Starting phenix.real_space_refine on Fri Feb 6 06:47:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hu4_52399/02_2026/9hu4_52399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hu4_52399/02_2026/9hu4_52399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hu4_52399/02_2026/9hu4_52399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hu4_52399/02_2026/9hu4_52399.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hu4_52399/02_2026/9hu4_52399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hu4_52399/02_2026/9hu4_52399.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 14815 2.51 5 N 4052 2.21 5 O 4435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23399 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5965 Classifications: {'peptide': 766} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 735} Chain: "B" Number of atoms: 5965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5965 Classifications: {'peptide': 766} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 735} Chain: "C" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 289 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "D" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1118 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "E" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1118 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "F" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1118 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "G" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1118 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "H" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1118 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "I" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1118 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "J" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1118 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "K" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1118 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "L" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1118 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "M" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1118 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Time building chain proxies: 5.66, per 1000 atoms: 0.24 Number of scatterers: 23399 At special positions: 0 Unit cell: (169.4, 170.8, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 4435 8.00 N 4052 7.00 C 14815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 14 sheets defined 66.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 removed outlier: 3.544A pdb=" N SER A 12 " --> pdb=" O ASP A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 17 Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.624A pdb=" N TRP A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 139 removed outlier: 3.695A pdb=" N ILE A 131 " --> pdb=" O PRO A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 removed outlier: 3.656A pdb=" N HIS A 147 " --> pdb=" O HIS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 removed outlier: 4.064A pdb=" N ARG A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 5.905A pdb=" N LEU A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN A 211 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 239 removed outlier: 4.177A pdb=" N ALA A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 290 through 302 removed outlier: 4.122A pdb=" N ASP A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.663A pdb=" N GLU A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 393 through 406 removed outlier: 3.919A pdb=" N ALA A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Proline residue: A 403 - end of helix removed outlier: 3.817A pdb=" N ASN A 406 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 412 Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.642A pdb=" N SER A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 450 removed outlier: 3.855A pdb=" N VAL A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 removed outlier: 4.321A pdb=" N ALA A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 460 " --> pdb=" O MET A 456 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 497 removed outlier: 3.558A pdb=" N TYR A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 626 through 652 removed outlier: 3.705A pdb=" N ARG A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 682 removed outlier: 3.769A pdb=" N ALA A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 668 " --> pdb=" O ASP A 664 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 705 removed outlier: 3.723A pdb=" N GLY A 704 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 705 " --> pdb=" O GLN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 720 through 734 removed outlier: 3.771A pdb=" N LEU A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 753 removed outlier: 3.915A pdb=" N LYS A 748 " --> pdb=" O GLU A 744 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 759 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.827A pdb=" N ALA B 21 " --> pdb=" O THR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 82 through 98 removed outlier: 3.702A pdb=" N SER B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 127 through 139 removed outlier: 3.834A pdb=" N ILE B 131 " --> pdb=" O PRO B 127 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 132 " --> pdb=" O PRO B 128 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.966A pdb=" N HIS B 147 " --> pdb=" O HIS B 143 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 203 removed outlier: 3.900A pdb=" N ASP B 194 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 202 " --> pdb=" O MET B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 218 Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.990A pdb=" N ILE B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 254 removed outlier: 4.080A pdb=" N SER B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 removed outlier: 3.659A pdb=" N GLY B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.520A pdb=" N LEU B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.848A pdb=" N ILE B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) Proline residue: B 319 - end of helix Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.545A pdb=" N ALA B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Proline residue: B 403 - end of helix removed outlier: 3.747A pdb=" N ASN B 406 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 422 removed outlier: 4.136A pdb=" N LYS B 415 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 451 removed outlier: 4.046A pdb=" N VAL B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 464 removed outlier: 4.241A pdb=" N LEU B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 498 removed outlier: 3.700A pdb=" N ASP B 478 " --> pdb=" O ARG B 474 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 481 " --> pdb=" O ASN B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.634A pdb=" N TYR B 551 " --> pdb=" O GLU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 612 removed outlier: 3.557A pdb=" N LEU B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 608 through 612' Processing helix chain 'B' and resid 626 through 652 Processing helix chain 'B' and resid 656 through 683 removed outlier: 3.649A pdb=" N LYS B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 661 " --> pdb=" O ASP B 657 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 662 " --> pdb=" O ALA B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 700 removed outlier: 3.529A pdb=" N LEU B 693 " --> pdb=" O SER B 689 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B 696 " --> pdb=" O HIS B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 735 removed outlier: 3.510A pdb=" N TRP B 726 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET B 735 " --> pdb=" O VAL B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 753 removed outlier: 3.847A pdb=" N SER B 753 " --> pdb=" O VAL B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'D' and resid 3 through 21 removed outlier: 4.095A pdb=" N ALA D 9 " --> pdb=" O VAL D 5 " (cutoff:3.500A) Proline