Starting phenix.real_space_refine on Tue Nov 18 23:51:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ify_9658/11_2025/6ify_9658.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ify_9658/11_2025/6ify_9658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ify_9658/11_2025/6ify_9658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ify_9658/11_2025/6ify_9658.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ify_9658/11_2025/6ify_9658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ify_9658/11_2025/6ify_9658.map" } resolution = 3.8 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= 0.013 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 11962 2.51 5 N 3241 2.21 5 O 3782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19085 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5733 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 8, 'TRANS': 724} Chain breaks: 3 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 5, 'TYR:plan': 2, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 989 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" 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: "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: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1694 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1593 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2292 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2772 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 715 Classifications: {'RNA': 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: {'RNA': 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 2846 SG CYS A 401 57.843 30.797 65.672 1.00 62.78 S ATOM 2869 SG CYS A 404 55.290 32.198 63.265 1.00 63.76 S ATOM 3013 SG CYS A 422 58.505 33.792 63.733 1.00 60.33 S Time building chain proxies: 3.96, per 1000 atoms: 0.21 Number of scatterers: 19085 At special positions: 0 Unit cell: (91.52, 134.16, 171.6, 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 3782 8.00 N 3241 7.00 C 11962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.76 Conformation dependent library (CDL) restraints added in 723.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 401 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 404 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 422 " 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4252 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 21 sheets defined 38.5% alpha, 10.7% beta 22 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.606A pdb=" N ILE A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 7 " --> pdb=" O LYS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.769A pdb=" N VAL A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 43 removed outlier: 4.191A pdb=" N VAL A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 69 through 79 removed outlier: 3.553A pdb=" N THR A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.633A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.598A pdb=" N LYS A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 removed outlier: 4.410A pdb=" N ASP A 227 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 223 through 228' Processing helix chain 'A' and resid 231 through 237 removed outlier: 4.466A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 266 through 291 removed outlier: 3.923A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 335 removed outlier: 4.041A pdb=" N THR A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 378 removed outlier: 3.751A pdb=" N TYR A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.858A pdb=" N ASP A 415 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 432 removed outlier: 4.758A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 removed outlier: 3.719A pdb=" N ASN A 497 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 498 " --> pdb=" O ILE A 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 498' Processing helix chain 'A' and resid 522 through 529 Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.559A pdb=" N GLN A 533 " --> pdb=" O GLY A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 557 removed outlier: 4.065A pdb=" N SER A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 584 through 603 removed outlier: 4.285A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 638 removed outlier: 3.644A pdb=" N HIS A 627 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 662 removed outlier: 4.326A pdb=" N THR A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.837A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 712 removed outlier: 3.952A pdb=" N MET A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 removed outlier: 3.583A pdb=" N SER A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TRP A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 37 through 57 removed outlier: 4.117A pdb=" N LEU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 78 removed outlier: 3.891A pdb=" N ILE D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 removed outlier: 4.603A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.514A pdb=" N LYS C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.857A pdb=" N ASN C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 80 removed outlier: 4.168A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.621A pdb=" N LYS C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 101 through 122 removed outlier: 3.561A pdb=" N TYR C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 65 removed outlier: 3.694A pdb=" N LEU G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 112 removed outlier: 3.623A pdb=" N SER G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 161 through 166 removed outlier: 3.661A pdb=" N ASP G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 175 Processing helix chain 'G' and resid 176 through 180 Processing helix chain 'F' and resid 48 through 65 removed outlier: 3.581A pdb=" N LEU