Starting phenix.real_space_refine on Sat Sep 12 21:48:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ify_9658/09_2026/6ify_9658.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ify_9658/09_2026/6ify_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ify_9658/09_2026/6ify_9658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ify_9658/09_2026/6ify_9658.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ify_9658/09_2026/6ify_9658.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ify_9658/09_2026/6ify_9658.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ify_9658/09_2026/6ify_9658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ify_9658/09_2026/6ify_9658.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 34} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 606 Classifications: {'RNAv2': 28} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 24} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 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: 3.68, per 1000 atoms: 0.19 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: 1.62 Conformation dependent library (CDL) restraints added in 703.7 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: 2.12 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: 2.79 Time building geometry restraints manager: 2.14 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: 26319 3.62 - 7.24: 344 7.24 - 10.86: 30 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 - 29.57: 10951 29.57 - 59.14: 616 59.14 - 88.71: 48 88.71 - 118.28: 0 118.28 - 147.85: 1 Dihedral angle restraints: 11616 sinusoidal: 5025 harmonic: 6591 Sorted by residual: dihedral pdb=" C4' G I 3 " pdb=" C3' G I 3 " pdb=" C2' G I 3 " pdb=" C1' G I 3 " ideal model delta sinusoidal sigma weight residual 36.35 -39.86 76.20 1 3.10e+00 1.04e-01 7.61e+02 dihedral pdb=" C4' A I 27 " pdb=" C3' A I 27 " pdb=" C2' A I 27 " pdb=" C1' A I 27 " ideal model delta sinusoidal sigma weight residual 36.35 -39.30 75.64 1 3.10e+00 1.04e-01 7.51e+02 dihedral pdb=" C4' G I 9 " pdb=" C3' G I 9 " pdb=" C2' G I 9 " pdb=" C1' G I 9 " ideal model delta sinusoidal sigma weight residual 36.34 -39.10 75.44 1 3.10e+00 1.04e-01 7.48e+02 ... (remaining 11613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 2874 0.160 - 0.321: 140 0.321 - 0.481: 7 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: 0.520 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.880 Find NCS groups from input model: 0.200 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 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= 0.275 Angle : 1.076 18.106 26707 Z= 0.591 Chirality : 0.074 0.802 3022 Planarity : 0.006 0.065 3214 Dihedral : 17.076 147.847 7364 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/Z covalent geometry : bond 0.00521 / 0.26 (19573) covalent geometry : angle 1.07623 / 0.59 (26707) hydrogen bonds : bond 0.17190 / 11.74 ( 663) hydrogen bonds : angle 8.22833 / 5.76 ( 1793) metal coordination : bond 0.19106 / 9.52 ( 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 : 0.701 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: 0.8062 (OUTLIER) cc_final: 0.7850 (pp) REVERT: B 249 ASN cc_start: 0.7139 (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: 0.1465 time to fit residues: 119.0073 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 : 0.554 ------------------------------------------------------------------------------- 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: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** A 699 ASN D 76 GLN C 26 ASN G 85 ASN G 124 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.115983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.104076 restraints weight = 54457.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.106197 restraints weight = 29291.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107600 restraints weight = 18765.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.108527 restraints weight = 13624.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.109147 restraints weight = 10857.928| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19576 Z= 0.213 Angle : 1.013 21.953 26707 Z= 0.464 Chirality : 0.085 1.284 3022 Planarity : 0.005 0.043 3214 Dihedral : 12.909 172.751 3204 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.34 % Favored : 89.62 % Rotamer: Outliers : 3.53 % Allowed : 18.35 % Favored : 78.12 % 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: -4.16 (0.15), residues: 2225 helix: -2.21 (0.15), residues: 816 sheet: -2.97 (0.25), residues: 342 loop : -3.12 (0.16), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 301 TYR 0.023 0.002 TYR H 33 PHE 0.020 0.002 PHE B 33 TRP 0.027 0.002 TRP A 732 