residue: D 12 - end of helix removed outlier: 3.767A pdb=" N THR D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 33 removed outlier: 3.957A pdb=" N VAL D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 48 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.704A pdb=" N GLN D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 62 No H-bonds generated for 'chain 'D' and resid 60 through 62' Processing helix chain 'D' and resid 63 through 74 Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'D' and resid 94 through 101 removed outlier: 3.534A pdb=" N GLY D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.518A pdb=" N LEU D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 131 removed outlier: 3.734A pdb=" N LEU D 122 " --> pdb=" O GLY D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 146 removed outlier: 4.126A pdb=" N TYR D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 21 removed outlier: 4.329A pdb=" N ALA E 9 " --> pdb=" O VAL E 5 " (cutoff:3.500A) Proline residue: E 12 - end of helix removed outlier: 3.763A pdb=" N THR E 21 " --> pdb=" O ALA E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 33 removed outlier: 4.229A pdb=" N SER E 26 " --> pdb=" O PRO E 22 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG E 27 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 29 " --> pdb=" O VAL E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 64 through 74 Processing helix chain 'E' and resid 74 through 85 removed outlier: 3.636A pdb=" N MET E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASP E 83 " --> pdb=" O GLU E 79 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 84 " --> pdb=" O MET E 80 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER E 85 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 100 Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 118 through 131 removed outlier: 3.649A pdb=" N LEU E 122 " --> pdb=" O GLY E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 145 removed outlier: 4.183A pdb=" N TYR E 136 " --> pdb=" O ASP E 132 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 21 removed outlier: 4.074A pdb=" N ALA F 9 " --> pdb=" O VAL F 5 " (cutoff:3.500A) Proline residue: F 12 - end of helix removed outlier: 3.629A pdb=" N THR F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 33 removed outlier: 3.733A pdb=" N SER F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 48 removed outlier: 3.503A pdb=" N ASN F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 59 Processing helix chain 'F' and resid 63 through 74 Processing helix chain 'F' and resid 76 through 85 removed outlier: 4.650A pdb=" N MET F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 100 Processing helix chain 'F' and resid 102 through 117 removed outlier: 3.716A pdb=" N LEU F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 130 removed outlier: 3.921A pdb=" N GLN F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 145 removed outlier: 3.980A pdb=" N TYR F 136 " --> pdb=" O ASP F 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 21 removed outlier: 4.340A pdb=" N ALA G 9 " --> pdb=" O VAL G 5 " (cutoff:3.500A) Proline residue: G 12 - end of helix removed outlier: 3.602A pdb=" N THR G 21 " --> pdb=" O ALA G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'G' and resid 37 through 48 removed outlier: 3.753A pdb=" N ALA G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.576A pdb=" N GLN G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 74 Processing helix chain 'G' and resid 77 through 85 removed outlier: 3.655A pdb=" N ASP G 83 " --> pdb=" O GLU G 79 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER G 85 " --> pdb=" O LEU G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 100 Processing helix chain 'G' and resid 102 through 117 Processing helix chain 'G' and resid 119 through 131 Processing helix chain 'G' and resid 132 through 145 removed outlier: 4.049A pdb=" N TYR G 136 " --> pdb=" O ASP G 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 21 removed outlier: 4.606A pdb=" N ALA H 9 " --> pdb=" O VAL H 5 " (cutoff:3.500A) Proline residue: H 12 - end of helix Processing helix chain 'H' and resid 23 through 33 removed outlier: 3.691A pdb=" N ARG H 27 " --> pdb=" O GLY H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 48 removed outlier: 3.676A pdb=" N ALA H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 63 through 74 Processing helix chain 'H' and resid 76 through 85 removed outlier: 4.568A pdb=" N MET H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 101 removed outlier: 4.511A pdb=" N GLY H 97 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY H 100 " --> pdb=" O ILE H 96 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN H 101 " --> pdb=" O GLY H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 117 removed outlier: 3.673A pdb=" N LEU H 108 " --> pdb=" O GLU H 104 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 131 removed outlier: 3.606A pdb=" N LEU H 122 " --> pdb=" O GLY H 118 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 145 removed outlier: 4.225A pdb=" N TYR H 136 " --> pdb=" O ASP H 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 21 removed outlier: 3.754A pdb=" N ALA I 9 " --> pdb=" O VAL I 5 " (cutoff:3.500A) Proline residue: I 12 - end of helix removed outlier: 3.828A pdb=" N THR I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 32 removed outlier: 3.793A pdb=" N VAL I 25 " --> pdb=" O THR I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 48 removed outlier: 3.519A pdb=" N ILE I 41 " --> pdb=" O SER I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 59 Processing helix chain 'I' and resid 63 through 74 Processing helix chain 'I' and resid 77 through 85 Processing helix chain 'I' and resid 94 through 102 removed outlier: 3.729A pdb=" N GLN I 101 " --> pdb=" O GLY I 97 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 117 removed outlier: 3.806A pdb=" N LEU I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 131 Processing helix chain 'I' and resid 132 through 145 removed outlier: 4.105A pdb=" N TYR I 136 " --> pdb=" O ASP I 132 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN I 143 " --> pdb=" O LYS I 139 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET I 145 " --> pdb=" O GLN I 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 19 Proline residue: J 12 - end of helix Processing helix chain 'J' and resid 21 through 33 removed outlier: 4.043A pdb=" N VAL J 25 " --> pdb=" O THR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 48 removed outlier: 4.045A pdb=" N LYS J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN J 48 " --> pdb=" O ALA J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 59 removed outlier: 3.818A pdb=" N ILE J 59 " --> pdb=" O THR J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 62 No H-bonds generated for 'chain 'J' and resid 60 through 62' Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 77 through 85 removed outlier: 3.842A pdb=" N SER J 85 " --> pdb=" O LEU J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 102 through 117 removed outlier: 3.545A pdb=" N LEU J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 130 removed outlier: 3.517A pdb=" N LEU J 122 " --> pdb=" O GLY J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 145 removed outlier: 4.077A pdb=" N TYR J 136 " --> pdb=" O ASP J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 21 removed outlier: 4.567A pdb=" N ALA K 9 " --> pdb=" O VAL K 5 " (cutoff:3.500A) Proline residue: K 12 - end of helix Processing helix chain 'K' and resid 22 through 32 removed outlier: 3.899A pdb=" N SER K 26 " --> pdb=" O PRO K 22 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG K 27 " --> pdb=" O GLY K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 48 Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 63 through 74 Processing helix chain 'K' and resid 77 through 85 removed outlier: 3.627A pdb=" N ASP K 83 " --> pdb=" O GLU K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 117 Processing helix chain 'K' and resid 118 through 131 Processing helix chain 'K' and resid 132 through 145 removed outlier: 3.988A pdb=" N TYR K 136 " --> pdb=" O ASP