F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYS F 62 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL F 63 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN F 65 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 removed outlier: 3.670A pdb=" N ASP F 75 " --> pdb=" O PRO F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 84 Processing helix chain 'F' and resid 166 through 180 removed outlier: 3.602A pdb=" N ASP F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.507A pdb=" N ARG F 188 " --> pdb=" O SER F 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 removed outlier: 3.687A pdb=" N LYS E 55 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 84 Processing helix chain 'E' and resid 88 through 92 removed outlier: 4.323A pdb=" N LYS E 92 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.714A pdb=" N GLY E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 161 removed outlier: 4.241A pdb=" N ASN E 161 " --> pdb=" O GLU E 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 158 through 161' Processing helix chain 'E' and resid 162 through 178 removed outlier: 3.531A pdb=" N LYS E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG E 171 " --> pdb=" O PHE E 167 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.738A pdb=" N ARG E 188 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY E 189 " --> pdb=" O GLY E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 189' Processing helix chain 'E' and resid 208 through 211 removed outlier: 4.155A pdb=" N THR E 211 " --> pdb=" O ASP E 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 212 through 217 Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.633A pdb=" N PHE B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 removed outlier: 3.585A pdb=" N PHE B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.696A pdb=" N LEU B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 177 removed outlier: 3.617A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TYR B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.503A pdb=" N ASP B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.885A 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 128 through 143 removed outlier: 3.677A pdb=" N LEU H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 148 removed outlier: 3.586A pdb=" N ASN H 148 " --> pdb=" O PRO H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 184 Processing helix chain 'H' and resid 236 through 245 Processing helix chain 'H' and resid 245 through 261 removed outlier: 4.862A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 289 Processing sheet with id=AA1, first strand: chain 'A' and resid 298 through 301 removed outlier: 3.990A pdb=" N ALA A 244 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 311 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.667A pdb=" N ALA A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 569 through 575 removed outlier: 6.750A pdb=" N PHE A 580 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 574 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 579 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 96 through 97 removed outlier: 6.608A pdb=" N LYS G 5 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 146 through 149 removed outlier: 3.746A pdb=" N LYS G 192 " --> pdb=" O GLU G 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 118 through 122 removed outlier: 3.605A pdb=" N ARG G 140 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS G 121 " --> pdb=" O ILE G 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 146 through 155 removed outlier: 7.090A pdb=" N LYS F 5 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR F 202 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS F 7 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA F 200 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER F 9 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU F 198 " --> pdb=" O SER F 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 118 through 123 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.505A pdb=" N LYS E 7 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 149 Processing sheet with id=AB3, first strand: chain 'E' and resid 118 through 123 Processing sheet with id=AB4, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.659A pdb=" N VAL B 158 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 7 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AB6, first strand: chain 'B' and resid 128 through 133 removed outlier: 3.509A pdb=" N LYS B 133 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 143 " --> pdb=" O LYS B 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 265 through 267 Processing sheet with id=AB8, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AB9, first strand: chain 'H' and resid 185 through 186 removed outlier: 3.733A pdb=" N THR H 233 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE H 232 " --> pdb=" O PHE H 8 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AC2, first strand: chain 'H' and resid 32 through 33 removed outlier: 3.512A pdb=" N PHE H 40 " --> pdb=" O TYR H 92 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 214 through 219 removed outlier: 4.550A pdb=" N LYS H 202 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU H 217 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL H 200 " --> pdb=" O LEU H 217 " (cutoff:3.500A) 611 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4064 1.33 - 1.45: 4727 1.45 - 1.57: 10594 1.57 - 1.69: 122 1.69 - 1.81: 66 Bond restraints: 19573 Sorted by residual: bond pdb=" CG ASP A 67 " pdb=" OD2 ASP A 67 " ideal model delta sigma weight residual 1.249 1.327 -0.078 1.90e-02 2.77e+03 1.67e+01 bond pdb=" N LYS H 313 " pdb=" CA LYS H 313 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.68e+00 bond pdb=" N VAL H 315 " pdb=" CA VAL H 315 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.22e-02 6.72e+03 8.19e+00 bond pdb=" N VAL H 311 " pdb=" CA VAL H 311 