (tmm) REVERT: H 158 ARG cc_start: 0.7564 (mpt180) cc_final: 0.6325 (ttp-170) REVERT: H 319 THR cc_start: 0.9284 (p) cc_final: 0.8499 (p) REVERT: H 345 MET cc_start: 0.8329 (tpt) cc_final: 0.7715 (tpt) outliers start: 18 outliers final: 8 residues processed: 539 average time/residue: 0.1667 time to fit residues: 133.1014 Evaluate side-chains 306 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 296 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 ASN Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain H residue 167 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 HIS A 175 ASN A 329 GLN A 436 HIS A 497 ASN A 676 HIS A 695 HIS A 699 ASN A 727 ASN D 72 GLN G 11 GLN G 159 ASN F 213 ASN E 144 ASN B 11 GLN B 81 HIS B 144 GLN B 152 ASN B 174 GLN B 284 HIS H 22 ASN H 148 ASN H 194 ASN H 275 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.121862 restraints weight = 31911.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123566 restraints weight = 26823.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124675 restraints weight = 16993.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124979 restraints weight = 14011.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125163 restraints weight = 12996.954| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19677 Z= 0.167 Angle : 0.914 17.471 26829 Z= 0.427 Chirality : 0.077 1.397 3029 Planarity : 0.005 0.081 3226 Dihedral : 12.610 147.114 3214 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.45 % Favored : 91.42 % Rotamer: Outliers : 2.62 % Allowed : 17.35 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -3.99 (0.15), residues: 2226 helix: -1.93 (0.16), residues: 764 sheet: -3.08 (0.24), residues: 346 loop : -3.04 (0.16), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 22 TYR 0.017 0.002 TYR A 74 PHE 0.023 0.002 PHE C 51 TRP 0.036 0.002 TRP A 732 HIS 0.007 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (19674) covalent geometry : angle 0.91405 / 0.43 (26829) hydrogen bonds : bond 0.04161 / 2.78 ( 630) hydrogen bonds : angle 5.39282 / 3.65 ( 1777) metal coordination : bond 0.00183 / 0.09 ( 2) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 383 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 183 PHE cc_start: 0.6575 (m-80) cc_final: 0.6239 (m-80) REVERT: A 228 LEU cc_start: 0.7522 (mp) cc_final: 0.7306 (tp) REVERT: A 278 PHE cc_start: 0.7837 (m-10) cc_final: 0.7625 (m-10) REVERT: A 384 TYR cc_start: 0.6298 (t80) cc_final: 0.5912 (t80) REVERT: A 388 MET cc_start: 0.7415 (ttm) cc_final: 0.7136 (ttm) REVERT: A 426 TYR cc_start: 0.7185 (t80) cc_final: 0.6915 (t80) REVERT: A 527 PHE cc_start: 0.6685 (t80) cc_final: 0.5398 (m-10) REVERT: A 622 ILE cc_start: 0.8702 (mp) cc_final: 0.8415 (mt) REVERT: A 641 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6652 (tptt) REVERT: A 728 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8166 (tp) REVERT: D 7 GLU cc_start: 0.7541 (pm20) cc_final: 0.7296 (pm20) REVERT: D 44 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8490 (tp) REVERT: G 64 TYR cc_start: 0.7493 (m-10) cc_final: 0.6963 (m-10) REVERT: G 124 ASN cc_start: 0.8364 (p0) cc_final: 0.8063 (p0) REVERT: G 171 ARG cc_start: 0.6656 (tmm-80) cc_final: 0.6431 (mmm160) REVERT: E 146 THR cc_start: 0.8069 (p) cc_final: 0.7798 (p) REVERT: E 174 LEU cc_start: 0.8800 (mt) cc_final: 0.8520 (mp) REVERT: B 219 LEU cc_start: 0.8048 (tt) cc_final: 0.7695 (mt) REVERT: B 278 ARG cc_start: 0.8071 (ttp-170) cc_final: 0.7748 (ttm170) REVERT: H 158 ARG cc_start: 0.7415 (mpt180) cc_final: 0.6373 (ttt90) REVERT: H 164 LYS cc_start: 0.7481 (mttt) cc_final: 0.7103 (tppt) REVERT: H 221 SER cc_start: 0.7661 (p) cc_final: 0.7374 (m) outliers start: 49 outliers final: 22 residues processed: 413 average time/residue: 0.1543 time to fit residues: 97.5951 Evaluate side-chains 314 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 289 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 641 LYS Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 138 ILE Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 199 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 197 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS A 158 ASN A 268 GLN A 312 ASN A 497 ASN C 42 ASN G 124 ASN G 137 GLN E 144 ASN B 152 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119128 restraints weight = 32363.