HIS 0.006 0.002 HIS A 695 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.21 (19573) covalent geometry : angle 1.01308 / 0.46 (26707) hydrogen bonds : bond 0.04669 / 3.22 ( 663) hydrogen bonds : angle 6.20315 / 4.35 ( 1793) metal coordination : bond 0.00258 / 0.12 ( 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 413 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 348 time to evaluate : 0.697 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: A 208 PHE cc_start: 0.7597 (m-80) cc_final: 0.7066 (m-10) REVERT: A 281 GLU cc_start: 0.7578 (tp30) cc_final: 0.7010 (tp30) REVERT: A 285 ASP cc_start: 0.7392 (m-30) cc_final: 0.6507 (m-30) REVERT: A 327 PHE cc_start: 0.7694 (t80) cc_final: 0.7254 (t80) REVERT: A 331 LEU cc_start: 0.9064 (mt) cc_final: 0.8748 (mt) REVERT: A 484 HIS cc_start: 0.4371 (p90) cc_final: 0.3878 (p-80) REVERT: A 593 VAL cc_start: 0.8039 (t) cc_final: 0.7125 (t) REVERT: D 34 PHE cc_start: 0.7671 (m-80) cc_final: 0.7293 (m-10) REVERT: D 87 ILE cc_start: 0.8488 (pt) cc_final: 0.7586 (pt) REVERT: C 47 THR cc_start: 0.8955 (p) cc_final: 0.8393 (t) REVERT: G 18 LEU cc_start: 0.8011 (pt) cc_final: 0.7758 (pt) REVERT: G 124 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7452 (p0) REVERT: G 176 LEU cc_start: 0.7718 (mp) cc_final: 0.7516 (mp) REVERT: G 177 LEU cc_start: 0.8260 (mt) cc_final: 0.7979 (mt) REVERT: G 207 TYR cc_start: 0.7917 (t80) cc_final: 0.7631 (t80) REVERT: F 8 PHE cc_start: 0.7873 (m-10) cc_final: 0.7544 (m-80) REVERT: F 55 LYS cc_start: 0.8329 (tppt) cc_final: 0.7847 (tptt) REVERT: E 178 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: E 212 LEU cc_start: 0.7670 (tp) cc_final: 0.7370 (tp) REVERT: B 5 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7796 (pp) REVERT: B 28 SER cc_start: 0.7777 (t) cc_final: 0.7550 (p) REVERT: H 184 ILE cc_start: 0.6628 (mp) cc_final: 0.6167 (tt) outliers start: 65 outliers final: 37 residues processed: 393 average time/residue: 0.1349 time to fit residues: 82.2566 Evaluate side-chains 330 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 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 A residue 647 PHE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain C residue 4 LEU 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 124 ASN Chi-restraints excluded: chain G residue 180 ASP Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain F residue 134 ASN 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 108 GLU 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 B residue 269 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: 9.9990 chunk 155 optimal weight: 9.9990 chunk 209 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 211 optimal weight: 20.0000 chunk 140 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS A 661 ASN A 677 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.113428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.101537 restraints weight = 55535.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103619 restraints weight = 30275.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.104975 restraints weight = 19571.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105805 restraints weight = 14338.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.106458 restraints weight = 11642.780| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19576 Z= 0.239 Angle : 0.906 18.461 26707 Z= 0.434 Chirality : 0.073 1.189 3022 Planarity : 0.004 0.044 3214 Dihedral : 12.715 170.780 3202 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.83 % Favored : 89.12 % Rotamer: Outliers : 3.91 % Allowed : 22.37 % Favored : 73.72 % 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: -3.77 (0.16), residues: 2225 helix: -1.75 (0.16), residues: 811 sheet: -2.99 (0.25), residues: 354 loop : -2.92 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 702 TYR 0.024 0.002 TYR A 74 PHE 0.023 0.002 PHE B 64 TRP 0.022 0.002 TRP A 732 HIS 0.008 0.002 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.24 (19573) covalent geometry : angle 0.90560 / 0.43 (26707) hydrogen bonds : bond 0.04555 / 3.10 ( 663) hydrogen bonds : angle 5.97860 / 4.18 ( 1793) metal coordination : bond 0.00423 / 0.22 ( 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 373 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 301 time to evaluate : 0.596 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 208 PHE cc_start: 0.7557 (m-80) cc_final: 0.7341 (m-80) REVERT: A 327 PHE cc_start: 0.7641 (t80) cc_final: 0.7233 (t80) REVERT: A 331 LEU cc_start: 0.9029 (mt) cc_final: 0.8750 (mt) REVERT: D 34 PHE cc_start: 0.7764 (m-80) cc_final: 0.7485 (m-80) REVERT: D 87 ILE cc_start: 0.8260 (pt) cc_final: 0.7841 (pt) REVERT: C 15 