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.08e+00 bond pdb=" C SER A 359 " pdb=" N PRO A 360 " ideal model delta sigma weight residual 1.335 1.370 -0.035 1.30e-02 5.92e+03 7.35e+00 ... (remaining 19568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 26387 3.62 - 7.24: 277 7.24 - 10.86: 29 10.86 - 14.48: 10 14.48 - 18.11: 4 Bond angle restraints: 26707 Sorted by residual: angle pdb=" C LYS A 133 " pdb=" N PRO A 134 " pdb=" CA PRO A 134 " ideal model delta sigma weight residual 119.84 137.95 -18.11 1.25e+00 6.40e-01 2.10e+02 angle pdb=" C TYR B 78 " pdb=" N PRO B 79 " pdb=" CA PRO B 79 " ideal model delta sigma weight residual 119.90 107.85 12.05 1.05e+00 9.07e-01 1.32e+02 angle pdb=" N PRO B 79 " pdb=" CA PRO B 79 " pdb=" C PRO B 79 " ideal model delta sigma weight residual 110.80 98.58 12.22 1.51e+00 4.39e-01 6.55e+01 angle pdb=" C ALA B 29 " pdb=" CA ALA B 29 " pdb=" CB ALA B 29 " ideal model delta sigma weight residual 111.23 99.54 11.69 1.63e+00 3.76e-01 5.14e+01 angle pdb=" N LYS A 133 " pdb=" CA LYS A 133 " pdb=" C LYS A 133 " ideal model delta sigma weight residual 108.45 121.60 -13.15 1.93e+00 2.68e-01 4.64e+01 ... (remaining 26702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.40: 11410 35.40 - 70.80: 365 70.80 - 106.19: 28 106.19 - 141.59: 1 141.59 - 176.99: 2 Dihedral angle restraints: 11806 sinusoidal: 5215 harmonic: 6591 Sorted by residual: dihedral pdb=" O4' C I 8 " pdb=" C1' C I 8 " pdb=" N1 C I 8 " pdb=" C2 C I 8 " ideal model delta sinusoidal sigma weight residual -128.00 48.99 -176.99 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 14 " pdb=" C1' C I 14 " pdb=" N1 C I 14 " pdb=" C2 C I 14 " ideal model delta sinusoidal sigma weight residual -128.00 4.64 -132.64 1 1.70e+01 3.46e-03 5.57e+01 dihedral pdb=" CA ILE H 20 " pdb=" C ILE H 20 " pdb=" N GLY H 21 " pdb=" CA GLY H 21 " ideal model delta harmonic sigma weight residual 180.00 143.88 36.12 0 5.00e+00 4.00e-02 5.22e+01 ... (remaining 11803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 2971 0.160 - 0.321: 46 0.321 - 0.481: 4 0.481 - 0.641: 0 0.641 - 0.802: 1 Chirality restraints: 3022 Sorted by residual: chirality pdb=" CA TYR B 78 " pdb=" N TYR B 78 " pdb=" C TYR B 78 " pdb=" CB TYR B 78 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CA LYS A 133 " pdb=" N LYS A 133 " pdb=" C LYS A 133 " pdb=" CB LYS A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 3019 not shown) Planarity restraints: 3214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 638 " 0.026 2.00e-02 2.50e+03 5.40e-02 2.91e+01 pdb=" C GLY A 638 " -0.093 2.00e-02 2.50e+03 pdb=" O GLY A 638 " 0.035 2.00e-02 2.50e+03 pdb=" N ASN A 639 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G I 21 " 0.041 2.00e-02 2.50e+03 1.87e-02 1.05e+01 pdb=" N9 G I 21 " -0.046 2.00e-02 2.50e+03 pdb=" C8 G I 21 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G I 21 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G I 21 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G I 21 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G I 21 " 0.014 2.00e-02 2.50e+03 pdb=" N1 G I 21 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G I 21 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G I 21 " -0.006 2.00e-02 2.50e+03 pdb=" N3 G I 21 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G I 21 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A I 27 " 0.040 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" N9 A I 27 " -0.049 2.00e-02 2.50e+03 pdb=" C8 A I 27 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A I 27 " 0.004 2.00e-02 2.50e+03 pdb=" C5 A I 27 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A I 27 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A I 27 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A I 27 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A I 27 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A I 27 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A I 27 " -0.001 2.00e-02 2.50e+03 ... (remaining 3211 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 59 2.37 - 3.00: 9650 3.00 - 3.63: 29658 3.63 - 4.27: 46529 4.27 - 4.90: 75103 Nonbonded interactions: 160999 Sorted by model distance: nonbonded pdb=" CD2 TYR H 33 " pdb=" O ALA H 108 " model vdw 1.733 3.340 nonbonded pdb=" CE2 TYR H 33 " pdb=" O ALA H 108 " model vdw 1.763 3.340 nonbonded pdb=" ND2 ASN A 639 " pdb=" OG SER A 643 " model vdw 1.812 3.120 nonbonded pdb=" OE2 GLU A 192 " pdb=" OE1 GLN A 538 " model vdw 2.016 3.040 nonbonded pdb=" OG1 THR C 5 " pdb=" OD1 ASN C 8 " model vdw 2.039 3.040 ... (remaining 160994 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' and (resid 3 through 101 or (resid 102 and (name N or name CA or name \ C or name O or name CB )) or resid 103 through 123)) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 2 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 217)) selection = (chain 'F' and (resid 2 through 25 or (resid 26 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 through 65 or resid 76 through 1 \ 31 or (resid 132 through 133 and (name N or name CA or name C or name O or name \ CB )) or resid 134 through 136 or (resid 137 and (name N or name CA or name C or \ name O or name CB )) or resid 138 through 156 or (resid 157 through 158 and (na \ me N or name CA or name C or name O or name CB )) or resid 159 or (resid 160 thr \ ough 161 and (name N or name CA or name C or name O or name CB )) or resid 162 t \ hrough 217)) selection = (chain 'G' and (resid 2 through 25 or (resid 26 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 through 65 or resid 76 through 1 \ 06 or (resid 107 and (name N or name CA or name C or name O or name CB )) or res \ id 108 through 131 or (resid 132 through 133 and (name N or name CA or name C or \ name O or name CB )) or resid 134 through 136 or (resid 137 and (name N or name \ CA or name C or name O or name CB )) or resid 138 through 160 or (resid 161 and \ (name N or name CA or name C