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120779 restraints weight = 25805.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121819 restraints weight = 18489.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122042 restraints weight = 14479.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122200 restraints weight = 14033.276| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19677 Z= 0.204 Angle : 0.847 14.500 26829 Z= 0.400 Chirality : 0.071 1.425 3029 Planarity : 0.004 0.063 3226 Dihedral : 12.709 158.173 3207 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.48 % Favored : 90.43 % Rotamer: Outliers : 3.59 % Allowed : 19.39 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -3.56 (0.16), residues: 2226 helix: -1.39 (0.17), residues: 781 sheet: -2.86 (0.24), residues: 352 loop : -2.94 (0.16), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 81 TYR 0.035 0.002 TYR A 74 PHE 0.018 0.002 PHE G 167 TRP 0.028 0.002 TRP A 732 HIS 0.005 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (19674) covalent geometry : angle 0.84718 / 0.40 (26829) hydrogen bonds : bond 0.03882 / 2.59 ( 630) hydrogen bonds : angle 5.06448 / 3.41 ( 1777) metal coordination : bond 0.00240 / 0.12 ( 2) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 318 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 PHE cc_start: 0.6603 (m-80) cc_final: 0.6222 (m-80) REVERT: A 228 LEU cc_start: 0.7551 (mp) cc_final: 0.7288 (tp) REVERT: A 278 PHE cc_start: 0.7880 (m-10) cc_final: 0.7614 (m-10) REVERT: A 384 TYR cc_start: 0.6464 (t80) cc_final: 0.6005 (t80) REVERT: A 388 MET cc_start: 0.7377 (ttm) cc_final: 0.7150 (ttm) REVERT: A 527 PHE cc_start: 0.5834 (t80) cc_final: 0.5395 (m-10) REVERT: A 633 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: A 728 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8267 (tp) REVERT: D 4 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8381 (pp) REVERT: D 7 GLU cc_start: 0.7583 (pm20) cc_final: 0.7288 (pm20) REVERT: C 46 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8836 (mt) REVERT: G 64 TYR cc_start: 0.7571 (m-10) cc_final: 0.7074 (m-10) REVERT: F 79 LEU cc_start: 0.7676 (mp) cc_final: 0.7420 (tt) REVERT: F 134 ASN cc_start: 0.7981 (t0) cc_final: 0.7711 (p0) REVERT: F 172 ASP cc_start: 0.6851 (m-30) cc_final: 0.6612 (m-30) REVERT: E 150 GLU cc_start: 0.7550 (pm20) cc_final: 0.7335 (pm20) REVERT: B 5 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7995 (pp) REVERT: B 34 SER cc_start: 0.7809 (t) cc_final: 0.7462 (m) REVERT: B 219 LEU cc_start: 0.8143 (tt) cc_final: 0.7867 (mt) REVERT: H 158 ARG cc_start: 0.7537 (mpt180) cc_final: 0.6568 (ttp-170) REVERT: H 164 LYS cc_start: 0.7616 (mttt) cc_final: 0.7212 (tppt) outliers start: 67 outliers final: 40 residues processed: 362 average time/residue: 0.1472 time to fit residues: 82.4471 Evaluate side-chains 328 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 283 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 311 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 160 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN D 72 GLN G 124 ASN F 33 ASN B 152 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.143867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124242 restraints weight = 31910.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.125497 restraints weight = 25681.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126853 restraints weight = 18833.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127020 restraints weight = 14709.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.127321 restraints weight = 14954.273| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 19677 Z= 0.132 Angle : 0.763 12.495 26829 Z= 0.360 Chirality : 0.063 1.292 3029 Planarity : 0.004 0.059 3226 Dihedral : 12.569 170.722 3201 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.86 % Favored : 92.05 % Rotamer: Outliers : 3.54 % Allowed : 19.71 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -3.14 (0.16), residues: 2226 helix: -0.95 (0.18), residues: 792 sheet: -2.68 (0.25), residues: 340 loop : -2.76 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 128 TYR 0.028 0.001 TYR A 74 PHE 0.030 0.001 PHE B 64 TRP 0.027 0.002 TRP A 732 HIS 0.004 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (19674) covalent geometry : angle 0.76300 / 0.36 (26829) hydrogen bonds : bond 0.03399 / 2.26 ( 630) hydrogen bonds : angle 4.67441 / 3.14 ( 1777) metal coordination : bond 0.00127 / 0.06 ( 2) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 345 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 PHE cc_start: 0.6583 (m-80) cc_final: 0.6139 (m-80) REVERT: A 351 LYS cc_start: 0.7316 (mmpt) cc_final: 0.6578 (tptt) REVERT: A 527 PHE cc_start: 0.5896 (t80) cc_final: 0.5385 (m-80) REVERT: A 622 ILE cc_start: 0.8691 (mp) cc_final: 0.8396 (mt) REVERT: A 728 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8214 (tp) REVERT: D 7 GLU cc_start: 0.7447 (pm20) cc_final: 0.7195 (pm20) REVERT: G 64 TYR cc_start: 0.7417 (m-10) cc_final: 0.6928 (m-10) REVERT: F 89 LYS cc_start: 0.7676 (tppp) cc_final: 0.7461 (mtpt) REVERT: F 93 MET cc_start: 0.6794 (tpt) cc_final: 0.6479 (tpt) REVERT: F 126 ILE cc_start: 0.7959 (mm) cc_final: 0.7693 (mm) REVERT: F 134 ASN cc_start: 0.7872 (t0) cc_final: 0.7626 (p0) REVERT: E 123 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6835 (mt-10) REVERT: E 190 TYR cc_start: 0.8995 (m-80) cc_final: 0.8671 (m-80) REVERT: B 5 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7982 (pp) REVERT: B 219 LEU cc_start: 0.8031 (tt) cc_final: 0.7798 (mt) REVERT: H 158 ARG cc_start: 0.7213 (mpt180) cc_final: 0.6485 (ttt-90) REVERT: H 164 LYS cc_start: 0.7396 (mttt) cc_final: 0.7062 (tppt) outliers start: 66 outliers final: 39 residues processed: 385 average time/residue: 0.1483 time to fit residues: 87.6577 Evaluate side-chains 345 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 144 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 201 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN G 85 ASN G 124 ASN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116806 restraints weight = 32310.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118000 restraints weight = 30054.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121204 restraints weight = 21723.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120544 restraints weight = 15894.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121134 restraints weight = 14199.987| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 19677 Z= 0.270 Angle : 0.883 16.087 26829 Z= 0.417 Chirality : 0.070 0.902 3029 Planarity : 0.004 0.061 3226 Dihedral : 12.474 160.621 3200 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.79 % Favored : 90.12 % Rotamer: Outliers : 4.93 % Allowed : 20.19 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -3.17 (0.16), residues: 2226 helix: -0.92 (0.18), residues: 782 sheet: -2.70 (0.25), residues: 353 loop : -2.82 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 188 TYR 0.028 0.002 TYR A 74 PHE 0.023 0.002 PHE B 64 TRP 0.018 0.002 TRP A 732 HIS 0.005 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (19674) covalent geometry : angle 0.88328 / 0.42 (26829) hydrogen bonds : bond 0.03979 / 2.64 ( 630) hydrogen bonds : angle 4.96083 / 3.34 ( 1777) metal coordination : bond 0.00325 / 0.16 ( 2) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 313 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 PHE cc_start: 0.6657 (m-80) cc_final: 0.6101 (m-80) REVERT: A 527 PHE cc_start: 0.5922 (t80) cc_final: 0.5364 (m-80) REVERT: A 633 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: A 728 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8167 (tp) REVERT: D 4 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8386 (pp) REVERT: D 85 ASP cc_start: 0.7391 (t0) cc_final: 0.7040 (t0) REVERT: G 64 TYR cc_start: 0.7545 (m-10) cc_final: 0.6911 (m-10) REVERT: G 164 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7083 (pm20) REVERT: G 168 LYS cc_start: 0.6961 (mmmt) cc_final: 0.6626 (tppt) REVERT: F 89 LYS cc_start: 0.7810 (tppp) cc_final: 0.7539 (mtpt) REVERT: F 129 ILE cc_start: 0.8094 (mm) cc_final: 0.7836 (pt) REVERT: E 123 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7053 (mt-10) REVERT: E 171 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6841 (mtp-110) REVERT: B 78 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6278 (t80) REVERT: B 219 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7955 (mt) REVERT: H 158 ARG cc_start: 0.7391 (mpt180) cc_final: 0.6477 (ttt-90) REVERT: H 164 LYS cc_start: 0.7598 (mttt) cc_final: 0.7188 (tppt) outliers start: 92 outliers final: 63 residues processed: 374 average time/residue: 0.1519 time to fit residues: 87.1183 Evaluate side-chains 356 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 286 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 19 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 311 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 47 optimal weight: 0.0020 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN G 124 ASN G 137 GLN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.140498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119863 restraints weight = 32030.