K 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 21 removed outlier: 4.479A pdb=" N ALA L 9 " --> pdb=" O VAL L 5 " (cutoff:3.500A) Proline residue: L 12 - end of helix Processing helix chain 'L' and resid 23 through 33 removed outlier: 4.365A pdb=" N ARG L 27 " --> pdb=" O GLY L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 48 removed outlier: 3.736A pdb=" N LYS L 46 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 56 Processing helix chain 'L' and resid 63 through 74 Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 94 through 100 Processing helix chain 'L' and resid 102 through 117 Processing helix chain 'L' and resid 119 through 131 removed outlier: 3.954A pdb=" N GLN L 127 " --> pdb=" O ILE L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 145 Processing helix chain 'M' and resid 3 through 21 removed outlier: 4.281A pdb=" N ALA M 9 " --> pdb=" O VAL M 5 " (cutoff:3.500A) Proline residue: M 12 - end of helix removed outlier: 3.800A pdb=" N THR M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 33 removed outlier: 4.232A pdb=" N SER M 26 " --> pdb=" O PRO M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 46 removed outlier: 3.640A pdb=" N LYS M 46 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 59 Processing helix chain 'M' and resid 60 through 62 No H-bonds generated for 'chain 'M' and resid 60 through 62' Processing helix chain 'M' and resid 63 through 74 Processing helix chain 'M' and resid 77 through 85 removed outlier: 3.527A pdb=" N LEU M 81 " --> pdb=" O VAL M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 100 Processing helix chain 'M' and resid 102 through 117 Processing helix chain 'M' and resid 118 through 130 removed outlier: 3.529A pdb=" N LEU M 122 " --> pdb=" O GLY M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 146 removed outlier: 3.820A pdb=" N TYR M 136 " --> pdb=" O ASP M 132 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY M 146 " --> pdb=" O LEU M 142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 removed outlier: 6.112A pdb=" N VAL A 358 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLY A 440 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL A 360 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 38 removed outlier: 3.944A pdb=" N VAL A 501 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER A 515 " --> pdb=" O HIS A 506 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 46 Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 364 through 365 Processing sheet with id=AA6, first strand: chain 'A' and resid 385 through 389 Processing sheet with id=AA7, first strand: chain 'A' and resid 591 through 597 Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.850A pdb=" N HIS B 357 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 36 through 37 removed outlier: 3.583A pdb=" N TYR B 517 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 42 through 46 removed outlier: 3.893A pdb=" N SER B 45 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 52 through 55 Processing sheet with id=AB3, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'B' and resid 386 through 389 Processing sheet with id=AB5, first strand: chain 'B' and resid 601 through 607 1281 hydrogen bonds defined for protein. 3792 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7816 1.34 - 1.45: 3008 1.45 - 1.57: 12791 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 23803 Sorted by residual: bond pdb=" C HIS L 74 " pdb=" N PRO L 75 " ideal model delta sigma weight residual 1.334 1.315 0.018 8.40e-03 1.42e+04 4.76e+00 bond pdb=" C HIS M 74 " pdb=" N PRO M 75 " ideal model delta sigma weight residual 1.336 1.315 0.021 9.80e-03 1.04e+04 4.62e+00 bond pdb=" CB TYR B 170 " pdb=" CG TYR B 170 " ideal model delta sigma weight residual 1.512 1.467 0.045 2.20e-02 2.07e+03 4.13e+00 bond pdb=" C ASP A 270 " pdb=" N PRO A 271 " ideal model delta sigma weight residual 1.334 1.317 0.016 8.40e-03 1.42e+04 3.69e+00 bond pdb=" CD1 TYR B 170 " pdb=" CE1 TYR B 170 " ideal model delta sigma weight residual 1.382 1.327 0.055 3.00e-02 1.11e+03 3.40e+00 ... (remaining 23798 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 30422 1.62 - 3.24: 1601 3.24 - 4.86: 233 4.86 - 6.48: 38 6.48 - 8.10: 10 Bond angle restraints: 32304 Sorted by residual: angle pdb=" N GLU K 90 " pdb=" CA GLU K 90 " pdb=" CB GLU K 90 " ideal model delta sigma weight residual 114.17 107.91 6.26 1.14e+00 7.69e-01 3.02e+01 angle pdb=" N GLU B 268 " pdb=" CA GLU B 268 " pdb=" C GLU B 268 " ideal model delta sigma weight residual 114.64 107.00 7.64 1.52e+00 4.33e-01 2.53e+01 angle pdb=" N GLU A 268 " pdb=" CA GLU A 268 " pdb=" C GLU A 268 " ideal model delta sigma weight residual 114.09 106.36 7.73 1.55e+00 4.16e-01 2.49e+01 angle pdb=" N SER A 432 " pdb=" CA SER A 432 " pdb=" C SER A 432 " ideal model delta sigma weight residual 114.64 107.26 7.38 1.52e+00 4.33e-01 2.36e+01 angle pdb=" N LEU B 737 " pdb=" CA LEU B 737 " pdb=" C LEU B 737 " ideal model delta sigma weight residual 114.56 108.40 6.16 1.27e+00 6.20e-01 2.35e+01 ... (remaining 32299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13012 17.97 - 35.94: 1198 35.94 - 53.90: 219 53.90 - 71.87: 49 71.87 - 89.84: 25 Dihedral angle restraints: 14503 sinusoidal: 5653 harmonic: 8850 Sorted by residual: dihedral pdb=" CA ILE K 91 " pdb=" C ILE K 91 " pdb=" N GLN K 92 " pdb=" CA GLN K 92 " ideal model delta harmonic sigma weight residual 180.00 152.10 27.90 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PHE B 386 " pdb=" C PHE B 386 " pdb=" N LEU B 387 " pdb=" CA LEU B 387 " ideal model delta harmonic sigma weight residual -180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA VAL A 759 " pdb=" C VAL A 759 " pdb=" N VAL A 760 " pdb=" CA VAL A 760 " ideal model delta harmonic sigma weight residual -180.00 -155.24 -24.76 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 14500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2585 0.045 - 0.090: 938 0.090 - 0.134: 201 0.134 - 0.179: 15 0.179 - 0.224: 2 Chirality restraints: 3741 Sorted by residual: chirality pdb=" CB ILE A 577 " pdb=" CA ILE A 577 " pdb=" CG1 ILE A 577 " pdb=" CG2 ILE A 577 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB ILE B 535 " pdb=" CA ILE B 535 " pdb=" CG1 ILE B 535 " pdb=" CG2 ILE B 535 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE B 336 " pdb=" CA ILE B 336 " pdb=" CG1 ILE B 336 " pdb=" CG2 ILE B 336 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 3738 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 578 " -0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO A 579 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 579 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 579 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 441 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO A 442 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 442 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 442 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 441 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO B 442 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 442 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 442 " -0.031 5.00e-02 4.00e+02 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 275 2.64 - 3.21: 22486 3.21 - 3.77: 34534 3.77 - 4.34: 47243 4.34 - 4.90: 77657 Nonbonded interactions: 182195 Sorted by model distance: nonbonded pdb=" O ASP D 89 " pdb=" OH TYR H 135 " model vdw 2.077 3.040 nonbonded pdb=" O ALA A 460 " pdb=" OG1 THR A 464 " model vdw 2.116 3.040 nonbonded pdb=" O ALA I 128 " pdb=" OH TYR I 136 " model vdw 2.134 3.040 nonbonded pdb=" O ALA J 43 " pdb=" OG SER J 47 " model vdw 2.140 3.040 nonbonded pdb=" ND2 ASN B 27 " pdb=" OH TYR B 532 " model vdw 2.158 3.120 ... (remaining 182190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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=0.00 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.350 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.008 0.085 23803 Z= 0.360 Angle : 0.829 8.105 32304 Z= 0.484 Chirality : 0.046 0.224 3741 Planarity : 0.005 0.069 4206 Dihedral : 14.706 89.841 8797 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.49 % Rotamer: Outliers : 0.16 % Allowed : 8.85 % Favored : 90.98 % 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: -3.88 (0.12), residues: 3025 helix: -2.20 (0.10), residues: 1971 sheet: -2.02 (0.33), residues: 215 loop : -3.16 (0.16), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 103 TYR 0.018 0.002 TYR B 92 PHE 0.030 0.002 PHE B 386 TRP 0.030 0.003 TRP A 578 HIS 0.008 0.001 HIS B 492 Details of bonding type rmsd covalent geometry : bond 0.00829 (23803) covalent geometry : angle 0.82869 (32304) hydrogen bonds : bond 0.14500 ( 1281) hydrogen bonds : angle 6.73065 ( 3792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 656 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8124 (mtmm) REVERT: A 65 MET cc_start: 0.8276 (ttp) cc_final: 0.8063 (ttm) REVERT: A 214 PHE cc_start: 0.7142 (m-10) cc_final: 0.6777 (m-10) REVERT: A 357 HIS cc_start: 0.7885 (m90) cc_final: 0.7668 (m-70) REVERT: A 377 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8357 (ttmt) REVERT: A 408 PHE cc_start: 0.8000 (m-80) cc_final: 0.7790 (m-80) REVERT: A 421 TYR cc_start: 0.8071 (m-10) cc_final: 0.7859 (m-10) REVERT: A 491 MET cc_start: 0.7808 (ttt) cc_final: 0.7584 (ttp) REVERT: A 589 TYR cc_start: 0.8402 (t80) cc_final: 0.7523 (t80) REVERT: A 634 GLN cc_start: 0.8355 (tp40) cc_final: 0.7828 (tp-100) REVERT: A 644 ASP cc_start: 0.8251 (t0) cc_final: 0.7808 (t0) REVERT: A 677 LYS cc_start: 0.7868 (mttt) cc_final: 0.7620 (mttm) REVERT: A 741 SER cc_start: 0.9152 (t) cc_final: 0.8862 (m) REVERT: B 196 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7550 (mtp180) REVERT: B 297 MET cc_start: 0.8786 (ttp) cc_final: 0.8570 (ttm) REVERT: B 421 TYR cc_start: 0.8119 (m-80) cc_final: 0.6936 (m-80) REVERT: B 449 TYR cc_start: 0.8919 (m-10) cc_final: 0.8576 (m-80) REVERT: B 452 ASP cc_start: 0.7722 (m-30) cc_final: 0.7358 (t0) REVERT: B 559 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7115 (mt-10) REVERT: B 575 ILE cc_start: 0.8650 (pt) cc_final: 0.8433 (mp) REVERT: B 598 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7162 (mtm180) REVERT: B 599 ASN cc_start: 0.8837 (t0) cc_final: 0.8372 (t0) REVERT: B 639 TRP cc_start: 0.8869 (m-10) cc_final: 0.8565 (m-10) REVERT: B 642 GLU cc_start: 0.7200 (tp30) cc_final: 0.6868 (tp30) REVERT: B 720 ARG cc_start: 0.7371 (ttm110) cc_final: 0.7103 (mtm110) REVERT: B 731 VAL cc_start: 0.9384 (p) cc_final: 0.9140 (t) REVERT: B 748 LYS cc_start: 0.7292 (tttm) cc_final: 0.6799 (mtpp) REVERT: F 16 SER cc_start: 0.8196 (t) cc_final: 0.7960 (p) REVERT: F 86 PHE cc_start: 0.7269 (t80) cc_final: 0.7020 (t80) REVERT: G 48 ASN cc_start: 0.7687 (t0) cc_final: 0.7290 (t0) REVERT: G 50 VAL cc_start: 0.8798 (t) cc_final: 0.8555 (t) REVERT: G 82 LYS cc_start: 0.8382 (tmmt) cc_final: 0.8180 (tttt) REVERT: G 99 LEU cc_start: 0.8480 (tp) cc_final: 0.8132 (tp) REVERT: H 124 ARG cc_start: 0.4772 (tpt170) cc_final: 0.3766 (mmm160) REVERT: J 79 GLU cc_start: 0.7388 (tp30) cc_final: 0.6701 (tp30) REVERT: J 84 LEU cc_start: 0.8434 (tp) cc_final: 0.8080 (tp) REVERT: K 145 MET cc_start: 0.8106 (mtp) cc_final: 0.7897 (mtt) REVERT: K 147 TYR cc_start: 0.8372 (m-80) cc_final: 0.7856 (m-10) REVERT: L 80 MET cc_start: 0.8664 (tpp) cc_final: 0.8398 (tpt) REVERT: L 130 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6854 (mt-10) REVERT: M 36 VAL cc_start: 0.9201 (t) cc_final: 0.8968 (p) outliers start: 4 outliers final: 4 residues processed: 656 average time/residue: 0.1928 time to fit residues: 189.0988 Evaluate side-chains 508 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 504 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain C residue 307 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.0570 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 87 ASN A 93 HIS A 94 GLN A 182 ASN A 228 HIS A 300 GLN A 416 ASN A 552 ASN A 570 ASN A 599 ASN A 630 HIS A 634 GLN A 754 ASN B 93 HIS B 115 ASN B 228 HIS B 384 GLN B 426 GLN B 521 ASN B 630 HIS B 715 HIS B 719 ASN E 69 GLN E 92 GLN F 58 GLN F 68 GLN G 58 GLN G 68 GLN H 143 ASN J 92 GLN J 98 ASN J 101 GLN M 69 GLN M 101 GLN M 141 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.156335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.141095 restraints weight = 27687.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.139843 restraints weight = 43213.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.139669 restraints weight = 48771.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.138762 restraints weight = 39344.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.137699 restraints weight = 50159.012| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23803 Z= 0.174 Angle : 0.613 8.593 32304 Z= 0.316 Chirality : 0.041 0.227 3741 Planarity : 0.004 0.060 4206 Dihedral : 5.206 64.284 3338 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.80 % Allowed : 14.22 % Favored : 82.98 % 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: -1.85 (0.14), residues: 3025 helix: -0.59 (0.11), residues: 2001 sheet: -1.68 (0.36), residues: 196 loop : -2.41 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 463 TYR 0.013 0.001 TYR B 92 PHE 0.022 0.002 PHE B 386 TRP 0.013 0.002 TRP A 103 HIS 0.005 0.001 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00407 (23803) covalent geometry : angle 0.61343 (32304) hydrogen bonds : bond 0.03679 ( 1281) hydrogen bonds : angle 4.45081 ( 3792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 515 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.8235 (ttp) cc_final: 0.8031 (ttm) REVERT: A 214 PHE cc_start: 0.6947 (m-10) cc_final: 0.6587 (m-10) REVERT: A 323 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 500 GLU cc_start: 0.7574 (pm20) cc_final: 0.7176 (pm20) REVERT: A 644 ASP cc_start: 0.7947 (t0) cc_final: 0.7641 (t0) REVERT: A 754 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8250 (t0) REVERT: B 158 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 235 THR cc_start: 0.9338 (t) cc_final: 0.8885 (m) REVERT: B 398 SER cc_start: 0.9182 (m) cc_final: 0.8861 (m) REVERT: B 449 TYR cc_start: 0.9131 (m-10) cc_final: 0.8850 (m-10) REVERT: B 452 ASP cc_start: 0.7735 (m-30) cc_final: 0.7508 (t0) REVERT: B 589 TYR cc_start: 0.9091 (t80) cc_final: 0.8767 (t80) REVERT: B 731 VAL cc_start: 0.9349 (p) cc_final: 0.9086 (t) REVERT: C 296 MET cc_start: 0.8027 (mmt) cc_final: 0.7777 (mmt) REVERT: D 47 SER cc_start: 0.8840 (m) cc_final: 0.8578 (p) REVERT: D 73 ASN cc_start: 0.8161 (m-40) cc_final: 0.7901 (m110) REVERT: H 85 SER cc_start: 0.8306 (p) cc_final: 0.7996 (p) REVERT: H 105 GLU cc_start: 0.5753 (tt0) cc_final: 0.4785 (mp0) REVERT: H 124 ARG cc_start: 0.5582 (tpt170) cc_final: 0.4620 (mmm160) REVERT: L 80 MET cc_start: 0.8562 (tpp) cc_final: 0.8315 (tpt) REVERT: L 119 MET cc_start: 0.8836 (tpt) cc_final: 0.8627 (tpt) REVERT: M 68 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8272 (mm-40) outliers start: 69 outliers final: 40 residues processed: 546 average time/residue: 0.1800 time to fit residues: 150.0117 Evaluate side-chains 500 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 458 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 710 ASP Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain A residue 754 ASN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 374 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 262 optimal weight: 0.0040 chunk 69 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 277 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS A 570 ASN B 115 ASN B 351 HIS B 556 GLN B 719 ASN F 68 GLN F 73 ASN H 58 GLN J 143 ASN L 68 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.157965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.142917 restraints weight = 27542.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 83)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.134027 restraints weight = 46187.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.131853 restraints weight = 38377.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.131234 restraints weight = 45761.