or name O or name CB )) or resid 162 through 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.570 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 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 : 0.006 0.217 19576 Z= 0.274 Angle : 1.031 18.106 26707 Z= 0.585 Chirality : 0.060 0.802 3022 Planarity : 0.006 0.065 3214 Dihedral : 16.968 176.990 7554 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.74 % Favored : 88.99 % Rotamer: Outliers : 0.81 % Allowed : 9.61 % Favored : 89.58 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.14 (0.13), residues: 2225 helix: -3.34 (0.12), residues: 776 sheet: -3.29 (0.23), residues: 363 loop : -3.49 (0.15), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 31 TYR 0.027 0.002 TYR H 218 PHE 0.029 0.003 PHE B 64 TRP 0.050 0.003 TRP A 732 HIS 0.007 0.002 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00514 (19573) covalent geometry : angle 1.03108 (26707) hydrogen bonds : bond 0.17190 ( 663) hydrogen bonds : angle 8.22833 ( 1793) metal coordination : bond 0.19106 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 535 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 PHE cc_start: 0.7554 (m-80) cc_final: 0.7208 (m-10) REVERT: A 275 TYR cc_start: 0.7778 (t80) cc_final: 0.7567 (t80) REVERT: D 34 PHE cc_start: 0.8091 (m-80) cc_final: 0.7547 (m-10) REVERT: C 63 LEU cc_start: 0.6952 (pt) cc_final: 0.6622 (mt) REVERT: C 111 TYR cc_start: 0.8838 (t80) cc_final: 0.8619 (t80) REVERT: G 36 VAL cc_start: 0.9050 (p) cc_final: 0.8836 (p) REVERT: F 55 LYS cc_start: 0.8202 (tppt) cc_final: 0.7961 (tptt) REVERT: E 154 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6980 (mt-10) REVERT: E 212 LEU cc_start: 0.7526 (tp) cc_final: 0.7284 (tp) REVERT: B 5 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7850 (pp) REVERT: B 249 ASN cc_start: 0.7140 (t0) cc_final: 0.6934 (t0) REVERT: H 19 HIS cc_start: 0.7349 (t-90) cc_final: 0.7114 (t-170) outliers start: 15 outliers final: 6 residues processed: 547 average time/residue: 0.1557 time to fit residues: 125.3201 Evaluate side-chains 311 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 304 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 647 PHE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain H residue 92 TYR Chi-restraints excluded: chain H residue 309 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 167 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS A 561 ASN ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN C 26 ASN G 85 ASN G 137 GLN F 33 ASN F 197 ASN E 85 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 HIS B 273 GLN H 142 ASN H 148 ASN H 271 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.116174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.103976 restraints weight = 54905.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.106120 restraints weight = 29875.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107504 restraints weight = 19336.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.108419 restraints weight = 14188.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108921 restraints weight = 11480.725| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19576 Z= 0.179 Angle : 0.736 13.084 26707 Z= 0.388 Chirality : 0.047 0.398 3022 Planarity : 0.005 0.041 3214 Dihedral : 14.907 172.332 3394 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.07 % Favored : 89.89 % Rotamer: Outliers : 3.26 % Allowed : 18.51 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.14 (0.15), residues: 2225 helix: -2.22 (0.15), residues: 815 sheet: -2.89 (0.25), residues: 338 loop : -3.12 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 302 TYR 0.026 0.002 TYR H 33 PHE 0.022 0.002 PHE B 33 TRP 0.027 0.002 TRP A 732 HIS 0.007 0.002 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00389 (19573) covalent geometry : angle 0.73591 (26707) hydrogen bonds : bond 0.04501 ( 663) hydrogen bonds : angle 6.15172 ( 1793) metal coordination : bond 0.00555 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 356 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 PHE cc_start: 0.7615 (m-80) cc_final: 0.7084 (m-10) REVERT: A 281 GLU cc_start: 0.7542 (tp30) cc_final: 0.7022 (tp30) REVERT: A 285 ASP cc_start: 0.7380 (m-30) cc_final: 0.6456 (m-30) REVERT: A 327 PHE cc_start: 0.7632 (t80) cc_final: 0.7209 (t80) REVERT: A 331 LEU cc_start: 0.9038 (mt) cc_final: 0.8766 (mt) REVERT: A 484 HIS cc_start: 0.4343 (p90) cc_final: 0.3793 (p-80) REVERT: A 593 VAL cc_start: 0.7949 (t) cc_final: 0.6931 (t) REVERT: D 34 PHE cc_start: 0.7757 (m-80) cc_final: 0.7361 (m-10) REVERT: D 39 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7790 (mmmt) REVERT: D 87 ILE cc_start: 0.8589 (pt) cc_final: 0.7649 (pt) REVERT: C 15 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6797 (mmtp) REVERT: C 47 THR cc_start: 0.8960 (p) cc_final: 0.8382 (t) REVERT: C 101 ASP cc_start: 0.7881 (p0) cc_final: 0.7609 (p0) REVERT: G 18 LEU cc_start: 0.7884 (pt) cc_final: 0.7626 (pt) REVERT: G 177 LEU cc_start: 0.8187 (mt) cc_final: 0.7919 (mt) REVERT: G 207 TYR cc_start: 0.7948 (t80) cc_final: 0.7676 (t80) REVERT: F 55 LYS cc_start: 0.8217 (tppt) cc_final: 0.7834 (tptt) REVERT: E 178 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: E 212 LEU cc_start: 0.7644 (tp) cc_final: 0.7335 (tp) REVERT: B 5 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7778 (pp) outliers start: 60 outliers final: 29 residues processed: 396 average time/residue: 0.1413 time to fit residues: 85.6450 Evaluate side-chains 326 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 294 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 142 ASN Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 257 TYR Chi-restraints excluded: chain H residue 309 LYS Chi-restraints excluded: chain H residue 334 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 223 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 15 optimal weight: 0.0970 chunk 217 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 overall best weight: 3.