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121317 restraints weight = 24458.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122566 restraints weight = 17671.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122805 restraints weight = 13898.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122963 restraints weight = 13336.019| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19677 Z= 0.169 Angle : 0.794 13.805 26829 Z= 0.375 Chirality : 0.062 0.765 3029 Planarity : 0.004 0.060 3226 Dihedral : 12.436 166.474 3200 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.72 % Favored : 91.19 % Rotamer: Outliers : 4.28 % Allowed : 22.23 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -2.92 (0.17), residues: 2226 helix: -0.69 (0.18), residues: 788 sheet: -2.59 (0.25), residues: 347 loop : -2.70 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 136 TYR 0.025 0.001 TYR A 74 PHE 0.032 0.002 PHE A 548 TRP 0.023 0.002 TRP A 732 HIS 0.005 0.001 HIS A 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (19674) covalent geometry : angle 0.79353 / 0.37 (26829) hydrogen bonds : bond 0.03569 / 2.37 ( 630) hydrogen bonds : angle 4.75620 / 3.21 ( 1777) metal coordination : bond 0.00125 / 0.06 ( 2) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 319 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 PHE cc_start: 0.6704 (m-80) cc_final: 0.6070 (m-80) REVERT: A 351 LYS cc_start: 0.7407 (mmpt) cc_final: 0.6510 (tptt) REVERT: A 527 PHE cc_start: 0.5884 (t80) cc_final: 0.5403 (m-80) REVERT: A 633 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: A 728 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8100 (tp) REVERT: D 4 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8423 (pp) REVERT: D 7 GLU cc_start: 0.7542 (pm20) cc_final: 0.7296 (pm20) REVERT: G 64 TYR cc_start: 0.7467 (m-10) cc_final: 0.6897 (m-10) REVERT: G 164 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: G 168 LYS cc_start: 0.6878 (mmmt) cc_final: 0.6590 (tppt) REVERT: F 89 LYS cc_start: 0.7751 (tppp) cc_final: 0.7511 (mtpt) REVERT: E 123 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6997 (mt-10) REVERT: E 171 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6563 (mtp-110) REVERT: B 78 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6697 (t80) REVERT: B 219 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7861 (mt) REVERT: H 158 ARG cc_start: 0.7392 (mpt180) cc_final: 0.6466 (ttt-90) REVERT: H 164 LYS cc_start: 0.7491 (mttt) cc_final: 0.7141 (tppt) outliers start: 80 outliers final: 54 residues processed: 374 average time/residue: 0.1411 time to fit residues: 81.1768 Evaluate side-chains 362 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 19 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 311 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 29 optimal weight: 0.0570 chunk 127 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN D 72 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 174 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 = 0.3750 r_free = 0.3750 target = 0.142247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121761 restraints weight = 32196.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123672 restraints weight = 24340.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124948 restraints weight = 16966.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125137 restraints weight = 12819.