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6691 (mmtp) REVERT: C 18 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7937 (mm) REVERT: C 47 THR cc_start: 0.9026 (p) cc_final: 0.8512 (t) REVERT: G 18 LEU cc_start: 0.7925 (pt) cc_final: 0.7688 (pt) REVERT: G 36 VAL cc_start: 0.9144 (p) cc_final: 0.8753 (m) REVERT: G 139 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7522 (tm-30) REVERT: E 56 MET cc_start: 0.7674 (ttm) cc_final: 0.7472 (ttm) REVERT: E 212 LEU cc_start: 0.7602 (tp) cc_final: 0.7251 (tp) REVERT: B 5 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7650 (pp) REVERT: H 320 LYS cc_start: 0.8218 (mttt) cc_final: 0.7674 (tttt) outliers start: 72 outliers final: 47 residues processed: 350 average time/residue: 0.1335 time to fit residues: 73.6658 Evaluate side-chains 319 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 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 A residue 710 LEU Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain C residue 15 LYS 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 170 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 134 ASN Chi-restraints excluded: chain F residue 163 VAL 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 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 173 LEU Chi-restraints excluded: chain B residue 221 VAL 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 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: 9.9990 chunk 137 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 205 optimal weight: 0.0040 chunk 93 optimal weight: 5.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN A 497 ASN A 677 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN F 197 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS H 69 ASN ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.116145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.104335 restraints weight = 54616.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.106457 restraints weight = 29748.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.107837 restraints weight = 19165.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.108719 restraints weight = 14003.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.109214 restraints weight = 11266.774| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3606 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= 0.155 Angle : 0.821 15.328 26707 Z= 0.391 Chirality : 0.064 1.028 3022 Planarity : 0.004 0.043 3214 Dihedral : 12.657 174.524 3198 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.39 % Favored : 90.56 % Rotamer: Outliers : 3.53 % Allowed : 24.70 % Favored : 71.77 % 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: -3.38 (0.16), residues: 2225 helix: -1.34 (0.17), residues: 814 sheet: -2.76 (0.26), residues: 339 loop : -2.79 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 81 TYR 0.020 0.002 TYR G 181 PHE 0.020 0.002 PHE F 195 TRP 0.019 0.002 TRP A 732 HIS 0.011 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (19573) covalent geometry : angle 0.82090 / 0.39 (26707) hydrogen bonds : bond 0.04028 / 2.76 ( 663) hydrogen bonds : angle 5.68257 / 3.96 ( 1793) metal coordination : bond 0.00124 / 0.06 ( 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 390 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 325 time to evaluate : 0.707 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 285 ASP cc_start: 0.7243 (m-30) cc_final: 0.6918 (m-30) REVERT: A 327 PHE cc_start: 0.7379 (t80) cc_final: 0.7018 (t80) REVERT: A 331 LEU cc_start: 0.8943 (mt) cc_final: 0.8704 (mt) REVERT: A 486 PHE cc_start: 0.7202 (m-80) cc_final: 0.7001 (m-10) REVERT: A 698 MET cc_start: 0.7688 (tpt) cc_final: 0.6851 (tpp) REVERT: A 728 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8011 (tt) REVERT: D 49 THR cc_start: 0.8066 (p) cc_final: 0.7858 (t) REVERT: D 88 GLU cc_start: 0.8146 (mp0) cc_final: 0.7880 (mp0) REVERT: C 47 THR cc_start: 0.8966 (p) cc_final: 0.8377 (t) REVERT: G 70 GLU cc_start: 0.6511 (tm-30) cc_final: 0.5653 (mm-30) REVERT: G 159 ASN cc_start: 0.4559 (OUTLIER) cc_final: 0.3789 (m-40) REVERT: E 212 LEU cc_start: 0.7567 (tp) cc_final: 0.7195 (tp) REVERT: B 5 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7425 (pp) REVERT: H 42 ASP cc_start: 0.7181 (t70) cc_final: 0.6931 (m-30) REVERT: H 289 LYS cc_start: 0.7371 (mmtm) cc_final: 0.7032 (mptt) REVERT: H 320 LYS cc_start: 0.8215 (mttt) cc_final: 0.7572 (tttt) REVERT: H 344 GLU cc_start: 0.7066 (tp30) cc_final: 0.6679 (tm-30) outliers start: 65 outliers final: 36 residues processed: 370 average time/residue: 0.1438 time to fit residues: 82.8895 Evaluate side-chains 303 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 113 VAL 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 728 LEU Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain G residue 180 ASP 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 198 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 173 LEU 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 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: 8.9990 chunk 149 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 677 GLN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.113359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101517 restraints weight = 54877.