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.131697 restraints weight = 38281.685| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23803 Z= 0.110 Angle : 0.523 7.817 32304 Z= 0.268 Chirality : 0.038 0.160 3741 Planarity : 0.004 0.042 4206 Dihedral : 4.773 59.292 3338 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.60 % Allowed : 16.49 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 3025 helix: 0.16 (0.12), residues: 1982 sheet: -1.32 (0.37), residues: 198 loop : -2.00 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 148 TYR 0.012 0.001 TYR A 421 PHE 0.018 0.001 PHE A 308 TRP 0.009 0.001 TRP A 54 HIS 0.004 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00252 (23803) covalent geometry : angle 0.52317 (32304) hydrogen bonds : bond 0.03119 ( 1281) hydrogen bonds : angle 3.95927 ( 3792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 492 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9152 (mt) REVERT: A 65 MET cc_start: 0.8366 (ttp) cc_final: 0.8141 (ttm) REVERT: A 134 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7620 (tp40) REVERT: A 323 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7569 (tm-30) REVERT: A 491 MET cc_start: 0.7720 (ttt) cc_final: 0.7287 (ttp) REVERT: A 500 GLU cc_start: 0.7362 (pm20) cc_final: 0.7069 (pm20) REVERT: B 158 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8576 (mm) REVERT: B 235 THR cc_start: 0.9313 (t) cc_final: 0.8823 (m) REVERT: B 449 TYR cc_start: 0.9046 (m-10) cc_final: 0.8729 (m-10) REVERT: B 452 ASP cc_start: 0.7725 (m-30) cc_final: 0.7372 (t0) REVERT: B 523 ARG cc_start: 0.6929 (mmm-85) cc_final: 0.6726 (mtp85) REVERT: B 589 TYR cc_start: 0.9056 (t80) cc_final: 0.8477 (t80) REVERT: B 705 ARG cc_start: 0.8341 (ttt90) cc_final: 0.8104 (ptm160) REVERT: B 731 VAL cc_start: 0.9308 (p) cc_final: 0.9072 (t) REVERT: D 47 SER cc_start: 0.8993 (m) cc_final: 0.8496 (p) REVERT: D 119 MET cc_start: 0.8710 (tpt) cc_final: 0.8483 (tpt) REVERT: F 16 SER cc_start: 0.8003 (t) cc_final: 0.7689 (p) REVERT: F 101 GLN cc_start: 0.6638 (mt0) cc_final: 0.6293 (pt0) REVERT: G 80 MET cc_start: 0.7222 (tpp) cc_final: 0.6764 (tpt) REVERT: G 82 LYS cc_start: 0.8366 (tppt) cc_final: 0.8163 (ttpt) REVERT: G 145 MET cc_start: 0.8639 (mtp) cc_final: 0.8358 (mtp) REVERT: H 85 SER cc_start: 0.8112 (p) cc_final: 0.7615 (p) REVERT: H 105 GLU cc_start: 0.5614 (tt0) cc_final: 0.4577 (mp0) REVERT: I 58 GLN cc_start: 0.7383 (mm-40) cc_final: 0.7007 (mm-40) REVERT: L 80 MET cc_start: 0.8646 (tpp) cc_final: 0.8382 (tpt) REVERT: L 119 MET cc_start: 0.8911 (tpt) cc_final: 0.8711 (tpt) REVERT: M 8 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8478 (mtp180) REVERT: M 47 SER cc_start: 0.8948 (p) cc_final: 0.8711 (p) REVERT: M 68 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8255 (mm-40) outliers start: 64 outliers final: 36 residues processed: 523 average time/residue: 0.1786 time to fit residues: 143.2317 Evaluate side-chains 508 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 470 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 107 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 171 optimal weight: 0.0020 chunk 98 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 ASN B 115 ASN F 68 GLN G 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.157059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.142219 restraints weight = 27331.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.140371 restraints weight = 44710.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.138946 restraints weight = 54488.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.138097 restraints weight = 49179.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.137065 restraints weight = 49554.463| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23803 Z= 0.116 Angle : 0.517 8.160 32304 Z= 0.263 Chirality : 0.039 0.216 3741 Planarity : 0.004 0.058 4206 Dihedral : 4.409 51.363 3338 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.37 % Allowed : 17.14 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3025 helix: 0.58 (0.12), residues: 1995 sheet: -1.06 (0.37), residues: 202 loop : -1.72 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 124 TYR 0.013 0.001 TYR K 67 PHE 0.015 0.001 PHE A 308 TRP 0.012 0.001 TRP A 54 HIS 0.004 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00271 (23803) covalent geometry : angle 0.51745 (32304) hydrogen bonds : bond 0.02990 ( 1281) hydrogen bonds : angle 3.75860 ( 3792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 491 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9207 (mt) REVERT: A 134 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7331 (tp40) REVERT: A 323 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 491 MET cc_start: 0.7876 (ttt) cc_final: 0.7372 (ttp) REVERT: A 710 ASP cc_start: 0.5922 (t0) cc_final: 0.5719 (t0) REVERT: B 158 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8710 (mm) REVERT: B 235 THR cc_start: 0.9291 (t) cc_final: 0.8802 (m) REVERT: B 421 TYR cc_start: 0.8661 (m-80) cc_final: 0.7485 (m-80) REVERT: B 439 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7452 (mp) REVERT: B 449 TYR cc_start: 0.9096 (m-10) cc_final: 0.8815 (m-10) REVERT: B 452 ASP cc_start: 0.7497 (m-30) cc_final: 0.7276 (t0) REVERT: B 456 MET cc_start: 0.7536 (ptp) cc_final: 0.7279 (ptp) REVERT: B 553 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7721 (mmtp) REVERT: B 589 TYR cc_start: 0.9033 (t80) cc_final: 0.8318 (t80) REVERT: B 731 VAL cc_start: 0.9264 (p) cc_final: 0.9062 (t) REVERT: C 311 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: D 47 SER cc_start: 0.8948 (m) cc_final: 0.8587 (p) REVERT: F 18 ILE cc_start: 0.8142 (mm) cc_final: 0.7689 (mt) REVERT: F 101 GLN cc_start: 0.6485 (mt0) cc_final: 0.6284 (pt0) REVERT: H 85 SER cc_start: 0.8534 (p) cc_final: 0.8142 (p) REVERT: H 105 GLU cc_start: 0.6113 (tt0) cc_final: 0.5030 (mp0) REVERT: I 58 GLN cc_start: 0.7367 (mm-40) cc_final: 0.6966 (mm-40) REVERT: I 124 ARG cc_start: 0.7718 (mtp85) cc_final: 0.7252 (mmm160) REVERT: L 80 MET cc_start: 0.8648 (tpp) cc_final: 0.8406 (tpt) REVERT: M 47 SER cc_start: 0.8953 (p) cc_final: 0.8743 (p) REVERT: M 68 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8244 (mm-40) REVERT: M 142 LEU cc_start: 0.8539 (mt) cc_final: 0.8145 (mp) outliers start: 83 outliers final: 54 residues processed: 539 average time/residue: 0.1737 time to fit residues: 144.7324 Evaluate side-chains 516 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 458 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 58 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 180 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN D 58 GLN D 73 ASN F 58 GLN F 68 GLN F 73 ASN I 73 ASN L 98 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.155995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.141215 restraints weight = 27307.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.139732 restraints weight = 48098.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.137903 restraints weight = 56428.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.136750 restraints weight = 65089.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.136705 restraints weight = 56494.428| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23803 Z= 0.129 Angle : 0.522 8.298 32304 Z= 0.264 Chirality : 0.039 0.162 3741 Planarity : 0.004 0.048 4206 Dihedral : 4.320 43.938 3337 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.37 % Allowed : 18.48 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3025 helix: 0.76 (0.12), residues: 2001 sheet: -0.88 (0.37), residues: 207 loop : -1.59 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 705 TYR 0.012 0.001 TYR B 92 PHE 0.013 0.001 PHE B 386 TRP 0.019 0.001 TRP A 54 HIS 0.005 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00308 (23803) covalent geometry : angle 0.52244 (32304) hydrogen bonds : bond 0.03011 ( 1281) hydrogen bonds : angle 3.71994 ( 3792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 491 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9149 (mp) REVERT: A 195 LEU cc_start: 0.8787 (tt) cc_final: 0.8537 (tp) REVERT: A 296 ASP cc_start: 0.7850 (t70) cc_final: 0.7605 (t0) REVERT: A 491 MET cc_start: 0.7795 (ttt) cc_final: 0.7404 (ttp) REVERT: A 644 ASP cc_start: 0.7539 (t0) cc_final: 0.7222 (t0) REVERT: B 118 ILE cc_start: 0.8493 (pt) cc_final: 