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125342 restraints weight = 12676.464| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19677 Z= 0.146 Angle : 0.770 12.722 26829 Z= 0.363 Chirality : 0.060 0.729 3029 Planarity : 0.004 0.057 3226 Dihedral : 12.342 168.730 3200 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.33 % Rotamer: Outliers : 4.12 % Allowed : 22.87 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -2.71 (0.17), residues: 2226 helix: -0.50 (0.18), residues: 791 sheet: -2.44 (0.25), residues: 345 loop : -2.60 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 136 TYR 0.025 0.001 TYR A 300 PHE 0.042 0.001 PHE A 548 TRP 0.022 0.002 TRP A 732 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (19674) covalent geometry : angle 0.77025 / 0.36 (26829) hydrogen bonds : bond 0.03499 / 2.32 ( 630) hydrogen bonds : angle 4.65727 / 3.14 ( 1777) metal coordination : bond 0.00160 / 0.08 ( 2) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 328 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.6935 (pp20) cc_final: 0.6684 (pp20) REVERT: A 178 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7973 (mm-30) REVERT: A 351 LYS cc_start: 0.7374 (mmpt) cc_final: 0.6507 (tptt) REVERT: A 728 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8021 (tp) REVERT: D 7 GLU cc_start: 0.7528 (pm20) cc_final: 0.7231 (pm20) REVERT: G 64 TYR cc_start: 0.7405 (m-10) cc_final: 0.6834 (m-10) REVERT: G 164 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: F 89 LYS cc_start: 0.7704 (tppp) cc_final: 0.7494 (mtpt) REVERT: E 123 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6983 (mt-10) REVERT: E 171 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6544 (mtp-110) REVERT: B 78 TYR cc_start: 0.7303 (OUTLIER) cc_final: 0.6704 (t80) REVERT: B 219 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7886 (mt) REVERT: H 164 LYS cc_start: 0.7459 (mttt) cc_final: 0.7183 (tppt) outliers start: 77 outliers final: 52 residues processed: 381 average time/residue: 0.1421 time to fit residues: 83.3060 Evaluate side-chains 364 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 306 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 19 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 173 LYS Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 311 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 180 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 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 = 0.3705 r_free = 0.3705 target = 0.138656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118508 restraints weight = 32178.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120235 restraints weight = 26979.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121121 restraints weight = 19413.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.121339 restraints weight = 15801.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121548 restraints weight = 15086.706| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19677 Z= 0.221 Angle : 0.841 14.514 26829 Z= 0.397 Chirality : 0.065 0.793 3029 Planarity : 0.004 0.057 3226 Dihedral : 12.374 164.099 3200 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.48 % Favored : 90.43 % Rotamer: Outliers : 4.28 % Allowed : 22.82 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -2.76 (0.17), residues: 2226 helix: -0.55 (0.18), residues: 791 sheet: -2.41 (0.26), residues: 351 loop : -2.63 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 188 TYR 0.023 0.002 TYR A 74 PHE 0.057 0.002 PHE A 548 TRP 0.024 0.002 TRP A 38 HIS 0.004 0.001 HIS A 627 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (19674) covalent geometry : angle 0.84062 / 0.40 (26829) hydrogen bonds : bond 0.03856 / 2.57 ( 630) hydrogen bonds : angle 4.87555 / 3.27 ( 1777) metal coordination : bond 0.00202 / 0.10 ( 2) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 301 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.6900 (pp20) cc_final: 0.6678 (pp20) REVERT: A 236 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.7165 (t80) REVERT: A 351 LYS cc_start: 0.7400 (mmpt) cc_final: 0.6537 (tptt) REVERT: A 728 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8073 (tp) REVERT: D 7 GLU cc_start: 0.7576 (pm20) cc_final: 0.7352 (pm20) REVERT: D 85 ASP cc_start: 0.7426 (t0) cc_final: 0.6544 (t0) REVERT: D 89 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7091 (mttt) REVERT: G 64 TYR cc_start: 0.7483 (m-10) cc_final: 0.6879 (m-10) REVERT: G 164 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: G 168 LYS cc_start: 0.6959 (mmmt) cc_final: 0.6584 (tppt) REVERT: F 89 LYS cc_start: 0.7817 (tppp) cc_final: 0.7556 (mtpt) REVERT: E 123 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7031 (mt-10) REVERT: E 171 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6545 (mtp-110) REVERT: B 78 