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.103617 restraints weight = 29940.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.104982 restraints weight = 19264.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.105789 restraints weight = 14068.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.106441 restraints weight = 11423.197| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19576 Z= 0.219 Angle : 0.861 16.267 26707 Z= 0.409 Chirality : 0.065 0.954 3022 Planarity : 0.004 0.042 3214 Dihedral : 12.730 177.599 3198 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.92 % Favored : 89.03 % Rotamer: Outliers : 4.29 % Allowed : 25.24 % Favored : 70.47 % 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 (0.17), residues: 2225 helix: -1.20 (0.17), residues: 811 sheet: -2.64 (0.26), residues: 332 loop : -2.75 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 756 TYR 0.031 0.002 TYR C 75 PHE 0.022 0.002 PHE A 655 TRP 0.017 0.002 TRP A 732 HIS 0.012 0.002 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.22 (19573) covalent geometry : angle 0.86107 / 0.41 (26707) hydrogen bonds : bond 0.04233 / 2.88 ( 663) hydrogen bonds : angle 5.72244 / 3.98 ( 1793) metal coordination : bond 0.00400 / 0.21 ( 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 363 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 284 time to evaluate : 0.769 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: 0.7537 (t80) cc_final: 0.7184 (t80) REVERT: A 331 LEU cc_start: 0.9003 (mt) cc_final: 0.8739 (mt) REVERT: A 669 GLN cc_start: 0.6841 (tt0) cc_final: 0.6232 (tt0) REVERT: D 88 GLU cc_start: 0.8343 (mp0) cc_final: 0.8131 (mp0) REVERT: C 47 THR cc_start: 0.8870 (p) cc_final: 0.8355 (t) REVERT: C 86 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8531 (tp) REVERT: G 59 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7138 (tt) REVERT: G 70 GLU cc_start: 0.6636 (tm-30) cc_final: 0.5763 (mm-30) REVERT: G 146 THR cc_start: 0.7029 (OUTLIER) cc_final: 0.6422 (t) REVERT: F 78 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7911 (tt) REVERT: F 190 TYR cc_start: 0.8849 (m-10) cc_final: 0.8590 (m-10) REVERT: E 212 LEU cc_start: 0.7584 (tp) cc_final: 0.7217 (tp) REVERT: B 5 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7648 (pp) REVERT: B 213 MET cc_start: 0.8144 (ttt) cc_final: 0.7808 (ttt) REVERT: H 289 LYS cc_start: 0.7467 (mmtm) cc_final: 0.7144 (mptt) REVERT: H 320 LYS cc_start: 0.8224 (mttt) cc_final: 0.7667 (tttt) REVERT: H 344 GLU cc_start: 0.6883 (tp30) cc_final: 0.6662 (tm-30) outliers start: 79 outliers final: 51 residues processed: 336 average time/residue: 0.1402 time to fit residues: 74.3299 Evaluate side-chains 311 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 255 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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 711 GLU 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 66 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 ILE 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 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 198 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 173 LEU 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 H residue 32 ILE Chi-restraints excluded: chain H residue 114 VAL 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=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: 0.9990 chunk 76 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.113556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.101610 restraints weight = 55341.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.103706 restraints weight = 30547.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.105050 restraints weight = 19842.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.105965 restraints weight = 14635.