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 ASN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 137 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.114902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.102888 restraints weight = 55342.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104985 restraints weight = 30276.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.106341 restraints weight = 19641.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.107253 restraints weight = 14453.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.107743 restraints weight = 11591.039| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19576 Z= 0.176 Angle : 0.696 12.799 26707 Z= 0.367 Chirality : 0.046 0.384 3022 Planarity : 0.004 0.039 3214 Dihedral : 14.757 175.709 3388 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.93 % Favored : 90.02 % Rotamer: Outliers : 3.91 % Allowed : 22.20 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.16), residues: 2225 helix: -1.71 (0.16), residues: 817 sheet: -2.90 (0.25), residues: 354 loop : -2.93 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 702 TYR 0.027 0.002 TYR A 74 PHE 0.026 0.002 PHE B 64 TRP 0.022 0.002 TRP A 732 HIS 0.008 0.001 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00383 (19573) covalent geometry : angle 0.69560 (26707) hydrogen bonds : bond 0.04131 ( 663) hydrogen bonds : angle 5.78991 ( 1793) metal coordination : bond 0.00270 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 304 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 PHE cc_start: 0.7452 (m-80) cc_final: 0.7235 (m-80) REVERT: A 327 PHE cc_start: 0.7479 (t80) cc_final: 0.7065 (t80) REVERT: A 331 LEU cc_start: 0.8980 (mt) cc_final: 0.8732 (mt) REVERT: D 34 PHE cc_start: 0.7696 (m-80) cc_final: 0.7445 (m-80) REVERT: D 87 ILE cc_start: 0.8133 (pt) cc_final: 0.7723 (pt) REVERT: C 18 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7746 (mm) REVERT: C 47 THR cc_start: 0.9025 (p) cc_final: 0.8547 (t) REVERT: E 212 LEU cc_start: 0.7600 (tp) cc_final: 0.7235 (tp) REVERT: B 5 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7604 (pp) REVERT: H 60 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7253 (pp20) REVERT: H 320 LYS cc_start: 0.8185 (mttt) cc_final: 0.7656 (tttm) outliers start: 72 outliers final: 47 residues processed: 353 average time/residue: 0.1324 time to fit residues: 72.9755 Evaluate side-chains 325 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 257 TYR Chi-restraints excluded: chain H residue 309 LYS Chi-restraints excluded: chain H residue 334 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 190 optimal weight: 0.0670 chunk 137 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 40.0000 chunk 153 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.115609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.103708 restraints weight = 54427.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.105820 restraints weight = 29533.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.107202 restraints weight = 18961.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.108100 restraints weight = 13828.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.108558 restraints weight = 11087.844| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19576 Z= 0.151 Angle : 0.662 10.944 26707 Z= 0.349 Chirality : 0.045 0.372 3022 Planarity : 0.004 0.038 3214 Dihedral : 14.638 176.168 3388 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.75 % Favored : 90.20 % Rotamer: Outliers : 4.13 % Allowed : 23.89 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.16), residues: 2225 helix: -1.34 (0.17), residues: 826 sheet: -2.70 (0.26), residues: 340 loop : -2.85 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 81 TYR 0.019 0.002 TYR G 181 PHE 0.020 0.001 PHE A 655 TRP 0.017 0.002 TRP A 732 HIS 0.011 0.001 HIS B 137 Details of bonding type rmsd covalent geometry : bond 0.00332 (19573) covalent geometry : angle 0.66178 (26707) hydrogen bonds : bond 0.03816 ( 663) hydrogen bonds : angle 5.56854 ( 1793) metal coordination : bond 0.00204 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 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: 76 poor density : 315 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7396 (t80) cc_final: 0.7035 (t80) REVERT: A 331 LEU cc_start: 0.8976 (mt) cc_final: 0.8709 (mt) REVERT: D 34 PHE cc_start: 0.7823 (m-80) cc_final: 0.7569 (m-80) REVERT: D 88 GLU cc_start: 0.8104 (mp0) cc_final: 0.7809 (mp0) REVERT: C 18 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7670 (mm) REVERT: C 47 THR cc_start: 0.8956 (p) cc_final: 0.8492 (t) REVERT: G 18 LEU cc_start: 0.7877 (pt) cc_final: 0.7671 (pt) REVERT: G 70 GLU cc_start: 0.6592 (tm-30) cc_final: 0.5500 (mm-30) REVERT: E 77 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7770 (t70) REVERT: E 212 LEU cc_start: 0.7546 (tp) cc_final: 0.7211 (tp) REVERT: B 5 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7429 (pp) REVERT: H 184 ILE cc_start: 0.6580 (mp) cc_final: 0.6251 (tt) REVERT: H 320 LYS cc_start: 0.8257 (mttt) cc_final: 0.7610 (tttt) REVERT: H 344 GLU cc_start: 0.7104 (tp30) cc_final: 0.6626 (tm-30) outliers start: 76 outliers final: 47 residues processed: 362 average time/residue: 0.1380 time to fit residues: 77.6200 Evaluate side-chains 323 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 257 TYR Chi-restraints excluded: chain H residue 309 LYS Chi-restraints excluded: chain H residue 334 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 35 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 305 HIS ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 677 GLN A 699 ASN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.113717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.101795 restraints weight = 54761.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.103888 restraints weight = 29733.