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6884 (t80) REVERT: B 219 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7878 (mt) REVERT: H 158 ARG cc_start: 0.7367 (mpt180) cc_final: 0.6439 (ttt-90) REVERT: H 164 LYS cc_start: 0.7542 (mttt) cc_final: 0.7191 (tppt) outliers start: 80 outliers final: 61 residues processed: 354 average time/residue: 0.1422 time to fit residues: 78.2676 Evaluate side-chains 359 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 291 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 89 LYS Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 19 HIS Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 173 LYS Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 311 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 225 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 174 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 94 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.6745 > 50:) chunk 7 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN G 124 ASN B 134 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122716 restraints weight = 32107.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124608 restraints weight = 25158.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125777 restraints weight = 17425.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125971 restraints weight = 13521.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126140 restraints weight = 13266.387| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19677 Z= 0.140 Angle : 0.774 14.066 26829 Z= 0.365 Chirality : 0.059 0.722 3029 Planarity : 0.004 0.052 3226 Dihedral : 12.318 169.894 3198 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.45 % Favored : 91.46 % Rotamer: Outliers : 3.96 % Allowed : 23.62 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -2.52 (0.17), residues: 2226 helix: -0.35 (0.18), residues: 790 sheet: -2.30 (0.26), residues: 345 loop : -2.49 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 136 TYR 0.025 0.001 TYR E 64 PHE 0.043 0.001 PHE A 548 TRP 0.022 0.002 TRP A 732 HIS 0.003 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (19674) covalent geometry : angle 0.77351 / 0.36 (26829) hydrogen bonds : bond 0.03612 / 2.38 ( 630) hydrogen bonds : angle 4.71563 / 3.16 ( 1777) metal coordination : bond 0.00118 / 0.06 ( 2) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 317 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7062 (pp20) cc_final: 0.6808 (pp20) REVERT: A 37 ASP cc_start: 0.6957 (m-30) cc_final: 0.6689 (t0) REVERT: A 351 LYS cc_start: 0.7333 (mmpt) cc_final: 0.6440 (tptt) REVERT: A 728 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8012 (tp) REVERT: G 64 TYR cc_start: 0.7436 (m-10) cc_final: 0.6832 (m-10) REVERT: G 164 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.6977 (pm20) REVERT: E 64 TYR cc_start: 0.8057 (m-10) cc_final: 0.7732 (m-10) REVERT: E 123 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6964 (mt-10) REVERT: E 171 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6623 (mtp-110) REVERT: B 38 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7795 (mt) REVERT: B 78 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.7038 (t80) REVERT: B 219 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7889 (mt) REVERT: H 164 LYS cc_start: 0.7404 (mttt) cc_final: 0.7139 (tppt) outliers start: 74 outliers final: 58 residues processed: 362 average time/residue: 0.1348 time to fit residues: 76.2877 Evaluate side-chains 366 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 302 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 21 GLU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 173 LYS Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 27 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 220 optimal weight: 0.0670 chunk 168 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 195 optimal weight: 0.5980 chunk 127 optimal weight: 8.9990 overall best weight: 1.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 72 GLN G 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.141470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121420 restraints weight = 32089.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123651 restraints weight = 25595.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124577 restraints weight = 18326.