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.106473 restraints weight = 11755.344| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19576 Z= 0.209 Angle : 0.861 15.918 26707 Z= 0.408 Chirality : 0.064 0.904 3022 Planarity : 0.004 0.045 3214 Dihedral : 12.650 172.901 3197 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.29 % Favored : 89.66 % Rotamer: Outliers : 4.51 % Allowed : 26.28 % Favored : 69.22 % 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: -1.16 (0.17), residues: 820 sheet: -2.63 (0.26), residues: 330 loop : -2.81 (0.17), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 302 TYR 0.029 0.002 TYR C 75 PHE 0.022 0.002 PHE A 655 TRP 0.021 0.002 TRP A 732 HIS 0.014 0.002 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (19573) covalent geometry : angle 0.86071 / 0.41 (26707) hydrogen bonds : bond 0.04167 / 2.82 ( 663) hydrogen bonds : angle 5.73918 / 3.99 ( 1793) metal coordination : bond 0.00393 / 0.21 ( 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 359 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 276 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.8930 (ttp) cc_final: 0.8679 (ttt) REVERT: A 327 PHE cc_start: 0.7557 (t80) cc_final: 0.7133 (t80) REVERT: A 331 LEU cc_start: 0.9028 (mt) cc_final: 0.8794 (mt) REVERT: D 88 GLU cc_start: 0.8336 (mp0) cc_final: 0.7903 (mp0) REVERT: C 47 THR cc_start: 0.8831 (p) cc_final: 0.8262 (t) REVERT: C 86 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8544 (tp) REVERT: G 70 GLU cc_start: 0.6656 (tm-30) cc_final: 0.5686 (mm-30) REVERT: G 170 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8552 (tp) REVERT: G 216 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6681 (mt) REVERT: F 78 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7928 (tt) REVERT: F 190 TYR cc_start: 0.8853 (m-10) cc_final: 0.8608 (m-80) REVERT: E 212 LEU cc_start: 0.7605 (tp) cc_final: 0.7251 (tp) REVERT: B 213 MET cc_start: 0.8144 (ttt) cc_final: 0.7901 (ttt) REVERT: B 288 ASN cc_start: 0.8536 (t0) cc_final: 0.8326 (t0) REVERT: H 184 ILE cc_start: 0.6674 (mp) cc_final: 0.6404 (tt) REVERT: H 289 LYS cc_start: 0.7506 (mmtm) cc_final: 0.7129 (mptt) REVERT: H 306 MET cc_start: 0.1736 (tpp) cc_final: 0.1384 (ttt) REVERT: H 320 LYS cc_start: 0.8203 (mttt) cc_final: 0.7655 (tttt) REVERT: H 342 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6663 (m-10) REVERT: H 344 GLU cc_start: 0.6920 (tp30) cc_final: 0.6680 (tm-30) outliers start: 83 outliers final: 57 residues processed: 330 average time/residue: 0.1404 time to fit residues: 72.9084 Evaluate side-chains 319 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 257 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 642 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 749 LEU 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 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 69 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 116 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 170 ILE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 173 LEU 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 32 ILE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 114 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 220 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 219 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.111773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099749 restraints weight = 55410.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.101914 restraints weight = 29893.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.103280 restraints weight = 19062.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.104188 restraints weight = 13869.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.104718 restraints weight = 11097.333| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19576 Z= 0.239 Angle : 0.894 15.826 26707 Z= 0.424 Chirality : 0.066 0.897 3022 Planarity : 0.004 0.050 3214 Dihedral : 12.642 169.684 3195 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.60 % Favored : 88.36 % Rotamer: Outliers : 4.34 % Allowed : 27.69 % Favored : 67.97 % 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: -3.27 (0.16), residues: 2225 helix: -1.19 (0.17), residues: 822 sheet: -2.71 (0.27), residues: 323 loop : -2.79 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 155 TYR 0.040 0.002 TYR C 68 PHE 0.026 0.002 PHE C 51 TRP 0.024 0.002 TRP H 287 HIS 0.011 0.002 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.24 (19573) covalent geometry : angle 0.89385 / 0.42 (26707) hydrogen bonds : bond 0.04352 / 2.95 ( 663) hydrogen bonds : angle 5.90553 / 4.12 ( 1793) metal coordination : bond 0.00518 / 0.27 ( 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 348 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 268 time to evaluate : 0.726 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 298 MET cc_start: 0.8962 (ttp) cc_final: 0.8732 (ttp) REVERT: A 327 PHE cc_start: 0.7657 (t80) cc_final: 0.7305 (t80) REVERT: A 331 LEU cc_start: 0.9062 (mt) cc_final: 0.8824 (mt) REVERT: D 88 GLU cc_start: 0.8399 (mp0) cc_final: 0.8018 (mp0) REVERT: C 68 TYR cc_start: 0.8499 (t80) cc_final: 0.7675 (t80) REVERT: C 86 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8493 (tp) REVERT: G 56 MET cc_start: 0.7085 (mmm) cc_final: 0.6760 (mmm) REVERT: G 70 GLU cc_start: 0.6830 (tm-30) cc_final: 0.5937 (mm-30) REVERT: G 216 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6765 (mt) REVERT: F 78 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8002 (tt) REVERT: F 190 TYR cc_start: 0.8881 (m-10) cc_final: 0.8610 (m-80) REVERT: E 212 LEU cc_start: 0.7644 (tp) cc_final: 0.7301 (tp) REVERT: B 213 MET cc_start: 0.8221 (ttt) cc_final: 0.8000 (ttt) REVERT: B 288 ASN cc_start: 0.8606 (t0) cc_final: 0.8387 (t0) REVERT: H 184 ILE cc_start: 0.6735 (mp) cc_final: 0.6463 (tt) REVERT: H 342 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6825 (m-10) outliers start: 80 outliers final: 60 residues processed: 326 average time/residue: 0.1402 time to fit residues: 72.8629 Evaluate side-chains 308 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 244 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 642 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 749 LEU 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 49 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 113 GLU 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 155 ILE Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 173 LEU 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 93 SER Chi-restraints excluded: chain H residue 114 VAL 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: 2.9990 chunk 157 optimal weight: 2.9990 chunk 5 optimal weight: 50.0000 chunk 152 optimal weight: 8.9990 chunk 19 optimal weight: 0.0870 chunk 140 optimal weight: 1.9990 chunk 167 optimal weight: 20.0000 chunk 212 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 135 GLN ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 251 GLN H 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.115306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.103511 restraints weight = 54786.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.105642 restraints weight = 29781.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.106894 restraints weight = 19120.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.107898 restraints weight = 14157.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.108492 restraints weight = 11223.167| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19576 Z= 0.155 Angle : 0.835 14.590 26707 Z= 0.393 Chirality : 0.061 0.852 3022 Planarity : 0.004 0.046 3214 Dihedral : 12.382 173.090 3195 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.62 % Favored : 90.34 % Rotamer: Outliers : 3.42 % Allowed : 28.88 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.17), residues: 2225 helix: -0.95 (0.17), residues: 825 sheet: -2.55 (0.27), residues: 328 loop : -2.66 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 155 TYR 0.024 0.002 TYR C 68 PHE 0.053 0.002 PHE B 64 TRP 0.035 0.002 TRP H 287 HIS 0.009 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (19573) covalent geometry : angle 0.83479 / 0.39 (26707) hydrogen bonds : bond 0.03927 / 2.67 ( 663) hydrogen bonds : angle 5.62532 / 3.91 ( 1793) metal coordination : bond 0.00246 / 0.13 ( 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 355 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 292 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: A 298 MET cc_start: 0.8859 (ttp) cc_final: 0.8640 (ttt) REVERT: A 327 PHE cc_start: 0.7406 (t80) cc_final: 0.7133 (t80) REVERT: A 331 LEU cc_start: 0.8999 (mt) cc_final: 0.8784 (mt) REVERT: D 88 GLU cc_start: 0.8256 (mp0) cc_final: 0.7834 (mp0) REVERT: D 103 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7772 (tm-30) REVERT: C 68 TYR cc_start: 0.8199 (t80) cc_final: 0.7982 (t80) REVERT: G 56 MET cc_start: 0.6784 (mmm) cc_final: 0.6537 (mmm) REVERT: G 70 GLU cc_start: 0.6916 (tm-30) cc_final: 0.5925 (mm-30) REVERT: F 190 TYR cc_start: 0.8736 (m-10) cc_final: 0.8498 (m-10) REVERT: E 212 LEU cc_start: 0.7584 (tp) cc_final: 0.7173 (tp) REVERT: H 184 ILE cc_start: 0.6664 (mp) cc_final: 0.6407 (tt) REVERT: H 306 MET cc_start: 0.1935 (tpp) cc_final: 0.1678 (ttt) REVERT: H 342 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6437 (m-10) REVERT: H 344 GLU cc_start: 0.7160 (tp30) cc_final: 0.6881 (tm-30) outliers start: 63 outliers final: 49 residues processed: 338 average time/residue: 0.1335 time to fit residues: 71.1663 Evaluate side-chains 310 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 260 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 201 HIS 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 516 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 749 LEU 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 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 69 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 108 LEU 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 93 SER Chi-restraints excluded: chain H residue 114 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 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: 5.