0.8267 (pt) REVERT: B 158 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8701 (mm) REVERT: B 170 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6260 (t80) REVERT: B 235 THR cc_start: 0.9306 (t) cc_final: 0.8804 (m) REVERT: B 449 TYR cc_start: 0.9096 (m-10) cc_final: 0.8794 (m-10) REVERT: B 452 ASP cc_start: 0.7507 (m-30) cc_final: 0.7244 (t0) REVERT: B 558 SER cc_start: 0.9253 (p) cc_final: 0.9019 (t) REVERT: B 589 TYR cc_start: 0.9267 (t80) cc_final: 0.8493 (t80) REVERT: C 311 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: D 47 SER cc_start: 0.8884 (m) cc_final: 0.8287 (p) REVERT: F 18 ILE cc_start: 0.8225 (mm) cc_final: 0.7764 (mt) REVERT: F 86 PHE cc_start: 0.8344 (t80) cc_final: 0.8134 (t80) REVERT: F 101 GLN cc_start: 0.6647 (mt0) cc_final: 0.6441 (pt0) REVERT: F 145 MET cc_start: 0.8716 (mtt) cc_final: 0.8212 (mtp) REVERT: H 85 SER cc_start: 0.8378 (p) cc_final: 0.7998 (p) REVERT: H 105 GLU cc_start: 0.6266 (tt0) cc_final: 0.4973 (mp0) REVERT: I 58 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7234 (mm-40) REVERT: I 104 GLU cc_start: 0.6364 (pm20) cc_final: 0.5689 (pm20) REVERT: I 124 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7233 (mmm160) REVERT: I 139 LYS cc_start: 0.8188 (tptm) cc_final: 0.6915 (mttt) REVERT: J 141 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: L 80 MET cc_start: 0.8621 (tpp) cc_final: 0.8408 (tpt) REVERT: M 47 SER cc_start: 0.9051 (p) cc_final: 0.8846 (p) REVERT: M 68 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8267 (mm-40) REVERT: M 142 LEU cc_start: 0.8501 (mt) cc_final: 0.8076 (mp) outliers start: 83 outliers final: 60 residues processed: 531 average time/residue: 0.1771 time to fit residues: 144.7829 Evaluate side-chains 534 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 469 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 532 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 141 GLN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 98 ASN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 40 optimal weight: 4.9990 chunk 93 optimal weight: 0.0470 chunk 56 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 255 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN B 115 ASN F 73 ASN I 73 ASN J 121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.154585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.139556 restraints weight = 27443.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.137651 restraints weight = 46015.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.136402 restraints weight = 56040.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.135485 restraints weight = 50483.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.134965 restraints weight = 49415.792| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23803 Z= 0.146 Angle : 0.539 8.142 32304 Z= 0.272 Chirality : 0.039 0.160 3741 Planarity : 0.004 0.042 4206 Dihedral : 4.306 36.006 3337 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.90 % Allowed : 18.44 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3025 helix: 0.85 (0.12), residues: 2009 sheet: -0.90 (0.38), residues: 197 loop : -1.56 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 463 TYR 0.014 0.001 TYR B 92 PHE 0.020 0.001 PHE A 308 TRP 0.019 0.002 TRP A 54 HIS 0.005 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00354 (23803) covalent geometry : angle 0.53922 (32304) hydrogen bonds : bond 0.03118 ( 1281) hydrogen bonds : angle 3.74661 ( 3792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 485 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 16 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9170 (mp) REVERT: A 296 ASP cc_start: 0.7863 (t70) cc_final: 0.7650 (t0) REVERT: A 301 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7332 (mmm-85) REVERT: A 491 MET cc_start: 0.7804 (ttt) cc_final: 0.7449 (ttp) REVERT: A 644 ASP cc_start: 0.7467 (t0) cc_final: 0.7166 (t0) REVERT: A 702 MET cc_start: 0.8476 (tpp) cc_final: 0.8156 (mmt) REVERT: B 115 ASN cc_start: 0.7577 (OUTLIER) cc_final: 0.7339 (t0) REVERT: B 118 ILE cc_start: 0.8654 (pt) cc_final: 0.8408 (pt) REVERT: B 158 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8809 (mm) REVERT: B 170 TYR cc_start: 0.7078 (OUTLIER) cc_final: 0.6511 (t80) REVERT: B 235 THR cc_start: 0.9284 (t) cc_final: 0.8748 (m) REVERT: B 449 TYR cc_start: 0.9070 (m-10) cc_final: 0.8787 (m-10) REVERT: B 589 TYR cc_start: 0.9228 (t80) cc_final: 0.8503 (t80) REVERT: B 598 ARG cc_start: 0.7268 (mtm180) cc_final: 0.6935 (mtt90) REVERT: C 311 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: D 47 SER cc_start: 0.8921 (m) cc_final: 0.8342 (p) REVERT: D 104 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6507 (pm20) REVERT: E 139 LYS cc_start: 0.8500 (tptt) cc_final: 0.8257 (tttp) REVERT: F 27 ARG cc_start: 0.7157 (ttp80) cc_final: 0.6835 (ttp80) REVERT: F 42 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7638 (mt) REVERT: G 114 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8214 (ttp80) REVERT: H 85 SER cc_start: 0.8691 (p) cc_final: 0.8394 (p) REVERT: H 105 GLU cc_start: 0.6545 (tt0) cc_final: 0.5153 (mp0) REVERT: I 58 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7348 (mm-40) REVERT: I 104 GLU cc_start: 0.6479 (pm20) cc_final: 0.5759 (pm20) REVERT: I 139 LYS cc_start: 0.8200 (tptm) cc_final: 0.6932 (mttt) REVERT: J 121 ASN cc_start: 0.8585 (m110) cc_final: 0.8132 (m-40) REVERT: J 141 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: L 32 ILE cc_start: 0.8617 (mm) cc_final: 0.8272 (mm) REVERT: L 80 MET cc_start: 0.8610 (tpp) cc_final: 0.8261 (tpt) REVERT: M 68 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8184 (mm-40) REVERT: M 142 LEU cc_start: 0.8707 (mt) cc_final: 0.8208 (mp) outliers start: 96 outliers final: 73 residues processed: 540 average time/residue: 0.1718 time to fit residues: 143.7896 Evaluate side-chains 540 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 459 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 532 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 141 GLN Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 87 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 121 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 188 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 243 optimal weight: 30.0000 chunk 278 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN A 513 GLN A 570 ASN B 115 ASN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN H 58 GLN I 143 ASN L 98 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.152336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.137125 restraints weight = 27427.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.135092 restraints weight = 48821.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.133904 restraints weight = 60854.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.133256 restraints weight = 51410.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.132868 restraints weight = 50570.164| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23803 Z= 0.185 Angle : 0.579 9.802 32304 Z= 0.294 Chirality : 0.041 0.183 3741 Planarity : 0.004 0.041 4206 Dihedral : 4.410 32.426 3337 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.10 % Allowed : 18.77 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 3025 helix: 0.85 (0.12), residues: 2005 sheet: -0.83 (0.36), residues: 210 loop : -1.56 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 27 TYR 0.014 0.001 TYR B 92 PHE 0.017 0.002 PHE B 386 TRP 0.022 0.002 TRP A 54 HIS 0.006 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00452 (23803) covalent geometry : angle 0.57946 (32304) hydrogen bonds : bond 0.03376 ( 1281) hydrogen bonds : angle 3.86431 ( 3792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 468 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8044 (mt0) cc_final: 0.7810 (mt0) REVERT: A 198 MET cc_start: 0.8017 (ttm) cc_final: 0.7802 (ttm) REVERT: A 267 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7153 (tppt) REVERT: A 290 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8827 (tp) REVERT: A 296 ASP cc_start: 0.7924 (t70) cc_final: 0.7710 (t0) REVERT: A 301 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7346 (mmm-85) REVERT: A 491 MET cc_start: 0.7746 (ttt) cc_final: 0.7476 (ttp) REVERT: A 644 ASP cc_start: 0.7510 (t0) cc_final: 0.7166 (t0) REVERT: B 118 ILE cc_start: 0.8760 (pt) cc_final: 0.8510 (pt) REVERT: B 170 TYR cc_start: 0.7280 (OUTLIER) cc_final: 0.6442 (t80) REVERT: B 188 ASP cc_start: 0.6814 (m-30) cc_final: 0.6563 (m-30) REVERT: B 235 THR cc_start: 0.9280 (t) cc_final: 0.8727 (m) REVERT: B 449 TYR cc_start: 0.9030 (m-10) cc_final: 0.8738 (m-10) REVERT: B 589 TYR cc_start: 0.9235 (t80) cc_final: 0.8517 (t80) REVERT: B 689 SER cc_start: 0.9391 (t) cc_final: 0.9058 (m) REVERT: B 758 MET cc_start: 0.8467 (mtp) cc_final: 0.8235 (mtp) REVERT: C 311 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: D 47 SER cc_start: 0.8921 (m) cc_final: 0.8372 (p) REVERT: D 73 ASN cc_start: 0.8264 (m-40) cc_final: 0.8064 (m110) REVERT: E 139 LYS cc_start: 0.8610 (tptt) cc_final: 0.8395 (tttp) REVERT: F 42 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7704 (mt) REVERT: F 58 GLN cc_start: 0.7761 (tp40) cc_final: 0.7516 (tp40) REVERT: F 104 GLU cc_start: 0.6910 (pm20) cc_final: 0.6572 (pm20) REVERT: G 1 MET cc_start: 0.7957 (tpp) cc_final: 0.7747 (tpt) REVERT: G 114 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8318 (ttp80) REVERT: H 85 SER cc_start: 0.8837 (p) cc_final: 0.8610 (p) REVERT: H 105 GLU cc_start: 0.6569 (tt0) cc_final: 0.4990 (mp0) REVERT: H 108 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8446 (tp) REVERT: I 104 GLU cc_start: 0.6535 (pm20) cc_final: 0.6292 (pm20) REVERT: I 139 LYS cc_start: 0.8139 (tptm) cc_final: 0.7843 (tmtt) REVERT: J 121 ASN cc_start: 0.8560 (m110) cc_final: 0.8342 (m-40) REVERT: J 141 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: L 80 MET cc_start: 0.8602 (tpp) cc_final: 0.8290 (tpt) REVERT: M 68 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8210 (mm-40) outliers start: 101 outliers final: 78 residues processed: 528 average time/residue: 0.1713 time to fit residues: 139.9912 Evaluate side-chains 534 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 449 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 532 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 141 GLN Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain M residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 61 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 271 optimal weight: 0.5980 chunk 250 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 141 optimal weight: 0.2980 chunk 113 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN K 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.152593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.137145 restraints weight = 27417.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.135415 restraints weight = 51630.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.134334 restraints weight = 60043.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.133305 restraints weight = 51950.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.133066 restraints weight = 54693.973| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23803 Z= 0.168 Angle : 0.566 11.209 32304 Z= 0.286 Chirality : 0.040 0.177 3741 Planarity : 0.004 0.040 4206 Dihedral : 4.377 32.597 3336 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.86 % Allowed : 19.54 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3025 helix: 0.91 (0.12), residues: 2002 sheet: -0.88 (0.37), residues: 200 loop : -1.53 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 27 TYR 0.015 0.001 TYR G 67 PHE 0.017 0.001 PHE B 386 TRP 0.018 0.002 TRP A 54 HIS 0.006 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00411 (23803) covalent geometry : angle 0.56603 (32304) hydrogen bonds : bond 0.03289 ( 1281) hydrogen bonds : angle 3.84697 ( 3792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 457 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8032 (mt0) cc_final: 0.7818 (mt0) REVERT: A 267 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7122 (tppt) REVERT: A 290 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8823 (tp) REVERT: A 296 ASP cc_start: 0.7923 (t70) cc_final: 0.7704 (t0) REVERT: A 301 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7324 (mmm-85) REVERT: A 491 MET cc_start: 0.7741 (ttt) cc_final: 0.7494 (ttp) REVERT: A 644 ASP cc_start: 0.7522 (t0) cc_final: 0.7181 (t0) REVERT: B 118 ILE cc_start: 0.8711 (pt) cc_final: 0.8403 (pt) REVERT: B 170 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6417 (t80) REVERT: B 188 ASP cc_start: 0.6787 (m-30) cc_final: 0.6519 (m-30) REVERT: B 235 THR cc_start: 0.9356 (t) cc_final: 0.8805 (m) REVERT: B 314 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8076 (t) REVERT: B 449 TYR cc_start: 0.9029 (m-10) cc_final: 0.8729 (m-10) REVERT: B 589 TYR cc_start: 0.9159 (t80) cc_final: 0.8518 (t80) REVERT: B 598 ARG cc_start: 0.7318 (mtm180) cc_final: 0.6965 (mtt90) REVERT: B 689 SER cc_start: 0.9367 (t) cc_final: 0.9053 (m) REVERT: C 311 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7292 (mt-10) REVERT: D 47 SER cc_start: 0.8908 (m) cc_final: 0.8351 (p) REVERT: E 68 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7310 (mm-40) REVERT: E 139 LYS cc_start: 0.8672 (tptt) cc_final: 0.8443 (tttp) REVERT: F 42 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7783 (mt) REVERT: F 104 GLU cc_start: 0.6881 (pm20) cc_final: 0.6496 (pm20) REVERT: G 1 MET cc_start: 0.8013 (tpp) cc_final: 0.7204 (tpt) REVERT: G 114 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8269 (ttp80) REVERT: H 105 GLU cc_start: 0.6600 (tt0) cc_final: 0.4997 (mp0) REVERT: I 104 GLU cc_start: 0.6474 (pm20) cc_final: 0.6237 (pm20) REVERT: I 139 LYS cc_start: 0.8163 (tptm) cc_final: 0.7888 (tmtt) REVERT: J 121 ASN cc_start: 0.8600 (m110) cc_final: 0.8398 (m-40) REVERT: J 141 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: L 80 MET cc_start: 0.8584 (tpp) cc_final: 0.8292 (tpt) REVERT: M 68 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8193 (mm-40) outliers start: 95 outliers final: 73 residues processed: 513 average time/residue: 0.1603 time to fit residues: 127.5061 Evaluate side-chains 524 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 444 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 532 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 141 GLN Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain M residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 200 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 163 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN B 115 ASN E 73 ASN F 58 GLN F 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.154349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.138831 restraints weight = 27391.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.136719 restraints weight = 54422.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.136398 restraints weight = 58132.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.135534 restraints weight = 47997.