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105245 restraints weight = 19176.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.106132 restraints weight = 14013.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106621 restraints weight = 11282.731| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19576 Z= 0.194 Angle : 0.709 13.263 26707 Z= 0.368 Chirality : 0.046 0.385 3022 Planarity : 0.004 0.041 3214 Dihedral : 14.659 178.410 3388 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.16 % Favored : 89.80 % Rotamer: Outliers : 4.45 % Allowed : 24.86 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.16), residues: 2225 helix: -1.20 (0.17), residues: 815 sheet: -2.53 (0.27), residues: 332 loop : -2.79 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 81 TYR 0.020 0.002 TYR G 181 PHE 0.022 0.002 PHE A 655 TRP 0.025 0.002 TRP A 732 HIS 0.011 0.002 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00425 (19573) covalent geometry : angle 0.70912 (26707) hydrogen bonds : bond 0.04011 ( 663) hydrogen bonds : angle 5.58963 ( 1793) metal coordination : bond 0.00336 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 284 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7549 (tp30) cc_final: 0.7293 (tm-30) REVERT: A 327 PHE cc_start: 0.7494 (t80) cc_final: 0.7090 (t80) REVERT: A 331 LEU cc_start: 0.8991 (mt) cc_final: 0.8733 (mt) REVERT: D 88 GLU cc_start: 0.8276 (mp0) cc_final: 0.7908 (mp0) REVERT: C 47 THR cc_start: 0.8908 (p) cc_final: 0.8444 (t) REVERT: G 59 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7126 (tt) REVERT: G 70 GLU cc_start: 0.6662 (tm-30) cc_final: 0.5789 (mm-30) REVERT: G 146 THR cc_start: 0.7041 (OUTLIER) cc_final: 0.6531 (t) REVERT: F 55 LYS cc_start: 0.8121 (tppt) cc_final: 0.7709 (tptt) REVERT: F 190 TYR cc_start: 0.8858 (m-10) cc_final: 0.8590 (m-10) REVERT: E 212 LEU cc_start: 0.7601 (tp) cc_final: 0.7215 (tp) REVERT: H 184 ILE cc_start: 0.6553 (mp) cc_final: 0.6273 (tt) REVERT: H 344 GLU cc_start: 0.7155 (tp30) cc_final: 0.6603 (tm-30) outliers start: 82 outliers final: 52 residues processed: 339 average time/residue: 0.1371 time to fit residues: 72.6424 Evaluate side-chains 311 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 257 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 309 LYS Chi-restraints excluded: chain H residue 334 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 6 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 163 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN G 19 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.112614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.100758 restraints weight = 55354.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.102770 restraints weight = 30838.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.104078 restraints weight = 20186.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.104937 restraints weight = 14935.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105523 restraints weight = 12105.859| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 19576 Z= 0.214 Angle : 0.726 11.587 26707 Z= 0.377 Chirality : 0.047 0.403 3022 Planarity : 0.004 0.044 3214 Dihedral : 14.692 178.523 3386 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.65 % Favored : 89.30 % Rotamer: Outliers : 4.34 % Allowed : 25.73 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.16), residues: 2225 helix: -1.16 (0.17), residues: 828 sheet: -2.51 (0.27), residues: 336 loop : -2.87 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 185 TYR 0.021 0.002 TYR C 68 PHE 0.023 0.002 PHE A 655 TRP 0.023 0.002 TRP A 732 HIS 0.009 0.002 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00470 (19573) covalent geometry : angle 0.72622 (26707) hydrogen bonds : bond 0.04021 ( 663) hydrogen bonds : angle 5.68050 ( 1793) metal coordination : bond 0.00423 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 272 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 PHE cc_start: 0.7579 (t80) cc_final: 0.7184 (t80) REVERT: A 331 LEU cc_start: 0.9021 (mt) cc_final: 0.8754 (mt) REVERT: D 88 GLU cc_start: 0.8341 (mp0) cc_final: 0.7933 (mp0) REVERT: C 47 THR cc_start: 0.8927 (p) cc_final: 0.8437 (t) REVERT: G 70 GLU cc_start: 0.6730 (tm-30) cc_final: 0.5905 (mm-30) REVERT: F 78 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7992 (tt) REVERT: F 190 TYR cc_start: 0.8884 (m-10) cc_final: 0.8644 (m-10) REVERT: E 212 LEU cc_start: 0.7628 (tp) cc_final: 0.7288 (tp) REVERT: B 213 MET cc_start: 0.8100 (ttt) cc_final: 0.7817 (ttt) REVERT: H 184 ILE cc_start: 0.6715 (mp) cc_final: 0.6469 (tt) REVERT: H 342 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6591 (m-10) REVERT: H 344 GLU cc_start: 0.6930 (tp30) cc_final: 0.6610 (tm-30) outliers start: 80 outliers final: 56 residues processed: 330 average time/residue: 0.1315 time to fit residues: 67.7734 Evaluate side-chains 305 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 309 LYS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain H residue 342 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 220 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 78 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 484 HIS A 677 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 273 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.111986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.100064 restraints weight = 55500.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.102072 restraints weight = 31215.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103378 restraints weight = 20469.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104236 restraints weight = 15177.