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 chunk 161 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN E 11 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 = 0.3908 r_free = 0.3908 target = 0.115097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.103453 restraints weight = 55166.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.105563 restraints weight = 30192.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.106930 restraints weight = 19497.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.107831 restraints weight = 14198.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108436 restraints weight = 11340.910| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19576 Z= 0.160 Angle : 0.840 14.464 26707 Z= 0.396 Chirality : 0.061 0.833 3022 Planarity : 0.004 0.046 3214 Dihedral : 12.268 172.179 3195 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.61 % Favored : 89.30 % Rotamer: Outliers : 3.15 % Allowed : 28.94 % Favored : 67.92 % 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: -2.98 (0.17), residues: 2225 helix: -0.90 (0.17), residues: 837 sheet: -2.58 (0.27), residues: 346 loop : -2.66 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 155 TYR 0.032 0.002 TYR B 78 PHE 0.038 0.002 PHE B 64 TRP 0.033 0.002 TRP H 287 HIS 0.016 0.001 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (19573) covalent geometry : angle 0.84044 / 0.40 (26707) hydrogen bonds : bond 0.03920 / 2.64 ( 663) hydrogen bonds : angle 5.57336 / 3.87 ( 1793) metal coordination : bond 0.00261 / 0.14 ( 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 344 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 286 time to evaluate : 0.659 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: 0.8681 (mm) cc_final: 0.8368 (pt) REVERT: A 298 MET cc_start: 0.8926 (ttp) cc_final: 0.8698 (ttt) REVERT: A 327 PHE cc_start: 0.7506 (t80) cc_final: 0.7203 (t80) REVERT: A 331 LEU cc_start: 0.9001 (mt) cc_final: 0.8749 (mt) REVERT: G 56 MET cc_start: 0.6774 (mmm) cc_final: 0.6531 (mmm) REVERT: G 70 GLU cc_start: 0.6839 (tm-30) cc_final: 0.5980 (mm-30) REVERT: G 216 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6623 (mt) REVERT: F 190 TYR cc_start: 0.8776 (m-10) cc_final: 0.8515 (m-10) REVERT: E 212 LEU cc_start: 0.7629 (tp) cc_final: 0.7265 (tp) REVERT: B 238 LYS cc_start: 0.7817 (tttp) cc_final: 0.7275 (mtmm) REVERT: H 184 ILE cc_start: 0.6556 (mp) cc_final: 0.6321 (tt) REVERT: H 306 MET cc_start: 0.1656 (tpp) cc_final: 0.1361 (ttt) REVERT: H 342 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.6431 (m-10) REVERT: H 344 GLU cc_start: 0.7136 (tp30) cc_final: 0.6870 (tm-30) outliers start: 58 outliers final: 54 residues processed: 328 average time/residue: 0.1295 time to fit residues: 67.2272 Evaluate side-chains 319 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 201 HIS 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 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 608 THR Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 749 LEU 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 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 69 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain F residue 134 ASN Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 THR 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 93 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 154 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 242 LEU 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: 3.9990 chunk 187 optimal weight: 7.9990 chunk 149 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 220 optimal weight: 0.0060 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.114767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.102974 restraints weight = 54707.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105076 restraints weight = 29801.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106406 restraints weight = 19233.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.107225 restraints weight = 14114.