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.134238 restraints weight = 53131.728| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23803 Z= 0.121 Angle : 0.535 8.986 32304 Z= 0.271 Chirality : 0.039 0.203 3741 Planarity : 0.004 0.051 4206 Dihedral : 4.211 31.682 3336 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.21 % Allowed : 20.06 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3025 helix: 1.14 (0.12), residues: 1991 sheet: -0.87 (0.37), residues: 200 loop : -1.48 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 148 TYR 0.010 0.001 TYR B 92 PHE 0.023 0.001 PHE A 308 TRP 0.018 0.001 TRP A 54 HIS 0.005 0.001 HIS B 497 Details of bonding type rmsd covalent geometry : bond 0.00287 (23803) covalent geometry : angle 0.53474 (32304) hydrogen bonds : bond 0.03001 ( 1281) hydrogen bonds : angle 3.72987 ( 3792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 456 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 73 TYR cc_start: 0.8239 (t80) cc_final: 0.7782 (t80) REVERT: A 88 GLN cc_start: 0.8040 (mt0) cc_final: 0.7814 (mt0) REVERT: A 267 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7094 (tppt) REVERT: A 290 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8758 (mt) REVERT: A 296 ASP cc_start: 0.7879 (t70) cc_final: 0.7641 (t0) REVERT: A 456 MET cc_start: 0.7665 (tpp) cc_final: 0.7436 (tpt) REVERT: A 491 MET cc_start: 0.7773 (ttt) cc_final: 0.7454 (ttp) REVERT: A 644 ASP cc_start: 0.7443 (t0) cc_final: 0.7142 (t0) REVERT: B 118 ILE cc_start: 0.8618 (pt) cc_final: 0.8377 (pt) REVERT: B 170 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6307 (t80) REVERT: B 235 THR cc_start: 0.9335 (t) cc_final: 0.8918 (m) REVERT: B 314 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.7936 (t) REVERT: B 449 TYR cc_start: 0.9040 (m-10) cc_final: 0.8707 (m-10) REVERT: B 589 TYR cc_start: 0.9157 (t80) cc_final: 0.8451 (t80) REVERT: B 598 ARG cc_start: 0.7202 (mtm180) cc_final: 0.6853 (mtt90) REVERT: B 689 SER cc_start: 0.9367 (t) cc_final: 0.9071 (m) REVERT: B 700 ASP cc_start: 0.8860 (p0) cc_final: 0.8570 (t0) REVERT: C 311 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7258 (mt-10) REVERT: D 47 SER cc_start: 0.8893 (m) cc_final: 0.8307 (p) REVERT: D 73 ASN cc_start: 0.8361 (m-40) cc_final: 0.8135 (m110) REVERT: E 68 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7410 (mm-40) REVERT: E 139 LYS cc_start: 0.8656 (tptt) cc_final: 0.8397 (tttp) REVERT: F 27 ARG cc_start: 0.7443 (ttp80) cc_final: 0.6814 (ttp80) REVERT: F 42 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7779 (mt) REVERT: G 1 MET cc_start: 0.8058 (tpp) cc_final: 0.7322 (tpt) REVERT: G 114 ARG cc_start: 0.8571 (ttp80) cc_final: 0.8293 (ttp80) REVERT: H 105 GLU cc_start: 0.6493 (tt0) cc_final: 0.4927 (mp0) REVERT: H 108 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8476 (tp) REVERT: I 58 GLN cc_start: 0.7407 (mm-40) cc_final: 0.7077 (mm-40) REVERT: I 104 GLU cc_start: 0.6348 (pm20) cc_final: 0.6139 (pm20) REVERT: I 139 LYS cc_start: 0.8102 (tptm) cc_final: 0.7801 (tmtt) REVERT: L 80 MET cc_start: 0.8601 (tpp) cc_final: 0.8288 (tpt) REVERT: M 68 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8177 (mm-40) outliers start: 79 outliers final: 54 residues processed: 505 average time/residue: 0.1687 time to fit residues: 131.2499 Evaluate side-chains 504 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 443 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 532 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 73 ASN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 96 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 209 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 127 GLN J 121 ASN K 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.149620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.133878 restraints weight = 27676.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.131560 restraints weight = 60874.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.125495 restraints weight = 63668.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.123588 restraints weight = 44721.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.123416 restraints weight = 46253.415| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 23803 Z= 0.242 Angle : 0.643 10.107 32304 Z= 0.325 Chirality : 0.044 0.244 3741 Planarity : 0.005 0.064 4206 Dihedral : 4.536 32.717 3336 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.80 % Allowed : 20.55 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3025 helix: 0.88 (0.12), residues: 1999 sheet: -0.95 (0.35), residues: 213 loop : -1.61 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 27 TYR 0.017 0.002 TYR B 92 PHE 0.024 0.002 PHE A 308 TRP 0.019 0.002 TRP A 54 HIS 0.010 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00597 (23803) covalent geometry : angle 0.64325 (32304) hydrogen bonds : bond 0.03773 ( 1281) hydrogen bonds : angle 4.00241 ( 3792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6050 Ramachandran restraints generated. 3025 Oldfield, 0 Emsley, 3025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 445 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 TYR cc_start: 0.8278 (t80) cc_final: 0.7843 (t80) REVERT: A 88 GLN cc_start: 0.8045 (mt0) cc_final: 0.7776 (mt0) REVERT: A 101 GLU cc_start: 0.7539 (pm20) cc_final: 0.7301 (pm20) REVERT: A 267 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7405 (tppt) REVERT: A 290 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8810 (tp) REVERT: A 296 ASP cc_start: 0.8002 (t70) cc_final: 0.7735 (t0) REVERT: A 456 MET cc_start: 0.7761 (tpp) cc_final: 0.7520 (tpt) REVERT: A 491 MET cc_start: 0.7770 (ttt) cc_final: 0.7507 (ttp) REVERT: A 644 ASP cc_start: 0.7540 (t0) cc_final: 0.7216 (t0) REVERT: A 714 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8304 (mp) REVERT: B 118 ILE cc_start: 0.8681 (pt) cc_final: 0.8413 (pt) REVERT: B 170 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6533 (t80) REVERT: B 188 ASP cc_start: 0.6927 (m-30) cc_final: 0.6658 (m-30) REVERT: B 235 THR cc_start: 0.9299 (t) cc_final: 0.8759 (m) REVERT: B 589 TYR cc_start: 0.9236 (t80) cc_final: 0.8520 (t80) REVERT: C 311 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7299 (mt-10) REVERT: D 47 SER cc_start: 0.8869 (m) cc_final: 0.8158 (p) REVERT: D 73 ASN cc_start: 0.8218 (m-40) cc_final: 0.7957 (m110) REVERT: D 105 GLU cc_start: 0.6324 (tt0) cc_final: 0.4537 (mp0) REVERT: E 68 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7685 (mm-40) REVERT: F 42 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7710 (mt) REVERT: F 104 GLU cc_start: 0.6648 (pm20) cc_final: 0.6370 (pm20) REVERT: G 1 MET cc_start: 0.8194 (tpp) cc_final: 0.7759 (tpt) REVERT: G 114 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8390 (ttp80) REVERT: H 105 GLU cc_start: 0.6546 (tt0) cc_final: 0.4673 (mp0) REVERT: H 108 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8590 (tp) REVERT: I 139 LYS cc_start: 0.8037 (tptm) cc_final: 0.7645 (tmtt) REVERT: L 80 MET cc_start: 0.8621 (tpp) cc_final: 0.7933 (tpt) REVERT: M 68 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8240 (mm-40) outliers start: 69 outliers final: 56 residues processed: 493 average time/residue: 0.1718 time to fit residues: 131.1012 Evaluate side-chains 499 residues out of total 2462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 436 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 532 TYR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 226 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 343 ILE Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 623 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 73 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 98 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 272 optimal weight: 0.0040 chunk 268 optimal weight: 8.9990 chunk 217 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 239 optimal weight: 0.9990 chunk 204 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 571 HIS J 121 ASN K 68 GLN K 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.150095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.133941 restraints weight = 27438.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.132701 restraints weight = 61452.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.132723 restraints weight = 57740.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.132337 restraints weight = 48699.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.132188 restraints weight = 42372.675| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 23803 Z= 0.212 Angle : 0.767 59.200 32304 Z= 0.420 Chirality : 0.044 0.903 3741 Planarity : 0.005 0.062 4206 Dihedral : 4.578 40.892 3336 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 2.97 % Allowed : 20.43 % Favored : 76.60 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 3025 helix: 0.90 (0.12), residues: 1999 sheet: -0.97 (0.35), residues: 213 loop : -1.61 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 27 TYR 0.038 0.001 TYR A 551 PHE 0.021 0.002 PHE B 386 TRP 0.016 0.002 TRP A 54 HIS 0.008 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00514 (23803) covalent geometry : angle 0.76662 (32304) hydrogen bonds : bond 0.03734 ( 1281) hydrogen bonds : angle 4.01156 ( 3792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4634.40 seconds wall clock time: 80 minutes 29.47 seconds (4829.47 seconds total)