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.104689 restraints weight = 12332.639| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 19576 Z= 0.226 Angle : 0.738 13.795 26707 Z= 0.383 Chirality : 0.047 0.407 3022 Planarity : 0.004 0.051 3214 Dihedral : 14.710 178.497 3385 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.24 % Favored : 88.72 % Rotamer: Outliers : 4.34 % Allowed : 26.82 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.16), residues: 2225 helix: -1.15 (0.17), residues: 820 sheet: -2.51 (0.27), residues: 336 loop : -2.84 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 155 TYR 0.038 0.002 TYR C 68 PHE 0.023 0.002 PHE A 655 TRP 0.024 0.002 TRP H 287 HIS 0.007 0.001 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00495 (19573) covalent geometry : angle 0.73769 (26707) hydrogen bonds : bond 0.04084 ( 663) hydrogen bonds : angle 5.73511 ( 1793) metal coordination : bond 0.00447 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 259 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.7709 (tp30) cc_final: 0.7284 (tm-30) REVERT: A 298 MET cc_start: 0.8941 (ttp) cc_final: 0.8686 (ttt) REVERT: A 327 PHE cc_start: 0.7456 (t80) cc_final: 0.7124 (t80) REVERT: A 331 LEU cc_start: 0.9010 (mt) cc_final: 0.8786 (mt) REVERT: A 510 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7516 (tp) REVERT: D 88 GLU cc_start: 0.8411 (mp0) cc_final: 0.7932 (mp0) REVERT: C 47 THR cc_start: 0.8925 (p) cc_final: 0.8464 (t) REVERT: C 68 TYR cc_start: 0.8450 (t80) cc_final: 0.7733 (t80) REVERT: G 70 GLU cc_start: 0.6622 (tm-30) cc_final: 0.5780 (mm-30) REVERT: F 78 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7992 (tt) REVERT: F 190 TYR cc_start: 0.8866 (m-10) cc_final: 0.8601 (m-10) REVERT: E 212 LEU cc_start: 0.7649 (tp) cc_final: 0.7312 (tp) REVERT: B 213 MET cc_start: 0.8227 (ttt) cc_final: 0.7941 (ttt) REVERT: H 342 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6726 (m-10) REVERT: H 344 GLU cc_start: 0.7001 (tp30) cc_final: 0.6642 (tm-30) outliers start: 80 outliers final: 58 residues processed: 317 average time/residue: 0.1302 time to fit residues: 64.8606 Evaluate side-chains 303 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 242 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 309 LYS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain H residue 342 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 70 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 5 optimal weight: 40.0000 chunk 152 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 167 optimal weight: 20.0000 chunk 212 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 HIS A 562 GLN A 677 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.114601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.102712 restraints weight = 55048.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.104776 restraints weight = 30788.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106095 restraints weight = 20107.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.106997 restraints weight = 14911.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.107490 restraints weight = 12012.870| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19576 Z= 0.150 Angle : 0.700 13.614 26707 Z= 0.361 Chirality : 0.046 0.386 3022 Planarity : 0.004 0.046 3214 Dihedral : 14.588 177.139 3385 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.57 % Favored : 90.34 % Rotamer: Outliers : 3.20 % Allowed : 28.18 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.17), residues: 2225 helix: -0.98 (0.17), residues: 823 sheet: -2.39 (0.28), residues: 331 loop : -2.74 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 155 TYR 0.025 0.002 TYR A 363 PHE 0.021 0.002 PHE A 486 TRP 0.030 0.002 TRP H 287 HIS 0.006 0.001 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00333 (19573) covalent geometry : angle 0.70035 (26707) hydrogen bonds : bond 0.03622 ( 663) hydrogen bonds : angle 5.53992 ( 1793) metal coordination : bond 0.00235 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 287 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.8873 (ttp) cc_final: 0.8648 (ttt) REVERT: A 510 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7523 (tp) REVERT: C 47 THR cc_start: 0.8939 (p) cc_final: 0.8698 (m) REVERT: G 56 MET cc_start: 0.6791 (mmm) cc_final: 0.6547 (mmm) REVERT: G 70 GLU cc_start: 0.6829 (tm-30) cc_final: 0.5754 (mm-30) REVERT: F 190 TYR cc_start: 0.8724 (m-10) cc_final: 0.8480 (m-10) REVERT: E 212 LEU cc_start: 0.7564 (tp) cc_final: 0.7096 (tp) REVERT: H 342 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6509 (m-10) outliers start: 59 outliers final: 45 residues processed: 328 average time/residue: 0.1300 time to fit residues: 67.5281 Evaluate side-chains 310 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 309 LYS Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain H residue 342 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 129 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 30.0000 chunk 161 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 174 optimal weight: 8.9990 chunk 159 optimal weight: 0.0980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 484 HIS A 562 GLN A 677 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.116503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.104660 restraints weight = 54609.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.106715 restraints weight = 30484.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.108063 restraints weight = 20007.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108904 restraints weight = 14823.