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124751 restraints weight = 13821.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124967 restraints weight = 13850.729| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19677 Z= 0.173 Angle : 0.806 13.619 26829 Z= 0.381 Chirality : 0.063 1.156 3029 Planarity : 0.004 0.053 3226 Dihedral : 12.272 167.202 3198 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.94 % Favored : 90.97 % Rotamer: Outliers : 3.70 % Allowed : 24.10 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -2.53 (0.17), residues: 2226 helix: -0.35 (0.18), residues: 791 sheet: -2.29 (0.26), residues: 351 loop : -2.51 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 115 TYR 0.024 0.002 TYR E 64 PHE 0.018 0.001 PHE A 246 TRP 0.020 0.002 TRP A 732 HIS 0.004 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (19674) covalent geometry : angle 0.80630 / 0.38 (26829) hydrogen bonds : bond 0.03747 / 2.48 ( 630) hydrogen bonds : angle 4.79066 / 3.21 ( 1777) metal coordination : bond 0.00205 / 0.10 ( 2) Misc. bond : bond 0.00021 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 305 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.6980 (pp20) cc_final: 0.6743 (pp20) REVERT: A 37 ASP cc_start: 0.6698 (m-30) cc_final: 0.6454 (t0) REVERT: A 351 LYS cc_start: 0.7327 (mmpt) cc_final: 0.6501 (tptt) REVERT: A 728 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8042 (tp) REVERT: G 64 TYR cc_start: 0.7399 (m-10) cc_final: 0.6770 (m-10) REVERT: G 164 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: E 123 GLU cc_start: 0.7247 (mt-10) cc_final: 0.7043 (mt-10) REVERT: E 171 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6503 (mtp-110) REVERT: B 38 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7812 (mt) REVERT: B 219 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7908 (mt) REVERT: H 164 LYS cc_start: 0.7448 (mttt) cc_final: 0.7188 (tppt) outliers start: 69 outliers final: 57 residues processed: 348 average time/residue: 0.1405 time to fit residues: 76.5254 Evaluate side-chains 360 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 298 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 657 ARG Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 125 THR Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 136 ARG Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 171 ARG Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 173 LYS Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 87 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 185 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 33 optimal weight: 0.0570 chunk 115 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN G 124 ASN E 162 GLN ** B 174 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 = 0.3769 r_free = 0.3769 target = 0.143622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123707 restraints weight = 32135.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125521 restraints weight = 25899.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126653 restraints weight = 18153.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126660 restraints weight = 14605.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126913 restraints weight = 14141.552| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19677 Z= 0.139 Angle : 0.775 14.489 26829 Z= 0.365 Chirality : 0.061 1.126 3029 Planarity : 0.004 0.050 3226 Dihedral : 12.245 169.686 3198 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.31 % Favored : 91.60 % Rotamer: Outliers : 3.70 % Allowed : 24.10 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % 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: -2.41 (0.17), residues: 2226 helix: -0.25 (0.18), residues: 794 sheet: -2.22 (0.26), residues: 342 loop : -2.45 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 550 TYR 0.025 0.001 TYR E 64 PHE 0.020 0.001 PHE A 548 TRP 0.023 0.002 TRP A 732 HIS 0.004 0.001 HIS A 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (19674) covalent geometry : angle 0.77499 / 0.37 (26829) hydrogen bonds : bond 0.03427 / 2.29 ( 630) hydrogen bonds : angle 4.68529 / 3.12 ( 1777) metal coordination : bond 0.00131 / 0.06 ( 2) Misc. bond : bond 0.00020 / 0.01 ( 1) =============================================================================== Job complete usr+sys time: 3009.69 seconds wall clock time: 53 minutes 13.79 seconds (3193.79 seconds total)