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.107878 restraints weight = 11468.726| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 19576 Z= 0.189 Angle : 0.868 14.340 26707 Z= 0.411 Chirality : 0.062 0.833 3022 Planarity : 0.004 0.060 3214 Dihedral : 12.317 170.687 3195 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.52 % Favored : 89.44 % Rotamer: Outliers : 3.37 % Allowed : 29.37 % Favored : 67.26 % 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: -2.94 (0.17), residues: 2225 helix: -0.90 (0.17), residues: 837 sheet: -2.50 (0.28), residues: 324 loop : -2.65 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 110 TYR 0.041 0.002 TYR C 68 PHE 0.038 0.002 PHE B 64 TRP 0.034 0.002 TRP H 287 HIS 0.017 0.002 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (19573) covalent geometry : angle 0.86772 / 0.41 (26707) hydrogen bonds : bond 0.03993 / 2.68 ( 663) hydrogen bonds : angle 5.64087 / 3.92 ( 1793) metal coordination : bond 0.00351 / 0.18 ( 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 328 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 266 time to evaluate : 0.558 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 156 ILE cc_start: 0.8659 (mm) cc_final: 0.8355 (pt) REVERT: A 298 MET cc_start: 0.8937 (ttp) cc_final: 0.8733 (ttt) REVERT: A 327 PHE cc_start: 0.7609 (t80) cc_final: 0.7290 (t80) REVERT: A 331 LEU cc_start: 0.9028 (mt) cc_final: 0.8780 (mt) REVERT: G 56 MET cc_start: 0.6824 (mmm) cc_final: 0.6560 (mmm) REVERT: G 70 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6002 (mm-30) REVERT: G 216 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6638 (mt) REVERT: F 190 TYR cc_start: 0.8827 (m-10) cc_final: 0.8579 (m-80) REVERT: E 212 LEU cc_start: 0.7589 (tp) cc_final: 0.7242 (tp) REVERT: B 213 MET cc_start: 0.7629 (ttt) cc_final: 0.7295 (ttt) REVERT: H 184 ILE cc_start: 0.6584 (mp) cc_final: 0.6345 (tt) REVERT: H 306 MET cc_start: 0.1616 (tpp) cc_final: 0.1351 (ttt) REVERT: H 344 GLU cc_start: 0.7123 (tp30) cc_final: 0.6873 (tm-30) outliers start: 62 outliers final: 58 residues processed: 308 average time/residue: 0.1272 time to fit residues: 61.6811 Evaluate side-chains 317 residues out of total 1949 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 201 HIS 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 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 608 THR Chi-restraints excluded: chain A residue 642 ASP Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 711 GLU Chi-restraints excluded: chain A residue 749 LEU 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 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 69 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 157 TYR 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 34 GLU Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain H residue 154 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 242 LEU 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: 0.9980 chunk 30 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 218 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 168 optimal weight: 0.4980 chunk 4 optimal weight: 6.9990 chunk 221 optimal weight: 30.0000 chunk 68 optimal weight: 5.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN H 115 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 = 0.114583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.102779 restraints weight = 55337.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.104800 restraints weight = 30953.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.106111 restraints weight = 20397.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.106902 restraints weight = 15090.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.107524 restraints weight = 12345.106| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 19576 Z= 0.192 Angle : 0.869 13.721 26707 Z= 0.412 Chirality : 0.062 0.834 3022 Planarity : 0.004 0.077 3214 Dihedral : 12.356 170.581 3195 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.79 % Favored : 89.17 % Rotamer: Outliers : 3.75 % Allowed : 29.04 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.17), residues: 2225 helix: -0.88 (0.17), residues: 839 sheet: -2.48 (0.27), residues: 330 loop : -2.66 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 110 TYR 0.021 0.002 TYR A 282 PHE 0.041 0.002 PHE B 64 TRP 0.033 0.002 TRP H 287 HIS 0.018 0.002 HIS H 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (19573) covalent geometry : angle 0.86850 / 0.41 (26707) hydrogen bonds : bond 0.03999 / 2.69 ( 663) hydrogen bonds : angle 5.61435 / 3.90 ( 1793) metal coordination : bond 0.00356 / 0.19 ( 3) =============================================================================== Job complete usr+sys time: 3088.65 seconds wall clock time: 54 minutes 34.99 seconds (3274.99 seconds total)