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.109544 restraints weight = 12073.954| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19576 Z= 0.135 Angle : 0.707 13.988 26707 Z= 0.362 Chirality : 0.045 0.351 3022 Planarity : 0.004 0.047 3214 Dihedral : 14.527 176.449 3385 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.80 % Favored : 90.11 % Rotamer: Outliers : 2.99 % Allowed : 29.15 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.17), residues: 2225 helix: -0.87 (0.17), residues: 827 sheet: -2.30 (0.28), residues: 331 loop : -2.65 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 110 TYR 0.032 0.002 TYR B 78 PHE 0.050 0.002 PHE B 64 TRP 0.028 0.002 TRP H 287 HIS 0.005 0.001 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00296 (19573) covalent geometry : angle 0.70651 (26707) hydrogen bonds : bond 0.03580 ( 663) hydrogen bonds : angle 5.45156 ( 1793) metal coordination : bond 0.00157 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 303 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ILE cc_start: 0.8680 (mm) cc_final: 0.8375 (pt) REVERT: A 510 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7478 (tp) REVERT: C 45 SER cc_start: 0.7773 (m) cc_final: 0.7236 (t) REVERT: C 47 THR cc_start: 0.8848 (p) cc_final: 0.8635 (m) REVERT: G 56 MET cc_start: 0.6630 (mmm) cc_final: 0.6397 (mmm) REVERT: G 70 GLU cc_start: 0.6913 (tm-30) cc_final: 0.5915 (mm-30) REVERT: G 135 PRO cc_start: 0.8261 (Cg_exo) cc_final: 0.7836 (Cg_endo) REVERT: E 150 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: E 212 LEU cc_start: 0.7466 (tp) cc_final: 0.7077 (tp) REVERT: B 238 LYS cc_start: 0.7603 (tttp) cc_final: 0.7205 (mtmm) REVERT: B 287 LEU cc_start: 0.8244 (mm) cc_final: 0.7949 (mm) REVERT: H 342 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6403 (m-10) outliers start: 55 outliers final: 36 residues processed: 345 average time/residue: 0.1335 time to fit residues: 72.6844 Evaluate side-chains 308 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 309 LYS Chi-restraints excluded: chain H residue 342 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 147 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 chunk 187 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 225 optimal weight: 20.0000 chunk 157 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 628 GLN A 677 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 HIS H 115 ASN ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.113422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101465 restraints weight = 55278.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.103466 restraints weight = 31042.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104806 restraints weight = 20499.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105593 restraints weight = 15149.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.106233 restraints weight = 12386.818| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 19576 Z= 0.213 Angle : 0.763 13.543 26707 Z= 0.395 Chirality : 0.047 0.365 3022 Planarity : 0.004 0.063 3214 Dihedral : 14.652 178.530 3385 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.47 % Favored : 89.44 % Rotamer: Outliers : 2.82 % Allowed : 29.64 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.17), residues: 2225 helix: -0.94 (0.17), residues: 823 sheet: -2.25 (0.28), residues: 328 loop : -2.71 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 110 TYR 0.034 0.002 TYR C 75 PHE 0.046 0.002 PHE B 64 TRP 0.025 0.002 TRP H 287 HIS 0.006 0.001 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00479 (19573) covalent geometry : angle 0.76322 (26707) hydrogen bonds : bond 0.04015 ( 663) hydrogen bonds : angle 5.68802 ( 1793) metal coordination : bond 0.00388 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ILE cc_start: 0.8716 (mm) cc_final: 0.8386 (pt) REVERT: A 510 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7500 (tp) REVERT: D 91 GLN cc_start: 0.8182 (mp10) cc_final: 0.7970 (mp10) REVERT: C 47 THR cc_start: 0.8914 (p) cc_final: 0.8453 (t) REVERT: G 56 MET cc_start: 0.6749 (mmm) cc_final: 0.6459 (mmm) REVERT: G 70 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6021 (mm-30) REVERT: G 98 PHE cc_start: 0.7615 (m-10) cc_final: 0.7357 (m-80) REVERT: G 135 PRO cc_start: 0.8579 (Cg_exo) cc_final: 0.8227 (Cg_endo) REVERT: B 213 MET cc_start: 0.7027 (ttt) cc_final: 0.6771 (ttm) REVERT: H 19 HIS cc_start: 0.7562 (t-170) cc_final: 0.7356 (t-170) REVERT: H 342 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6442 (m-10) outliers start: 52 outliers final: 44 residues processed: 304 average time/residue: 0.1355 time to fit residues: 64.7819 Evaluate side-chains 300 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 329 GLN Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 137 GLN Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 309 LYS Chi-restraints excluded: chain H residue 342 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 106 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 677 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.114434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.102483 restraints weight = 54642.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.104581 restraints weight = 29685.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.105952 restraints weight = 19156.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.106771 restraints weight = 13996.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.107420 restraints weight = 11352.328| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 19576 Z= 0.172 Angle : 0.747 13.218 26707 Z= 0.385 Chirality : 0.047 0.362 3022 Planarity : 0.004 0.045 3214 Dihedral : 14.607 177.197 3385 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.48 % Favored : 90.38 % Rotamer: Outliers : 2.88 % Allowed : 29.75 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.17), residues: 2225 helix: -0.89 (0.17), residues: 826 sheet: -2.23 (0.28), residues: 329 loop : -2.67 (0.18), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 110 TYR 0.055 0.002 TYR B 78 PHE 0.047 0.002 PHE B 64 TRP 0.025 0.002 TRP H 287 HIS 0.006 0.001 HIS H 19 Details of bonding type rmsd covalent geometry : bond 0.00390 (19573) covalent geometry : angle 0.74672 (26707) hydrogen bonds : bond 0.03790 ( 663) hydrogen bonds : angle 5.60136 ( 1793) metal coordination : bond 0.00271 ( 3) =============================================================================== Job complete usr+sys time: 3081.59 seconds wall clock time: 54 minutes 30.27 seconds (3270.27 seconds total)